diff --git a/README.rst b/README.rst index f7458aff4..c89c3dbe4 100644 --- a/README.rst +++ b/README.rst @@ -31,13 +31,13 @@ The quickest and easiest way to get RGT is to to use pip. First some dependencie :: - pip install --user cython numpy scipy + pip3 install --user cython numpy scipy Then install the full RGT suite with all other dependencies: :: - pip install --user RGT + pip3 install --user RGT Alternatively (but not recommended), you can clone this repository: @@ -53,7 +53,7 @@ to manual installation: :: cd reg-gen - python setup.py install --user + python3 setup.py install --user Detailed installation instructions and basic problem solving can be found `on our website `__. diff --git a/data/motifs/createMtf.py b/data/motifs/createMtf.py index 0f2078299..a39a517b0 100644 --- a/data/motifs/createMtf.py +++ b/data/motifs/createMtf.py @@ -40,6 +40,7 @@ parser.add_option("--hoc", dest="hoc", action="store_true", default=False, help="Create hocomoco.mtf") parser.add_option("--jv", dest="jv", action="store_true", default=False, help="Create jaspar_vertebrates.mtf") parser.add_option("--jp", dest="jp", action="store_true", default=False, help="Create jaspar_plants.mtf") +parser.add_option("--ji", dest="ji", action="store_true", default=False, help="Create jaspar_insects.mtf") parser.add_option("--t", dest="t", action="store_true", default=False, help="Create transfac.mtf") parser.add_option("--up", dest="up", action="store_true", default=False, help="Create uniprobe_primary.mtf") parser.add_option("--us", dest="us", action="store_true", default=False, help="Create uniprobe_secondary.mtf") @@ -50,6 +51,7 @@ options.hoc = True options.jv = True options.jp = True + options.ji = True options.t = True options.up = True options.us = True @@ -227,6 +229,62 @@ outputFile.write("\t".join(resultVec) + "\n") outputFile.close() +################################################################################################### +# JASPAR INSECTS +################################################################################################### +if options.ji: + # Fetching file names + source = "jaspar_insects" + inputLocation = dataLocation + source + "/" + resultMatrix = [] + jaspar_anno = {} + with open("jaspar_anno.csv", "r") as f: + csvf = csv.reader(f, dialect="unix") + for l in csvf: + if not l: + continue + jaspar_anno[l[0]] = l[1:] + for inputFileName in glob(inputLocation + "*.pwm"): + raw_name = inputFileName.split("/")[-1] + full_name, pwm_name, _, _ = re.match("((.+?)(\(var\.(\d+)\))?).pwm", raw_name).groups() + name_fields = pwm_name.split(".") + matrix_id = name_fields[0] + version = name_fields[1] + gene_names = name_fields[2] + group = jaspar_anno[full_name][1] + if not group: + group = "." + uniprot = jaspar_anno[full_name][2] + data_source = jaspar_anno[full_name][3] + taxGroup = jaspar_anno[full_name][4] + species = jaspar_anno[full_name][5] + + # Creating PSSM + pfm = parsers.pfm(inputFileName) + bg = tools.flat_bg(len(pfm)) # total number of "points" to add, not per-row + pssm = tools.log_odds(pfm, bg, pseudocounts, 2) + threshold_list = [] + + # Evaluating thresholds + for fpr in fprList: + # Note: this requires a modified version of MOODS. Only use it if you know what you are doing + # resVec.append(str(tools.threshold_from_p(pssm, bg, fpr, 10000.0))) + threshold = tools.threshold_from_p(pssm, bg, fpr) + threshold_list.append(str(threshold)) + threshold = ",".join(threshold_list) + + resultMatrix.append([matrix_id, pwm_name, version, gene_names, group, uniprot, data_source, taxGroup, + species, threshold]) + # Sorting results by ID + resultMatrix = sorted(resultMatrix, key=lambda x: x[0]) + + # Writing to output file + outputFileName = dataLocation + source + ".mtf" + outputFile = open(outputFileName, "w") + for resultVec in resultMatrix: + outputFile.write("\t".join(resultVec) + "\n") + outputFile.close() + ################################################################################################### # TRANSFAC PUBLIC ################################################################################################### diff --git a/data/motifs/jaspar_insects.mtf b/data/motifs/jaspar_insects.mtf new file mode 100644 index 000000000..e4e0d03fb --- /dev/null +++ b/data/motifs/jaspar_insects.mtf @@ -0,0 +1,143 @@ +MA0010 MA0010.1.br 1 br Other factors with up to three adjacent zinc fingers Q01295 COMPILED insects Drosophila melanogaster 3.7795,6.893,8.0365,10.3905,11.273,13.094 +MA0011 MA0011.1.br 1 br Other factors with up to three adjacent zinc fingers Q01295 COMPILED insects Drosophila melanogaster 4.96,7.225,8.24,9.5355,10.1875,11.256709931422208 +MA0012 MA0012.1.br 1 br Other factors with up to three adjacent zinc fingers Q01295 COMPILED insects Drosophila melanogaster 4.617,7.3135,8.274,10.152,10.779,12.0015 +MA0013 MA0013.1.br 1 br Other factors with up to three adjacent zinc fingers Q24206 COMPILED insects Drosophila melanogaster 4.5325,7.172,8.143,10.1735,10.952,12.4 +MA0015 MA0015.1.Cf2 1 Cf2 Factors with multiple dispersed zinc fingers P20385 SELEX insects Drosophila melanogaster 2.827,6.4575,7.906,10.5335,11.5055,13.7845 +MA0016 MA0016.1.usp 1 usp . P20153 SELEX insects Drosophila melanogaster 0.658,5.2,6.842,9.893,11.718,14.0185 +MA0022 MA0022.1.dl 1 dl . P15330 SELEX insects Drosophila melanogaster 3.1955,6.5915,7.865,10.4665,11.3535,13.3885 +MA0023 MA0023.1.dl 1 dl . P15330 SELEX insects Drosophila melanogaster 3.2,6.535,8.058,10.7315,11.346,13.454 +MA0026 MA0026.1.Eip74EF 1 Eip74EF Ets-related factors P20105 SELEX insects Drosophila melanogaster 3.536,7.3165,8.539,10.867,11.348977218945329,11.348977218945329 +MA0049 MA0049.1.hb 1 hb Factors with multiple dispersed zinc fingers P05084 COMPILED insects Drosophila melanogaster 3.992,7.1515,8.343,10.596,11.2565,12.6925 +MA0085 MA0085.1.Su(H) 1 Su(H) . P28159 COMPILED insects Drosophila melanogaster 1.5975,5.4425,6.9765,10.0875,11.1995,13.7355 +MA0086 MA0086.2.sna 2 sna More than 3 adjacent zinc finger factors P08044 SMiLE-seq insects Drosophila melanogaster -0.047,4.813,6.555,10.1855,11.646,14.2835 +MA0094 MA0094.2.Ubx 2 Ubx HOX-related factors P83949 bacterial 1-hybrid insects Drosophila melanogaster 3.2675,6.0475,7.3715,11.1985,12.0155,12.796050508619922 +MA0126 MA0126.1.ovo 1 ovo More than 3 adjacent zinc finger factors P51521 SELEX insects Drosophila melanogaster 3.947,7.5605,8.682,10.4615,11.0835,12.102 +MA0165 MA0165.1.Abd-B 1 Abd-B HOX-related factors P09087 bacterial 1-hybrid insects Drosophila melanogaster 3.856,7.5565,8.886,10.7415,11.057640416899243,11.057640416899243 +MA0166 MA0166.1.Antp 1 Antp HOX-related factors P02833 bacterial 1-hybrid insects Drosophila melanogaster 2.82,6.429,7.242,12.1,12.274575895467333,12.274575895467333 +MA0167 MA0167.1.Awh 1 Awh . Q8IRC7 bacterial 1-hybrid insects Drosophila melanogaster 2.97,7.019,8.594,11.6045,11.797715492039334,11.797715492039334 +MA0168 MA0168.1.B-H1 1 B-H1 HOX-related factors Q24255 bacterial 1-hybrid insects Drosophila melanogaster 3.643,6.6485,9.026,10.853,11.193999676923875,11.193999676923875 +MA0169 MA0169.1.B-H2 1 B-H2 HOX-related factors Q24256 bacterial 1-hybrid insects Drosophila melanogaster 3.3505,7.159,8.6975,11.0195,11.503930581626033,11.503930581626033 +MA0170 MA0170.1.C15 1 C15 . Q7KS72 bacterial 1-hybrid insects Drosophila melanogaster 4.4375,7.618,8.995,10.5565,10.63003311680588,10.63003311680588 +MA0171 MA0171.1.CG11085 1 CG11085 . Q9VYL0 bacterial 1-hybrid insects Drosophila melanogaster 4.4915,6.8065,8.6325,10.507,11.335086578254826,11.335086578254826 +MA0172 MA0172.1.CG11294 1 CG11294 . Q9W3C6 bacterial 1-hybrid insects Drosophila melanogaster 1.4505,7.065,7.065,11.0815,12.039181923505781,12.039181923505781 +MA0173 MA0173.1.CG11617 1 CG11617 . Q9VPL4 bacterial 1-hybrid insects Drosophila melanogaster 1.654,6.6245,6.7105,11.463,12.098022509757325,12.098022509757325 +MA0174 MA0174.1.Dbx 1 Dbx . Q9W064 bacterial 1-hybrid insects Drosophila melanogaster 4.493,7.8525,8.641,10.5155,10.71471549412226,10.71471549412226 +MA0175 MA0175.1.lms 1 lms . Q8MZ02 bacterial 1-hybrid insects Drosophila melanogaster 3.748,7.4075,9.046,10.841,11.157269928546292,11.157269928546292 +MA0176 MA0176.1.CG15696-RA 1 CG15696-RA . Q9VDH9 bacterial 1-hybrid insects Drosophila melanogaster 4.403,7.6825,8.532,10.547647455560648,10.547647455560648,10.547647455560648 +MA0177 MA0177.1.CG18599 1 CG18599 . Q9VEA3 bacterial 1-hybrid insects Drosophila melanogaster 3.841,6.033,8.281,11.159859685939104,11.159859685939104,11.159859685939104 +MA0178 MA0178.1.CG32105 1 CG32105 . Q9VTW5 bacterial 1-hybrid insects Drosophila melanogaster 3.8225,6.761,8.4015,10.629,11.448416893269393,11.448416893269393 +MA0179 MA0179.1.CG32532 1 CG32532 . Q9VWH1 bacterial 1-hybrid insects Drosophila melanogaster 3.641,6.016,8.574,11.5565,11.685340054451578,11.685340054451578 +MA0180 MA0180.1.Vsx2 1 Vsx2 Paired-related HD factors Q9W4B3 bacterial 1-hybrid insects Drosophila melanogaster 2.4815,6.8915,7.3965,10.58,11.6545,13.2845 +MA0181 MA0181.1.Vsx1 1 Vsx1 Paired-related HD factors Q5U1D9 bacterial 1-hybrid insects Drosophila melanogaster 3.5595,7.3125,8.599,11.3215,11.606813807544386,11.606813807544386 +MA0182 MA0182.1.CG4328-RA 1 CG4328-RA . Q9VTW3 bacterial 1-hybrid insects Drosophila melanogaster 3.8195,7.9735,8.3835,9.944575518674847,9.944575518674847,9.944575518674847 +MA0183 MA0183.1.HHEX 1 HHEX . Q9VDF0 bacterial 1-hybrid insects Drosophila melanogaster 4.6565,7.434,8.409,10.0735,10.8345,11.482571708932143 +MA0184 MA0184.1.CG9876 1 CG9876 . Q7YU61 bacterial 1-hybrid insects Drosophila melanogaster 3.9235,6.6385,8.544,11.207,11.489483940644048,11.489483940644048 +MA0185 MA0185.1.Deaf1 1 Deaf1 DEAF Q24180 DNaseI footprinting insects Drosophila melanogaster 3.796,7.7365,8.267,8.460315999632515,8.460315999632515,8.460315999632515 +MA0186 MA0186.1.Dfd 1 Dfd HOX-related factors P07548 bacterial 1-hybrid insects Drosophila melanogaster 3.6155,6.182,8.09,10.6565,11.62375084429744,11.62375084429744 +MA0187 MA0187.1.Dll 1 Dll . P20009 bacterial 1-hybrid insects Drosophila melanogaster 4.306,7.5755,8.608,10.868,10.941783965117658,10.941783965117658 +MA0188 MA0188.1.Dr 1 Dr NK-related factors Q03372 bacterial 1-hybrid insects Drosophila melanogaster 2.7665,6.1725,6.5595,11.498,12.039189485424846,12.039189485424846 +MA0189 MA0189.1.E5 1 E5 . Q9VFQ3 bacterial 1-hybrid insects Drosophila melanogaster 3.694,7.395,8.9335,10.822,10.910121836915714,10.910121836915714 +MA0190 MA0190.1.Gsc 1 Gsc Paired-related HD factors P54366 bacterial 1-hybrid insects Drosophila melanogaster 3.4055,4.5945,8.407,10.475668520459644,10.475668520459644,10.475668520459644 +MA0191 MA0191.1.HGTX 1 HGTX NK-related factors Q9NHP8 bacterial 1-hybrid insects Drosophila melanogaster 3.8855,6.9535,8.8885,10.68,11.2216568081487,11.2216568081487 +MA0192 MA0192.1.Hmx 1 Hmx NK-related factors Q9VEI9 bacterial 1-hybrid insects Drosophila melanogaster 2.9705,6.585,7.9635,10.7585,11.725922186843473,11.725922186843473 +MA0193 MA0193.1.schlank 1 schlank . Q9W423 bacterial 1-hybrid insects Drosophila melanogaster 4.224,7.2215,8.805,10.9415,11.014385824375502,11.014385824375502 +MA0194 MA0194.1.Lim1 1 Lim1 HD-LIM factors Q9V472 bacterial 1-hybrid insects Drosophila melanogaster 1.133,7.1555,7.1555,10.493,11.91830106430854,11.91830106430854 +MA0195 MA0195.1.Lim3 1 Lim3 HD-LIM factors Q9VJ02 bacterial 1-hybrid insects Drosophila melanogaster 4.669,7.599,8.7565,10.6915,10.784659056811046,10.784659056811046 +MA0196 MA0196.1.NK7.1 1 NK7 NK-related factors O61640 bacterial 1-hybrid insects Drosophila melanogaster 4.272,7.526,8.8315,10.6635,11.036628863787035,11.036628863787035 +MA0197 MA0197.2.nub 2 nub POU domain factors P31368 bacterial 1-hybrid insects Drosophila melanogaster 0.7875,5.0975,6.716,10.0275,11.2755,13.8465 +MA0198 MA0198.1.OdsH 1 OdsH Paired-related HD factors O96616 bacterial 1-hybrid insects Drosophila melanogaster 4.0535,5.458,7.123,11.2995,11.61657096272472,11.61657096272472 +MA0199 MA0199.1.Optix 1 Optix HD-SINE factors Q95RW8 bacterial 1-hybrid insects Drosophila melanogaster 2.983,7.3755,8.41604930858146,8.41604930858146,8.41604930858146,8.41604930858146 +MA0200 MA0200.1.Pph13 1 Pph13 . Q8T0V5 bacterial 1-hybrid insects Drosophila melanogaster 4.041,6.7845,8.1285,11.134,11.333438026104142,11.333438026104142 +MA0201 MA0201.1.Ptx1 1 Ptx1 Paired-related HD factors O18400 bacterial 1-hybrid insects Drosophila melanogaster 1.3275,6.713,6.713,11.6125,12.332418314138454,12.332418314138454 +MA0202 MA0202.1.Rx 1 Rx Paired-related HD factors Q9W2Q1 bacterial 1-hybrid insects Drosophila melanogaster 3.231,5.2585,5.9185,11.791,11.907848401706008,11.907848401706008 +MA0203 MA0203.1.Scr 1 Scr HOX-related factors P09077 bacterial 1-hybrid insects Drosophila melanogaster 3.3275,5.7325,7.69,11.318,11.853110440352813,11.853110440352813 +MA0204 MA0204.1.Six4 1 Six4 HD-SINE factors Q9Y1P6 bacterial 1-hybrid insects Drosophila melanogaster 4.142,6.1855,9.36,10.305999195939098,10.305999195939098,10.305999195939098 +MA0205 MA0205.2.Trl 2 Trl . Q08605 ChIP-seq insects Drosophila melanogaster 0.4555,5.0495,6.6905,10.2005,11.582,14.123 +MA0206 MA0206.1.abd-A 1 abd-A HOX-related factors P29555 bacterial 1-hybrid insects Drosophila melanogaster 3.7785,6.541,8.4225,11.1835,11.667959162134153,11.667959162134153 +MA0207 MA0207.1.achi 1 achi . A1Z916 bacterial 1-hybrid insects Drosophila melanogaster 4.5535,5.5375,8.7075,10.19520595147858,10.19520595147858,10.19520595147858 +MA0208 MA0208.1.al 1 al Paired-related HD factors Q06453 bacterial 1-hybrid insects Drosophila melanogaster 0.803,6.9115,6.9115,10.8435,12.04733470131145,12.04733470131145 +MA0209 MA0209.1.ap 1 ap . P29673 bacterial 1-hybrid insects Drosophila melanogaster 3.93,6.252,8.4395,11.346,11.594742284217666,11.594742284217666 +MA0210 MA0210.1.ara 1 ara TALE-type homeo domain factors Q24248 bacterial 1-hybrid insects Drosophila melanogaster 5.5315,8.0195,8.068653651128592,8.068653651128592,8.068653651128592,8.068653651128592 +MA0211 MA0211.1.bap 1 bap NK-related factors P22809 bacterial 1-hybrid insects Drosophila melanogaster 1.1785,6.497,6.56,11.8715,12.453539005394841,12.453539005394841 +MA0212 MA0212.1.bcd 1 bcd Paired-related HD factors P09081 bacterial 1-hybrid insects Drosophila melanogaster 4.1875,5.105,7.3575,9.859497930995987,9.859497930995987,9.859497930995987 +MA0213 MA0213.1.brk 1 brk . Q9XTN4 DNaseI footprinting insects Drosophila melanogaster 4.0955,6.8705,8.496,11.2185,11.5235,11.92711429431131 +MA0214 MA0214.1.bsh 1 bsh NK-related factors Q04787 bacterial 1-hybrid insects Drosophila melanogaster 4.315,7.6455,8.803,10.5975,10.703524850594057,10.703524850594057 +MA0215 MA0215.1.btn 1 btn . Q9U984 bacterial 1-hybrid insects Drosophila melanogaster 3.8055,7.03,8.4085,10.975,11.417319702819537,11.417319702819537 +MA0216 MA0216.2.cad 2 cad HOX-related factors P09085 ChIP-chip insects Drosophila melanogaster -5.5745,1.44,4.9515,10.372,11.7865,14.369 +MA0217 MA0217.1.caup 1 caup TALE-type homeo domain factors P54269 bacterial 1-hybrid insects Drosophila melanogaster 5.3465,7.112,7.874695504495408,7.874695504495408,7.874695504495408,7.874695504495408 +MA0218 MA0218.1.ct 1 ct HD-CUT factors P10180 bacterial 1-hybrid insects Drosophila melanogaster 4.6605,6.856,8.6055,9.653324165607355,9.653324165607355,9.653324165607355 +MA0219 MA0219.1.ems 1 ems NK-related factors P18488 bacterial 1-hybrid insects Drosophila melanogaster 4.2825,7.728,8.9785,10.4875,10.561571646518482,10.561571646518482 +MA0220 MA0220.1.en 1 en NK-related factors P02836 bacterial 1-hybrid insects Drosophila melanogaster 2.9595,5.759,8.4515,11.3205,11.50587800144205,11.50587800144205 +MA0221 MA0221.1.eve 1 eve HOX-related factors P06602 bacterial 1-hybrid insects Drosophila melanogaster 4.3635,7.243,8.6175,10.773,10.846590884597669,10.846590884597669 +MA0222 MA0222.1.exd 1 exd TALE-type homeo domain factors P40427 bacterial 1-hybrid insects Drosophila melanogaster 3.3305,6.2985,8.048,11.254,12.102,12.254040902198351 +MA0224 MA0224.1.exex 1 exex . Q9VSC2 bacterial 1-hybrid insects Drosophila melanogaster 2.4905,5.6295,7.5815,11.669,11.918905178279184,11.918905178279184 +MA0225 MA0225.1.ftz 1 ftz HOX-related factors P02835 bacterial 1-hybrid insects Drosophila melanogaster 3.3225,6.3845,8.13,11.0428726702125,11.0428726702125,11.0428726702125 +MA0226 MA0226.1.hbn 1 hbn . Q9W2P8 bacterial 1-hybrid insects Drosophila melanogaster 3.624,5.946,9.167,11.703,11.878717550502595,11.878717550502595 +MA0227 MA0227.1.hth 1 hth TALE-type homeo domain factors O46339 bacterial 1-hybrid insects Drosophila melanogaster 3.9715,5.717,8.629,10.28285159622916,10.28285159622916,10.28285159622916 +MA0228 MA0228.1.ind 1 ind . O96620 bacterial 1-hybrid insects Drosophila melanogaster 2.732,5.829,7.7765,11.557,11.758790080966829,11.758790080966829 +MA0229 MA0229.1.inv 1 inv NK-related factors P05527 bacterial 1-hybrid insects Drosophila melanogaster 2.092,6.202,7.3015,11.6365,12.202,13.040097574800019 +MA0230 MA0230.1.lab 1 lab HOX-related factors P10105 bacterial 1-hybrid insects Drosophila melanogaster 3.066,6.3585,7.0235,11.6675,12.023382642235942,12.023382642235942 +MA0231 MA0231.1.lbe 1 lbe . Q9VDA1 bacterial 1-hybrid insects Drosophila melanogaster 5.0445,7.9975,8.3025,9.193669786993617,9.193669786993617,9.193669786993617 +MA0232 MA0232.1.lbl 1 lbl . P91626 bacterial 1-hybrid insects Drosophila melanogaster 3.4815,8.1065,8.556,9.642395864276734,9.642395864276734,9.642395864276734 +MA0233 MA0233.1.mirr 1 mirr . O01667 bacterial 1-hybrid insects Drosophila melanogaster 4.5745,8.275,8.311062520216813,8.311062520216813,8.311062520216813,8.311062520216813 +MA0234 MA0234.1.oc 1 oc Paired-related HD factors P22810 bacterial 1-hybrid insects Drosophila melanogaster 4.6285,5.245,7.567,9.88332677934384,9.88332677934384,9.88332677934384 +MA0235 MA0235.1.onecut 1 onecut HD-CUT factors Q9NJB5 bacterial 1-hybrid insects Drosophila melanogaster 3.285,5.981,8.0625,11.66,11.786483338206384,11.786483338206384 +MA0236 MA0236.1.otp 1 otp Paired-related HD factors P56672 bacterial 1-hybrid insects Drosophila melanogaster 3.7105,7.2895,8.724,11.046,11.469443908075423,11.469443908075423 +MA0237 MA0237.2.pan 2 pan . Q8IMA8 ChIP-chip insects Drosophila melanogaster -2.2365,3.6415,5.4335,9.5445,11.4965,14.3035 +MA0238 MA0238.1.pb 1 pb HOX-related factors P31264 bacterial 1-hybrid insects Drosophila melanogaster 3.708,5.1125,5.9845,11.4765,11.59431075428868,11.59431075428868 +MA0239 MA0239.1.prd 1 prd . P23758 bacterial 1-hybrid insects Drosophila melanogaster 3.947,7.5605,8.682,10.4615,11.0835,12.102 +MA0240 MA0240.1.repo 1 repo . Q24477 bacterial 1-hybrid insects Drosophila melanogaster 2.7245,6.0415,8.221,11.1155,11.89151107723395,11.89151107723395 +MA0241 MA0241.1.ro 1 ro . P10181 bacterial 1-hybrid insects Drosophila melanogaster 3.1045,5.943,8.1895,11.5265,11.90487970258495,11.90487970258495 +MA0242 MA0242.1.Bgb::run 1 Bgb::run Runt-related factors Q24040 bacterial 1-hybrid insects Drosophila melanogaster 1.01,5.188,7.132,9.99,11.1205,14.4885 +MA0243 MA0243.1.sd 1 sd . P30052 DNaseI footprinting insects Drosophila melanogaster 4.9455,7.386,8.2115,9.7865,10.343,11.317 +MA0244 MA0244.1.slbo 1 slbo C/EBP-related factors Q02637 DNaseI footprinting insects Drosophila melanogaster 4.8985,7.2205,8.32,9.829,10.108,11.390695979938483 +MA0245 MA0245.1.slou 1 slou NK-related factors P22807 bacterial 1-hybrid insects Drosophila melanogaster 4.2265,7.648,8.496,10.490177090974505,10.490177090974505,10.490177090974505 +MA0246 MA0246.1.so 1 so HD-SINE factors Q27350 bacterial 1-hybrid insects Drosophila melanogaster 4.479,5.89,6.855,10.417910338696988,10.417910338696988,10.417910338696988 +MA0247 MA0247.2.tin 2 tin . P22711 ChIP-chip insects Drosophila melanogaster -3.1185,2.202,4.6015,10.8195,12.043,14.2915 +MA0248 MA0248.1.tup 1 tup HD-LIM factors Q9VJ37 bacterial 1-hybrid insects Drosophila melanogaster 4.6715,7.499,8.4565,10.9925,11.084684466467323,11.084684466467323 +MA0249 MA0249.2.twi 2 twi . P10627 ChIP-seq insects Drosophila melanogaster 2.28,6.48,7.6565,10.7405,12.1305,13.6445 +MA0250 MA0250.1.unc-4 1 unc-4 Paired-related HD factors O77215 bacterial 1-hybrid insects Drosophila melanogaster 3.389,5.983,8.305,11.134,11.727685973507285,11.727685973507285 +MA0251 MA0251.1.unpg 1 unpg . Q4V5A3 bacterial 1-hybrid insects Drosophila melanogaster 4.1305,6.522,7.9995,11.0965,11.452382132892698,11.452382132892698 +MA0252 MA0252.1.vis 1 vis . A1Z913 bacterial 1-hybrid insects Drosophila melanogaster 3.285,4.242,8.843,10.239323013600979,10.239323013600979,10.239323013600979 +MA0253 MA0253.1.vnd 1 vnd NK-related factors P22808 bacterial 1-hybrid insects Drosophila melanogaster 2.4415,6.0995,8.073,11.4015,11.634,14.34 +MA0254 MA0254.1.vvl 1 vvl POU domain factors P16241 DNaseI footprinting insects Drosophila melanogaster 4.5865,7.5425,7.8865,9.103846474724131,9.103846474724131,9.103846474724131 +MA0255 MA0255.1.z 1 z . P09956 DNaseI footprinting insects Drosophila melanogaster 4.378,7.5065,8.531,10.381,10.9725,12.0255 +MA0256 MA0256.1.zen 1 zen . P09089 bacterial 1-hybrid insects Drosophila melanogaster 4.14,6.1795,6.71,11.385,11.792337666923427,11.792337666923427 +MA0257 MA0257.1.zen2 1 zen2 . P09090 bacterial 1-hybrid insects Drosophila melanogaster 3.8765,7.1155,8.9955,10.818,11.133719775415031,11.133719775415031 +MA0443 MA0443.1.btd 1 btd Other factors with up to three adjacent zinc fingers Q24266 bacterial 1-hybrid insects Drosophila melanogaster 1.602,5.894,7.246,10.855,12.171,13.769 +MA0444 MA0444.1.CG34031 1 CG34031 . M9NDG6 bacterial 1-hybrid insects Drosophila melanogaster 3.1185,6.408,8.3355,11.302,11.926382148617673,11.926382148617673 +MA0445 MA0445.1.D 1 D . Q24533 bacterial 1-hybrid insects Drosophila melanogaster 1.908,5.9475,7.5365,10.6125,11.6945,13.87 +MA0446 MA0446.1.fkh 1 fkh Forkhead box (FOX) factors P14734 bacterial 1-hybrid insects Drosophila melanogaster 2.3445,6.282,7.6875,10.7365,11.872,13.6135 +MA0447 MA0447.1.gt 1 gt . P39572 bacterial 1-hybrid insects Drosophila melanogaster 0.231,4.9425,6.376,10.05,11.1815,13.6885 +MA0448 MA0448.1.H2.0 1 H2 NK-related factors P10035 bacterial 1-hybrid insects Drosophila melanogaster 4.827,7.791,8.545,10.168,10.261683058201085,10.261683058201085 +MA0449 MA0449.1.h 1 h Helix-Loop-Helix P14003 bacterial 1-hybrid insects Drosophila melanogaster 3.873,6.957,8.247,10.2105,10.8855,13.114 +MA0450 MA0450.1.hkb 1 hkb . Q9VN10 bacterial 1-hybrid insects Drosophila melanogaster 0.349,5.2635,6.6075,10.189,11.7445,14.317 +MA0451 MA0451.1.kni 1 kni . P10734 bacterial 1-hybrid insects Drosophila melanogaster 1.5655,5.685,7.2105,10.359,11.5215,13.8615 +MA0452 MA0452.2.Kr 2 Kr More than 3 adjacent zinc finger factors P07247 ChIP-chip insects Drosophila melanogaster -5.036,1.7465,4.6865,9.9675,11.4975,14.183 +MA0454 MA0454.1.odd 1 odd More than 3 adjacent zinc finger factors P23803 bacterial 1-hybrid insects Drosophila melanogaster 0.8615,5.0345,6.6015,10.091,11.056,14.1075 +MA0456 MA0456.1.opa 1 opa More than 3 adjacent zinc finger factors P39768 bacterial 1-hybrid insects Drosophila melanogaster 1.6245,5.5685,7.021,10.044,11.267,13.61 +MA0457 MA0457.1.PHDP 1 PHDP . Q9W1H7 bacterial 1-hybrid insects Drosophila melanogaster 4.113,7.169,9.2645,10.778,10.884516222639265,10.884516222639265 +MA0458 MA0458.1.slp1 1 slp1 Forkhead box (FOX) factors P32030 bacterial 1-hybrid insects Drosophila melanogaster 2.3065,6.249,7.7955,10.89,11.859,13.556 +MA0459 MA0459.1.tll 1 tll . P18102 bacterial 1-hybrid insects Drosophila melanogaster -0.1835,4.007,6.024,9.917,10.765,14.561 +MA0460 MA0460.1.ttk 1 ttk Other factors with up to three adjacent zinc fingers P17789 bacterial 1-hybrid insects Drosophila melanogaster 1.029,5.759,7.1375,10.148,11.897,13.9345 +MA0529 MA0529.2.BEAF-32 2 BEAF-32 . Q94513 ChIP-seq insects Drosophila melanogaster 1.2205,5.5025,6.9875,10.1825,11.52,14.4 +MA0530 MA0530.1.cnc::maf-S 1 cnc::maf-S Jun-related factors;Maf-related factors P20482;Q4QPP9 ChIP-chip insects Drosophila melanogaster -3.56,2.6075,5.2215,10.181,11.611,14.245 +MA0531 MA0531.1.CTCF 1 CTCF More than 3 adjacent zinc finger factors Q9VS55 ChIP-chip insects Drosophila melanogaster -2.398,3.8505,6.0165,9.965,11.3165,13.9105 +MA0532 MA0532.1.Stat92E 1 Stat92E STAT factors Q24151 ChIP-chip insects Drosophila melanogaster -1.238,3.9405,5.8445,9.728,11.2255,14.096 +MA0533 MA0533.1.su(Hw) 1 su(Hw) Factors with multiple dispersed zinc fingers P08970 ChIP-chip insects Drosophila melanogaster -2.169,2.7625,4.6175,8.445,9.9195,13.0115 +MA0534 MA0534.1.EcR::usp 1 EcR::usp . P34021;P20153 ChIP-seq insects Drosophila melanogaster -2.111,3.561,5.547,9.873,11.4425,14.162 +MA0535 MA0535.1.Mad 1 Mad SMAD factors P42003 ChIP-chip insects Drosophila melanogaster 0.122,4.8575,7.039,10.877,11.947,13.8245 +MA0536 MA0536.1.pnr 1 pnr GATA-type zinc fingers Q9VEZ8 ChIP-chip insects Drosophila melanogaster -5.7575,1.172,3.5265,10.025,11.792,14.4185 +MA0915 MA0915.1.dve 1 dve . Q9W268 PBM insects Drosophila melanogaster -3.9895,1.064,1.1055,12.157,12.5715,12.799005525443059 +MA0916 MA0916.1.Ets21C 1 Ets21C Ets-related factors P29776 PBM insects Drosophila melanogaster -4.5455,3.7795,4.3635,10.272,12.422,14.235954588907973 +MA0917 MA0917.1.gcm2 1 gcm2 GCM factors Q9VLA2 PBM insects Drosophila melanogaster 1.583,7.0005,8.553,10.9315,11.2675,13.10116655261472 +MA1455 MA1455.1.dmrt99B 1 dmrt99B DMRT factors Q9VAI8 HT-SELEX insects Drosophila melanogaster -1.4425,3.407,5.237,9.0095,10.456,13.4625 +MA1456 MA1456.1.Dref 1 Dref BED zinc finger factors O96083 ChIP-seq insects Drosophila melanogaster -11.804,-1.081,0.5305,10.628,12.1495,14.564 +MA1457 MA1457.1.grh 1 grh Grainyhead-related factors P13002 ChIP-seq insects Drosophila melanogaster 1.191,5.3855,7.008,10.1265,11.414,14.019 +MA1458 MA1458.1.Hsf 1 Hsf HSF factors P22813 ChIP-seq insects Drosophila melanogaster 2.1965,5.675,7.736,9.848,10.8995,14.2725 +MA1459 MA1459.1.M1BP 1 M1BP . Q9VHM3 ChIP-seq insects Drosophila melanogaster -1.9865,3.0675,4.9705,8.889,10.3885,13.4885 +MA1460 MA1460.1.pho 1 pho . Q8ST83 ChIP-seq insects Drosophila melanogaster 3.7255,7.1585,8.2295,10.054,11.8935,13.2235 +MA1461 MA1461.1.sv 1 sv . O16804 HT-SELEX insects Drosophila melanogaster -7.2285,-0.8485,1.5525,6.508,8.41,12.3395 +MA1462 MA1462.1.vfl 1 vfl . Q9VWC6 ChIP-seq insects Drosophila melanogaster 1.9625,5.882,7.194,11.1065,12.262,13.5485 +MA1700 MA1700.1.Clamp 1 Clamp . Q8IGP5 ChIP-seq insects Drosophila melanogaster -0.042,4.3805,6.056,9.525,10.853,13.625 +MA1702 MA1702.1.Pdp1 1 Pdp1 . Q24217 ChIP-seq insects Drosophila melanogaster 2.0745,5.5835,7.526,10.108,11.0555,14.2675 diff --git a/data/motifs/jaspar_insects/MA0010.1.br.pwm b/data/motifs/jaspar_insects/MA0010.1.br.pwm new file mode 100644 index 000000000..e38d3f321 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0010.1.br.pwm @@ -0,0 +1,4 @@ +3 1 5 7 3 6 4 7 1 9 8 5 4 2 +1 1 2 0 0 0 1 0 8 0 0 0 0 3 +4 1 1 1 0 0 4 1 0 0 1 3 0 2 +1 6 1 1 6 3 0 1 0 0 0 1 5 2 diff --git a/data/motifs/jaspar_insects/MA0011.1.br(var.2).pwm b/data/motifs/jaspar_insects/MA0011.1.br(var.2).pwm new file mode 100644 index 000000000..977e8fd02 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0011.1.br(var.2).pwm @@ -0,0 +1,4 @@ +3 5 0 0 12 1 2 1 +1 2 10 1 0 1 0 2 +1 1 0 0 0 2 1 1 +7 4 2 11 0 8 9 8 diff --git a/data/motifs/jaspar_insects/MA0012.1.br(var.3).pwm b/data/motifs/jaspar_insects/MA0012.1.br(var.3).pwm new file mode 100644 index 000000000..fe12398c4 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0012.1.br(var.3).pwm @@ -0,0 +1,4 @@ +3 9 10 12 0 4 10 6 6 4 2 +1 2 0 0 10 0 0 0 1 3 3 +1 1 0 0 1 0 0 4 2 2 5 +7 0 2 0 1 8 2 2 3 3 2 diff --git a/data/motifs/jaspar_insects/MA0013.1.br(var.4).pwm b/data/motifs/jaspar_insects/MA0013.1.br(var.4).pwm new file mode 100644 index 000000000..36c4726c2 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0013.1.br(var.4).pwm @@ -0,0 +1,4 @@ +1 4 2 1 5 6 5 1 3 5 3 +1 0 0 0 0 0 0 3 0 0 1 +0 0 4 0 1 0 1 1 1 0 0 +4 2 0 5 0 0 0 1 2 1 2 diff --git a/data/motifs/jaspar_insects/MA0015.1.Cf2.pwm b/data/motifs/jaspar_insects/MA0015.1.Cf2.pwm new file mode 100644 index 000000000..91b5334c3 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0015.1.Cf2.pwm @@ -0,0 +1,4 @@ +25 1 74 0 78 1 41 2 53 12 +13 2 2 9 2 4 2 9 3 29 +40 1 4 4 0 1 36 1 20 15 +2 76 0 67 0 74 1 68 4 24 diff --git a/data/motifs/jaspar_insects/MA0016.1.usp.pwm b/data/motifs/jaspar_insects/MA0016.1.usp.pwm new file mode 100644 index 000000000..c8d985b6d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0016.1.usp.pwm @@ -0,0 +1,4 @@ +0 1 0 0 0 0 35 5 5 6 +1 0 0 0 0 36 0 25 8 10 +37 36 38 38 0 1 3 3 22 16 +0 1 0 0 38 1 0 5 3 6 diff --git a/data/motifs/jaspar_insects/MA0022.1.dl.pwm b/data/motifs/jaspar_insects/MA0022.1.dl.pwm new file mode 100644 index 000000000..b7d5149e7 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0022.1.dl.pwm @@ -0,0 +1,4 @@ +0 0 0 0 1 1 1 0 0 1 1 3 +5 0 1 0 1 0 0 0 3 9 9 5 +6 12 11 10 3 2 0 0 0 0 1 5 +2 1 1 3 8 10 12 13 10 3 2 0 diff --git a/data/motifs/jaspar_insects/MA0023.1.dl(var.2).pwm b/data/motifs/jaspar_insects/MA0023.1.dl(var.2).pwm new file mode 100644 index 000000000..b964a3d97 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0023.1.dl(var.2).pwm @@ -0,0 +1,4 @@ +0 0 0 0 4 2 0 0 0 1 +1 0 0 0 1 1 0 1 9 8 +7 7 9 8 0 0 0 0 0 0 +1 2 0 1 4 6 9 8 0 0 diff --git a/data/motifs/jaspar_insects/MA0026.1.Eip74EF.pwm b/data/motifs/jaspar_insects/MA0026.1.Eip74EF.pwm new file mode 100644 index 000000000..e1e925dd7 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0026.1.Eip74EF.pwm @@ -0,0 +1,4 @@ +2 5 0 0 17 17 5 +12 12 0 0 0 0 1 +2 0 17 17 0 0 10 +1 0 0 0 0 0 1 diff --git a/data/motifs/jaspar_insects/MA0049.1.hb.pwm b/data/motifs/jaspar_insects/MA0049.1.hb.pwm new file mode 100644 index 000000000..c1e2ebbc9 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0049.1.hb.pwm @@ -0,0 +1,4 @@ +1 6 9 4 13 16 16 14 15 9 +5 8 3 3 1 0 0 0 1 2 +8 2 4 1 0 0 0 2 0 2 +2 0 0 8 2 0 0 0 0 3 diff --git a/data/motifs/jaspar_insects/MA0085.1.Su(H).pwm b/data/motifs/jaspar_insects/MA0085.1.Su(H).pwm new file mode 100644 index 000000000..6dab1fc2d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0085.1.Su(H).pwm @@ -0,0 +1,4 @@ +1 0 0 0 0 3 0 10 10 5 1 1 4 3 4 2 +3 4 0 0 0 0 0 0 0 5 7 2 2 1 3 1 +3 0 10 0 10 7 10 0 0 0 1 4 2 4 2 2 +3 6 0 10 0 0 0 0 0 0 1 3 2 2 1 5 diff --git a/data/motifs/jaspar_insects/MA0086.2.sna.pwm b/data/motifs/jaspar_insects/MA0086.2.sna.pwm new file mode 100644 index 000000000..cf19599c4 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0086.2.sna.pwm @@ -0,0 +1,4 @@ +241 128 454 835 5 984 87 5 5 10 42 535 290 +200 324 57 7 984 4 4 4 4 5 455 139 244 +309 264 387 114 6 7 903 986 7 976 184 147 230 +250 284 102 44 5 5 6 5 984 10 319 179 236 diff --git a/data/motifs/jaspar_insects/MA0094.2.Ubx.pwm b/data/motifs/jaspar_insects/MA0094.2.Ubx.pwm new file mode 100644 index 000000000..9eea329ab --- /dev/null +++ b/data/motifs/jaspar_insects/MA0094.2.Ubx.pwm @@ -0,0 +1,4 @@ +3 0 0 17 20 0 0 14 +5 0 0 0 0 0 0 0 +3 0 0 0 0 0 6 6 +9 20 20 3 0 20 14 0 diff --git a/data/motifs/jaspar_insects/MA0126.1.ovo.pwm b/data/motifs/jaspar_insects/MA0126.1.ovo.pwm new file mode 100644 index 000000000..3b5d48bdc --- /dev/null +++ b/data/motifs/jaspar_insects/MA0126.1.ovo.pwm @@ -0,0 +1,4 @@ +10 1 4 20 21 0 7 0 5 +4 4 2 0 0 21 5 0 4 +0 14 2 0 0 0 3 21 2 +7 2 13 1 0 0 6 0 10 diff --git a/data/motifs/jaspar_insects/MA0165.1.Abd-B.pwm b/data/motifs/jaspar_insects/MA0165.1.Abd-B.pwm new file mode 100644 index 000000000..876d9230e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0165.1.Abd-B.pwm @@ -0,0 +1,4 @@ +1 0 5 21 0 3 13 +0 0 0 0 3 0 0 +0 0 0 0 0 11 5 +20 21 16 0 18 7 3 diff --git a/data/motifs/jaspar_insects/MA0166.1.Antp.pwm b/data/motifs/jaspar_insects/MA0166.1.Antp.pwm new file mode 100644 index 000000000..c27a6edb3 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0166.1.Antp.pwm @@ -0,0 +1,4 @@ +1 0 16 16 0 0 15 +1 0 0 0 0 0 0 +0 0 0 0 0 9 1 +14 16 0 0 16 7 0 diff --git a/data/motifs/jaspar_insects/MA0167.1.Awh.pwm b/data/motifs/jaspar_insects/MA0167.1.Awh.pwm new file mode 100644 index 000000000..060829199 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0167.1.Awh.pwm @@ -0,0 +1,4 @@ +3 1 33 40 0 0 34 +16 0 0 0 0 0 0 +0 0 7 0 1 8 4 +21 39 0 0 39 32 2 diff --git a/data/motifs/jaspar_insects/MA0168.1.B-H1.pwm b/data/motifs/jaspar_insects/MA0168.1.B-H1.pwm new file mode 100644 index 000000000..d18631000 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0168.1.B-H1.pwm @@ -0,0 +1,4 @@ +4 0 21 21 8 1 1 +4 0 0 0 0 7 0 +0 0 0 0 0 0 20 +13 21 0 0 13 13 0 diff --git a/data/motifs/jaspar_insects/MA0169.1.B-H2.pwm b/data/motifs/jaspar_insects/MA0169.1.B-H2.pwm new file mode 100644 index 000000000..f78277898 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0169.1.B-H2.pwm @@ -0,0 +1,4 @@ +6 0 21 21 5 3 0 +2 0 0 0 0 1 0 +1 0 0 0 0 2 21 +12 21 0 0 16 15 0 diff --git a/data/motifs/jaspar_insects/MA0170.1.C15.pwm b/data/motifs/jaspar_insects/MA0170.1.C15.pwm new file mode 100644 index 000000000..8a14f9f1f --- /dev/null +++ b/data/motifs/jaspar_insects/MA0170.1.C15.pwm @@ -0,0 +1,4 @@ +1 0 17 19 6 0 10 +1 0 0 0 2 3 0 +0 0 0 0 0 6 9 +17 19 2 0 11 10 0 diff --git a/data/motifs/jaspar_insects/MA0171.1.CG11085.pwm b/data/motifs/jaspar_insects/MA0171.1.CG11085.pwm new file mode 100644 index 000000000..1d51a50a5 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0171.1.CG11085.pwm @@ -0,0 +1,4 @@ +0 0 13 13 1 2 1 +3 0 0 0 0 1 0 +0 0 0 0 0 2 12 +10 13 0 0 12 8 0 diff --git a/data/motifs/jaspar_insects/MA0172.1.CG11294.pwm b/data/motifs/jaspar_insects/MA0172.1.CG11294.pwm new file mode 100644 index 000000000..75062e5b7 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0172.1.CG11294.pwm @@ -0,0 +1,4 @@ +0 0 15 15 0 0 15 +3 2 0 0 0 0 0 +0 0 0 0 0 0 0 +12 13 0 0 15 15 0 diff --git a/data/motifs/jaspar_insects/MA0173.1.CG11617.pwm b/data/motifs/jaspar_insects/MA0173.1.CG11617.pwm new file mode 100644 index 000000000..d5e2ab9e0 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0173.1.CG11617.pwm @@ -0,0 +1,4 @@ +1 0 10 17 0 17 0 +0 0 0 0 17 0 0 +0 0 3 0 0 0 0 +16 17 4 0 0 0 17 diff --git a/data/motifs/jaspar_insects/MA0174.1.Dbx.pwm b/data/motifs/jaspar_insects/MA0174.1.Dbx.pwm new file mode 100644 index 000000000..11c47445e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0174.1.Dbx.pwm @@ -0,0 +1,4 @@ +2 2 6 16 0 0 13 +0 0 0 0 0 2 0 +0 0 2 0 0 6 3 +14 14 8 0 16 8 0 diff --git a/data/motifs/jaspar_insects/MA0175.1.lms.pwm b/data/motifs/jaspar_insects/MA0175.1.lms.pwm new file mode 100644 index 000000000..203e23c1b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0175.1.lms.pwm @@ -0,0 +1,4 @@ +2 0 21 21 0 3 8 +7 0 0 0 0 0 0 +1 0 0 0 0 4 13 +11 21 0 0 21 14 0 diff --git a/data/motifs/jaspar_insects/MA0176.1.CG15696-RA.pwm b/data/motifs/jaspar_insects/MA0176.1.CG15696-RA.pwm new file mode 100644 index 000000000..df3ea5010 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0176.1.CG15696-RA.pwm @@ -0,0 +1,4 @@ +2 2 21 32 0 0 16 +3 3 0 0 0 0 0 +3 0 6 0 0 2 16 +24 27 5 0 32 30 0 diff --git a/data/motifs/jaspar_insects/MA0177.1.CG18599.pwm b/data/motifs/jaspar_insects/MA0177.1.CG18599.pwm new file mode 100644 index 000000000..66f359fa6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0177.1.CG18599.pwm @@ -0,0 +1,4 @@ +4 0 25 25 0 0 23 +10 0 0 0 0 1 0 +1 0 0 0 0 8 2 +10 25 0 0 25 16 0 diff --git a/data/motifs/jaspar_insects/MA0178.1.CG32105.pwm b/data/motifs/jaspar_insects/MA0178.1.CG32105.pwm new file mode 100644 index 000000000..42e90051d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0178.1.CG32105.pwm @@ -0,0 +1,4 @@ +2 2 17 19 0 0 15 +4 0 0 0 0 0 0 +0 0 0 0 1 1 4 +13 17 2 0 18 18 0 diff --git a/data/motifs/jaspar_insects/MA0179.1.CG32532.pwm b/data/motifs/jaspar_insects/MA0179.1.CG32532.pwm new file mode 100644 index 000000000..7116d23b8 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0179.1.CG32532.pwm @@ -0,0 +1,4 @@ +2 0 23 23 0 0 12 +6 0 0 0 0 0 0 +2 0 0 0 0 2 10 +13 23 0 0 23 21 1 diff --git a/data/motifs/jaspar_insects/MA0180.1.Vsx2.pwm b/data/motifs/jaspar_insects/MA0180.1.Vsx2.pwm new file mode 100644 index 000000000..bcb15c338 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0180.1.Vsx2.pwm @@ -0,0 +1,4 @@ +1 2 0 13 13 0 0 10 1 +1 2 0 0 0 0 0 0 2 +5 0 0 0 0 0 0 3 10 +6 9 13 0 0 13 13 0 0 diff --git a/data/motifs/jaspar_insects/MA0181.1.Vsx1.pwm b/data/motifs/jaspar_insects/MA0181.1.Vsx1.pwm new file mode 100644 index 000000000..9f5c2e914 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0181.1.Vsx1.pwm @@ -0,0 +1,4 @@ +1 0 22 22 0 2 15 +8 0 0 0 0 0 0 +1 0 0 0 0 3 6 +12 22 0 0 22 17 1 diff --git a/data/motifs/jaspar_insects/MA0182.1.CG4328-RA.pwm b/data/motifs/jaspar_insects/MA0182.1.CG4328-RA.pwm new file mode 100644 index 000000000..45125aa01 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0182.1.CG4328-RA.pwm @@ -0,0 +1,4 @@ +12 7 13 30 0 0 15 +2 1 0 0 0 0 0 +3 0 0 0 0 6 15 +13 22 17 0 30 24 0 diff --git a/data/motifs/jaspar_insects/MA0183.1.HHEX.pwm b/data/motifs/jaspar_insects/MA0183.1.HHEX.pwm new file mode 100644 index 000000000..69305561d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0183.1.HHEX.pwm @@ -0,0 +1,4 @@ +7 0 0 21 26 0 7 22 +3 7 6 0 0 3 0 0 +2 0 7 2 0 3 1 4 +14 19 13 3 0 20 18 0 diff --git a/data/motifs/jaspar_insects/MA0184.1.CG9876.pwm b/data/motifs/jaspar_insects/MA0184.1.CG9876.pwm new file mode 100644 index 000000000..659560e37 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0184.1.CG9876.pwm @@ -0,0 +1,4 @@ +2 0 18 20 0 0 14 +9 0 0 0 0 0 0 +3 0 0 0 0 1 6 +6 20 2 0 20 19 0 diff --git a/data/motifs/jaspar_insects/MA0185.1.Deaf1.pwm b/data/motifs/jaspar_insects/MA0185.1.Deaf1.pwm new file mode 100644 index 000000000..146358ed0 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0185.1.Deaf1.pwm @@ -0,0 +1,4 @@ +0 0 0 0 0 1 +3 0 10 0 0 3 +0 0 0 10 5 4 +7 10 0 0 5 2 diff --git a/data/motifs/jaspar_insects/MA0186.1.Dfd.pwm b/data/motifs/jaspar_insects/MA0186.1.Dfd.pwm new file mode 100644 index 000000000..e4a655115 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0186.1.Dfd.pwm @@ -0,0 +1,4 @@ +1 0 24 24 0 1 21 +4 0 0 0 0 0 0 +3 0 0 0 0 19 3 +16 24 0 0 24 4 0 diff --git a/data/motifs/jaspar_insects/MA0187.1.Dll.pwm b/data/motifs/jaspar_insects/MA0187.1.Dll.pwm new file mode 100644 index 000000000..bfca4c97f --- /dev/null +++ b/data/motifs/jaspar_insects/MA0187.1.Dll.pwm @@ -0,0 +1,4 @@ +1 22 23 0 3 10 1 +0 0 0 0 0 0 12 +0 1 0 0 3 9 4 +22 0 0 23 17 4 6 diff --git a/data/motifs/jaspar_insects/MA0188.1.Dr.pwm b/data/motifs/jaspar_insects/MA0188.1.Dr.pwm new file mode 100644 index 000000000..69bac1662 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0188.1.Dr.pwm @@ -0,0 +1,4 @@ +1 0 21 21 0 0 21 +13 16 0 0 0 0 0 +6 0 0 0 0 0 0 +1 5 0 0 21 21 0 diff --git a/data/motifs/jaspar_insects/MA0189.1.E5.pwm b/data/motifs/jaspar_insects/MA0189.1.E5.pwm new file mode 100644 index 000000000..2c3ae5398 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0189.1.E5.pwm @@ -0,0 +1,4 @@ +5 3 43 42 1 5 34 +15 0 0 0 0 0 0 +6 0 0 0 1 16 9 +17 40 0 1 41 22 0 diff --git a/data/motifs/jaspar_insects/MA0190.1.Gsc.pwm b/data/motifs/jaspar_insects/MA0190.1.Gsc.pwm new file mode 100644 index 000000000..5325f65c1 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0190.1.Gsc.pwm @@ -0,0 +1,4 @@ +0 22 22 0 0 0 +0 0 0 0 22 14 +0 0 0 0 0 2 +22 0 0 22 0 6 diff --git a/data/motifs/jaspar_insects/MA0191.1.HGTX.pwm b/data/motifs/jaspar_insects/MA0191.1.HGTX.pwm new file mode 100644 index 000000000..f4d8f8a6e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0191.1.HGTX.pwm @@ -0,0 +1,4 @@ +4 0 20 20 0 1 15 +2 0 0 0 0 0 0 +3 0 0 0 0 6 5 +11 20 0 0 20 13 0 diff --git a/data/motifs/jaspar_insects/MA0192.1.Hmx.pwm b/data/motifs/jaspar_insects/MA0192.1.Hmx.pwm new file mode 100644 index 000000000..afd0a5bb8 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0192.1.Hmx.pwm @@ -0,0 +1,4 @@ +1 0 20 20 1 0 4 +3 0 0 0 0 3 0 +0 0 0 0 0 0 16 +16 20 0 0 19 17 0 diff --git a/data/motifs/jaspar_insects/MA0193.1.schlank.pwm b/data/motifs/jaspar_insects/MA0193.1.schlank.pwm new file mode 100644 index 000000000..6e83581be --- /dev/null +++ b/data/motifs/jaspar_insects/MA0193.1.schlank.pwm @@ -0,0 +1,4 @@ +0 0 17 1 0 18 12 +19 9 2 18 12 0 0 +0 0 0 0 0 1 4 +0 10 0 0 7 0 3 diff --git a/data/motifs/jaspar_insects/MA0194.1.Lim1.pwm b/data/motifs/jaspar_insects/MA0194.1.Lim1.pwm new file mode 100644 index 000000000..2caffe52e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0194.1.Lim1.pwm @@ -0,0 +1,4 @@ +0 0 18 18 0 0 17 +2 0 0 0 0 0 0 +0 0 0 0 0 0 1 +16 18 0 0 18 18 0 diff --git a/data/motifs/jaspar_insects/MA0195.1.Lim3.pwm b/data/motifs/jaspar_insects/MA0195.1.Lim3.pwm new file mode 100644 index 000000000..a5a0f2138 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0195.1.Lim3.pwm @@ -0,0 +1,4 @@ +3 4 16 20 0 0 16 +7 0 0 0 0 2 0 +2 0 3 0 0 4 4 +8 16 1 0 20 14 0 diff --git a/data/motifs/jaspar_insects/MA0196.1.NK7.1.pwm b/data/motifs/jaspar_insects/MA0196.1.NK7.1.pwm new file mode 100644 index 000000000..a8f751690 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0196.1.NK7.1.pwm @@ -0,0 +1,4 @@ +5 0 33 35 4 6 13 +5 0 0 0 0 0 0 +1 0 2 0 5 7 22 +24 35 0 0 26 22 0 diff --git a/data/motifs/jaspar_insects/MA0197.2.nub.pwm b/data/motifs/jaspar_insects/MA0197.2.nub.pwm new file mode 100644 index 000000000..12a9ba099 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0197.2.nub.pwm @@ -0,0 +1,4 @@ +2 29 0 0 0 24 28 28 4 6 19 4 +1 0 0 0 19 0 0 0 1 5 5 3 +1 0 0 25 1 0 1 0 0 8 1 15 +25 0 29 4 9 5 0 1 24 10 4 7 diff --git a/data/motifs/jaspar_insects/MA0198.1.OdsH.pwm b/data/motifs/jaspar_insects/MA0198.1.OdsH.pwm new file mode 100644 index 000000000..3bbcdc44b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0198.1.OdsH.pwm @@ -0,0 +1,4 @@ +0 0 22 22 0 0 13 +11 0 0 0 0 0 0 +4 0 0 0 0 0 8 +7 22 0 0 22 22 1 diff --git a/data/motifs/jaspar_insects/MA0199.1.Optix.pwm b/data/motifs/jaspar_insects/MA0199.1.Optix.pwm new file mode 100644 index 000000000..d85987b2b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0199.1.Optix.pwm @@ -0,0 +1,4 @@ +0 0 27 0 26 +5 0 0 0 0 +0 27 0 0 1 +22 0 0 27 0 diff --git a/data/motifs/jaspar_insects/MA0200.1.Pph13.pwm b/data/motifs/jaspar_insects/MA0200.1.Pph13.pwm new file mode 100644 index 000000000..de39bedf5 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0200.1.Pph13.pwm @@ -0,0 +1,4 @@ +6 0 21 21 0 0 13 +8 0 0 0 0 1 1 +3 0 0 0 0 0 6 +4 21 0 0 21 20 1 diff --git a/data/motifs/jaspar_insects/MA0201.1.Ptx1.pwm b/data/motifs/jaspar_insects/MA0201.1.Ptx1.pwm new file mode 100644 index 000000000..51589482d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0201.1.Ptx1.pwm @@ -0,0 +1,4 @@ +0 0 20 20 0 0 0 +5 0 0 0 0 20 19 +1 0 0 0 0 0 0 +14 20 0 0 20 0 1 diff --git a/data/motifs/jaspar_insects/MA0202.1.Rx.pwm b/data/motifs/jaspar_insects/MA0202.1.Rx.pwm new file mode 100644 index 000000000..d20963302 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0202.1.Rx.pwm @@ -0,0 +1,4 @@ +3 0 27 27 0 0 17 +13 0 0 0 0 0 0 +0 0 0 0 0 0 10 +11 27 0 0 27 27 0 diff --git a/data/motifs/jaspar_insects/MA0203.1.Scr.pwm b/data/motifs/jaspar_insects/MA0203.1.Scr.pwm new file mode 100644 index 000000000..769066816 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0203.1.Scr.pwm @@ -0,0 +1,4 @@ +3 0 25 25 0 0 23 +7 0 0 0 0 0 0 +0 0 0 0 0 18 2 +15 25 0 0 25 7 0 diff --git a/data/motifs/jaspar_insects/MA0204.1.Six4.pwm b/data/motifs/jaspar_insects/MA0204.1.Six4.pwm new file mode 100644 index 000000000..698498fb0 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0204.1.Six4.pwm @@ -0,0 +1,4 @@ +0 0 20 0 20 1 +0 0 0 7 0 19 +0 20 0 4 0 0 +20 0 0 9 0 0 diff --git a/data/motifs/jaspar_insects/MA0205.2.Trl.pwm b/data/motifs/jaspar_insects/MA0205.2.Trl.pwm new file mode 100644 index 000000000..91ce1ca9f --- /dev/null +++ b/data/motifs/jaspar_insects/MA0205.2.Trl.pwm @@ -0,0 +1,4 @@ +2210 2618 4107 6613 91 6743 10 6603 141 5105 1888 2984 +1330 1348 597 47 54 21 38 182 29 845 621 870 +2687 1972 1902 44 6535 44 6783 45 6638 495 3800 2179 +631 920 252 154 178 50 27 28 50 413 549 825 diff --git a/data/motifs/jaspar_insects/MA0206.1.abd-A.pwm b/data/motifs/jaspar_insects/MA0206.1.abd-A.pwm new file mode 100644 index 000000000..26f8247ef --- /dev/null +++ b/data/motifs/jaspar_insects/MA0206.1.abd-A.pwm @@ -0,0 +1,4 @@ +1 0 16 18 1 0 15 +3 0 0 0 0 0 1 +0 0 0 0 0 6 2 +14 18 2 0 17 12 0 diff --git a/data/motifs/jaspar_insects/MA0207.1.achi.pwm b/data/motifs/jaspar_insects/MA0207.1.achi.pwm new file mode 100644 index 000000000..a807694e1 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0207.1.achi.pwm @@ -0,0 +1,4 @@ +0 0 23 0 23 3 +0 0 0 22 0 0 +0 23 0 0 0 12 +23 0 0 1 0 2 diff --git a/data/motifs/jaspar_insects/MA0208.1.al.pwm b/data/motifs/jaspar_insects/MA0208.1.al.pwm new file mode 100644 index 000000000..9dbef13b0 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0208.1.al.pwm @@ -0,0 +1,4 @@ +0 20 20 0 0 17 18 +0 0 0 0 0 0 0 +0 0 0 0 0 3 2 +20 0 0 20 20 0 0 diff --git a/data/motifs/jaspar_insects/MA0209.1.ap.pwm b/data/motifs/jaspar_insects/MA0209.1.ap.pwm new file mode 100644 index 000000000..0db9f4cd9 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0209.1.ap.pwm @@ -0,0 +1,4 @@ +2 1 19 19 0 0 16 +10 0 0 0 0 0 0 +0 0 0 0 0 6 3 +7 18 0 0 19 13 0 diff --git a/data/motifs/jaspar_insects/MA0210.1.ara.pwm b/data/motifs/jaspar_insects/MA0210.1.ara.pwm new file mode 100644 index 000000000..35ace0136 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0210.1.ara.pwm @@ -0,0 +1,4 @@ +14 23 34 0 34 +0 0 0 34 0 +5 0 0 0 0 +15 11 0 0 0 diff --git a/data/motifs/jaspar_insects/MA0211.1.bap.pwm b/data/motifs/jaspar_insects/MA0211.1.bap.pwm new file mode 100644 index 000000000..30593c898 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0211.1.bap.pwm @@ -0,0 +1,4 @@ +0 0 23 23 0 1 7 +0 0 0 0 0 0 0 +1 0 0 0 23 0 16 +22 23 0 0 0 22 0 diff --git a/data/motifs/jaspar_insects/MA0212.1.bcd.pwm b/data/motifs/jaspar_insects/MA0212.1.bcd.pwm new file mode 100644 index 000000000..799394e72 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0212.1.bcd.pwm @@ -0,0 +1,4 @@ +0 20 22 0 0 0 +0 0 0 0 22 21 +0 0 0 1 0 0 +22 2 0 21 0 1 diff --git a/data/motifs/jaspar_insects/MA0213.1.brk.pwm b/data/motifs/jaspar_insects/MA0213.1.brk.pwm new file mode 100644 index 000000000..dac5006db --- /dev/null +++ b/data/motifs/jaspar_insects/MA0213.1.brk.pwm @@ -0,0 +1,4 @@ +1 0 0 0 0 1 1 0 +5 4 0 0 10 0 8 5 +4 0 10 10 0 9 0 1 +0 6 0 0 0 0 1 4 diff --git a/data/motifs/jaspar_insects/MA0214.1.bsh.pwm b/data/motifs/jaspar_insects/MA0214.1.bsh.pwm new file mode 100644 index 000000000..301b66cd1 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0214.1.bsh.pwm @@ -0,0 +1,4 @@ +1 0 16 16 0 0 7 +3 0 0 0 1 3 0 +2 0 0 0 0 6 9 +10 16 0 0 15 7 0 diff --git a/data/motifs/jaspar_insects/MA0215.1.btn.pwm b/data/motifs/jaspar_insects/MA0215.1.btn.pwm new file mode 100644 index 000000000..912149058 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0215.1.btn.pwm @@ -0,0 +1,4 @@ +5 0 22 23 0 0 19 +1 0 0 0 1 0 0 +4 0 1 0 0 15 3 +13 23 0 0 22 8 1 diff --git a/data/motifs/jaspar_insects/MA0216.2.cad.pwm b/data/motifs/jaspar_insects/MA0216.2.cad.pwm new file mode 100644 index 000000000..38f7b87aa --- /dev/null +++ b/data/motifs/jaspar_insects/MA0216.2.cad.pwm @@ -0,0 +1,4 @@ +854 575 0 745 2117 0 2236 2303 2303 1637 1046 +0 341 1481 1475 0 95 0 0 0 115 755 +1143 1387 0 0 186 0 0 0 0 147 0 +306 0 822 83 0 2208 67 0 0 404 502 diff --git a/data/motifs/jaspar_insects/MA0217.1.caup.pwm b/data/motifs/jaspar_insects/MA0217.1.caup.pwm new file mode 100644 index 000000000..0aee92890 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0217.1.caup.pwm @@ -0,0 +1,4 @@ +4 14 19 0 19 +1 0 0 19 0 +2 2 0 0 0 +12 3 0 0 0 diff --git a/data/motifs/jaspar_insects/MA0218.1.ct.pwm b/data/motifs/jaspar_insects/MA0218.1.ct.pwm new file mode 100644 index 000000000..921c6594f --- /dev/null +++ b/data/motifs/jaspar_insects/MA0218.1.ct.pwm @@ -0,0 +1,4 @@ +0 1 9 20 17 0 +6 2 0 0 0 19 +0 0 11 0 1 1 +14 17 0 0 2 0 diff --git a/data/motifs/jaspar_insects/MA0219.1.ems.pwm b/data/motifs/jaspar_insects/MA0219.1.ems.pwm new file mode 100644 index 000000000..90627af48 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0219.1.ems.pwm @@ -0,0 +1,4 @@ +3 3 19 19 0 0 14 +7 0 0 0 0 1 0 +1 0 0 1 0 10 6 +9 17 1 0 20 9 0 diff --git a/data/motifs/jaspar_insects/MA0220.1.en.pwm b/data/motifs/jaspar_insects/MA0220.1.en.pwm new file mode 100644 index 000000000..19d93c40b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0220.1.en.pwm @@ -0,0 +1,4 @@ +2 0 23 23 0 0 13 +8 0 0 0 0 0 0 +2 0 0 0 0 2 10 +11 23 0 0 23 21 0 diff --git a/data/motifs/jaspar_insects/MA0221.1.eve.pwm b/data/motifs/jaspar_insects/MA0221.1.eve.pwm new file mode 100644 index 000000000..6d0394fb9 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0221.1.eve.pwm @@ -0,0 +1,4 @@ +3 1 22 22 0 0 17 +10 0 0 0 2 2 0 +0 0 0 0 1 11 4 +9 21 0 0 19 9 1 diff --git a/data/motifs/jaspar_insects/MA0222.1.exd.pwm b/data/motifs/jaspar_insects/MA0222.1.exd.pwm new file mode 100644 index 000000000..7d48626ac --- /dev/null +++ b/data/motifs/jaspar_insects/MA0222.1.exd.pwm @@ -0,0 +1,4 @@ +4 1 0 0 0 17 0 11 +4 0 0 0 0 0 12 0 +4 2 0 0 17 0 0 6 +5 14 17 17 0 0 5 0 diff --git a/data/motifs/jaspar_insects/MA0224.1.exex.pwm b/data/motifs/jaspar_insects/MA0224.1.exex.pwm new file mode 100644 index 000000000..0c3bcb41e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0224.1.exex.pwm @@ -0,0 +1,4 @@ +0 0 23 23 0 1 20 +7 0 0 0 0 1 0 +10 0 0 0 0 0 3 +6 23 0 0 23 21 0 diff --git a/data/motifs/jaspar_insects/MA0225.1.ftz.pwm b/data/motifs/jaspar_insects/MA0225.1.ftz.pwm new file mode 100644 index 000000000..3026b4ebe --- /dev/null +++ b/data/motifs/jaspar_insects/MA0225.1.ftz.pwm @@ -0,0 +1,4 @@ +1 1 18 18 0 0 14 +2 0 0 0 0 0 0 +0 0 0 0 0 9 4 +15 17 0 0 18 9 0 diff --git a/data/motifs/jaspar_insects/MA0226.1.hbn.pwm b/data/motifs/jaspar_insects/MA0226.1.hbn.pwm new file mode 100644 index 000000000..a7aafd842 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0226.1.hbn.pwm @@ -0,0 +1,4 @@ +2 0 17 17 0 0 9 +2 0 0 0 0 0 0 +2 0 0 0 0 0 7 +11 17 0 0 17 17 1 diff --git a/data/motifs/jaspar_insects/MA0227.1.hth.pwm b/data/motifs/jaspar_insects/MA0227.1.hth.pwm new file mode 100644 index 000000000..c42a30659 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0227.1.hth.pwm @@ -0,0 +1,4 @@ +0 0 17 0 14 0 +0 0 0 17 0 0 +0 17 0 0 3 8 +17 0 0 0 0 4 diff --git a/data/motifs/jaspar_insects/MA0228.1.ind.pwm b/data/motifs/jaspar_insects/MA0228.1.ind.pwm new file mode 100644 index 000000000..c0ec80464 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0228.1.ind.pwm @@ -0,0 +1,4 @@ +0 0 21 21 0 0 19 +12 0 0 0 0 0 0 +0 0 0 0 1 8 2 +9 21 0 0 20 13 0 diff --git a/data/motifs/jaspar_insects/MA0229.1.inv.pwm b/data/motifs/jaspar_insects/MA0229.1.inv.pwm new file mode 100644 index 000000000..a2fcaf27e --- /dev/null +++ b/data/motifs/jaspar_insects/MA0229.1.inv.pwm @@ -0,0 +1,4 @@ +4 1 0 16 16 0 0 11 +0 9 0 0 0 0 0 0 +3 0 0 0 0 0 0 5 +9 6 16 0 0 16 16 0 diff --git a/data/motifs/jaspar_insects/MA0230.1.lab.pwm b/data/motifs/jaspar_insects/MA0230.1.lab.pwm new file mode 100644 index 000000000..38b07420b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0230.1.lab.pwm @@ -0,0 +1,4 @@ +1 0 16 16 1 0 16 +3 0 0 0 0 0 0 +0 0 0 0 0 6 0 +12 16 0 0 15 10 0 diff --git a/data/motifs/jaspar_insects/MA0231.1.lbe.pwm b/data/motifs/jaspar_insects/MA0231.1.lbe.pwm new file mode 100644 index 000000000..ccd091986 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0231.1.lbe.pwm @@ -0,0 +1,4 @@ +0 22 22 1 4 19 +0 0 0 10 5 0 +0 0 0 2 3 3 +22 0 0 9 10 0 diff --git a/data/motifs/jaspar_insects/MA0232.1.lbl.pwm b/data/motifs/jaspar_insects/MA0232.1.lbl.pwm new file mode 100644 index 000000000..69eed7df7 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0232.1.lbl.pwm @@ -0,0 +1,4 @@ +0 23 23 0 1 17 +0 0 0 5 3 0 +0 0 0 0 7 6 +23 0 0 18 12 0 diff --git a/data/motifs/jaspar_insects/MA0233.1.mirr.pwm b/data/motifs/jaspar_insects/MA0233.1.mirr.pwm new file mode 100644 index 000000000..bc27a6fc4 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0233.1.mirr.pwm @@ -0,0 +1,4 @@ +20 29 41 0 41 +1 0 0 41 0 +1 2 0 0 0 +19 10 0 0 0 diff --git a/data/motifs/jaspar_insects/MA0234.1.oc.pwm b/data/motifs/jaspar_insects/MA0234.1.oc.pwm new file mode 100644 index 000000000..a24d41477 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0234.1.oc.pwm @@ -0,0 +1,4 @@ +0 19 19 0 0 0 +0 0 0 0 19 17 +0 0 0 2 0 1 +19 0 0 17 0 1 diff --git a/data/motifs/jaspar_insects/MA0235.1.onecut.pwm b/data/motifs/jaspar_insects/MA0235.1.onecut.pwm new file 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0 2 10 2 5 1 +1 0 3 7 0 2 1 0 +1 11 9 0 0 1 0 0 diff --git a/data/motifs/jaspar_insects/MA0245.1.slou.pwm b/data/motifs/jaspar_insects/MA0245.1.slou.pwm new file mode 100644 index 000000000..5a32b768a --- /dev/null +++ b/data/motifs/jaspar_insects/MA0245.1.slou.pwm @@ -0,0 +1,4 @@ +3 0 22 21 0 2 11 +5 1 0 0 0 1 0 +1 0 0 1 0 5 11 +13 21 0 0 22 14 0 diff --git a/data/motifs/jaspar_insects/MA0246.1.so.pwm b/data/motifs/jaspar_insects/MA0246.1.so.pwm new file mode 100644 index 000000000..cc5a1c228 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0246.1.so.pwm @@ -0,0 +1,4 @@ +0 0 27 0 27 0 +0 0 0 0 0 10 +1 27 0 1 0 0 +26 0 0 26 0 3 diff --git a/data/motifs/jaspar_insects/MA0247.2.tin.pwm b/data/motifs/jaspar_insects/MA0247.2.tin.pwm new file mode 100644 index 000000000..cba8b4805 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0247.2.tin.pwm @@ -0,0 +1,4 @@ +136 0 0 0 326 515 0 0 0 13 +54 188 51 425 0 0 0 0 0 157 +80 137 0 34 189 0 515 0 515 301 +245 190 464 56 0 0 0 515 0 44 diff --git 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--git a/data/motifs/jaspar_insects/MA0251.1.unpg.pwm b/data/motifs/jaspar_insects/MA0251.1.unpg.pwm new file mode 100644 index 000000000..a277108b6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0251.1.unpg.pwm @@ -0,0 +1,4 @@ +1 1 21 21 0 0 14 +6 0 0 0 0 0 0 +4 0 0 0 0 2 7 +10 20 0 0 21 19 0 diff --git a/data/motifs/jaspar_insects/MA0252.1.vis.pwm b/data/motifs/jaspar_insects/MA0252.1.vis.pwm new file mode 100644 index 000000000..1618f5288 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0252.1.vis.pwm @@ -0,0 +1,4 @@ +0 0 22 0 22 2 +0 0 0 22 0 4 +0 22 0 0 0 8 +22 0 0 0 0 2 diff --git a/data/motifs/jaspar_insects/MA0253.1.vnd.pwm b/data/motifs/jaspar_insects/MA0253.1.vnd.pwm new file mode 100644 index 000000000..d1756f3ce --- /dev/null +++ b/data/motifs/jaspar_insects/MA0253.1.vnd.pwm @@ -0,0 +1,4 @@ +4 1 0 0 19 19 0 2 9 +0 8 0 15 0 0 0 0 0 +2 1 0 2 0 0 19 0 10 +13 9 19 2 0 0 0 17 0 diff --git a/data/motifs/jaspar_insects/MA0254.1.vvl.pwm 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a/data/motifs/jaspar_insects/MA0530.1.cnc::maf-S.pwm b/data/motifs/jaspar_insects/MA0530.1.cnc::maf-S.pwm new file mode 100644 index 000000000..ce86cff55 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0530.1.cnc::maf-S.pwm @@ -0,0 +1,4 @@ +142 340 0 0 407 0 80 78 136 24 0 368 133 221 214 +113 20 0 0 46 292 0 215 33 0 474 0 128 63 12 +159 114 0 474 21 80 169 90 163 422 0 106 99 0 0 +60 0 474 0 0 102 225 91 142 28 0 0 114 190 248 diff --git a/data/motifs/jaspar_insects/MA0531.1.CTCF.pwm b/data/motifs/jaspar_insects/MA0531.1.CTCF.pwm new file mode 100644 index 000000000..11adbf1c6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0531.1.CTCF.pwm @@ -0,0 +1,4 @@ +306 313 457 676 257 1534 202 987 2 0 2 124 1 79 231 +876 1147 383 784 714 1 0 0 4 0 0 1645 0 1514 773 +403 219 826 350 87 192 1700 912 311 1902 1652 3 1807 8 144 +317 223 236 92 844 175 0 3 1585 0 248 130 94 301 754 diff --git a/data/motifs/jaspar_insects/MA0532.1.Stat92E.pwm b/data/motifs/jaspar_insects/MA0532.1.Stat92E.pwm new file mode 100644 index 000000000..767ad5a0b --- /dev/null +++ b/data/motifs/jaspar_insects/MA0532.1.Stat92E.pwm @@ -0,0 +1,4 @@ +15 24 27 91 47 0 0 0 0 38 41 0 113 118 63 +50 22 35 1 0 1 6 106 67 21 2 1 0 0 9 +24 59 41 17 27 1 0 0 14 30 70 117 2 0 10 +29 13 15 9 44 116 112 12 37 29 5 0 3 0 36 diff --git a/data/motifs/jaspar_insects/MA0533.1.su(Hw).pwm b/data/motifs/jaspar_insects/MA0533.1.su(Hw).pwm new file mode 100644 index 000000000..435a81223 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0533.1.su(Hw).pwm @@ -0,0 +1,4 @@ +336 243 778 855 2767 3438 4217 3904 410 17 4276 7 199 116 2821 3392 523 2535 1815 2231 1996 +1133 4116 3001 1480 586 208 93 19 235 441 21 11 5 4594 411 296 2430 354 1284 447 379 +2808 35 231 977 925 529 295 316 3759 96 95 1140 4526 6 8 713 191 1409 770 345 351 +460 343 727 1425 459 562 132 498 333 4183 345 3579 7 21 1497 336 1593 439 868 1714 2011 diff --git a/data/motifs/jaspar_insects/MA0534.1.EcR::usp.pwm b/data/motifs/jaspar_insects/MA0534.1.EcR::usp.pwm new file mode 100644 index 000000000..b6fec843a --- /dev/null +++ b/data/motifs/jaspar_insects/MA0534.1.EcR::usp.pwm @@ -0,0 +1,4 @@ +29 60 19 5 9 12 74 34 0 0 66 49 21 0 24 +36 12 10 3 0 66 0 11 0 0 33 55 57 34 28 +39 32 75 35 0 0 30 5 0 104 0 0 0 0 0 +0 0 0 61 95 26 0 54 104 0 5 0 26 70 52 diff --git a/data/motifs/jaspar_insects/MA0535.1.Mad.pwm b/data/motifs/jaspar_insects/MA0535.1.Mad.pwm new file mode 100644 index 000000000..6c224ebff --- /dev/null +++ b/data/motifs/jaspar_insects/MA0535.1.Mad.pwm @@ -0,0 +1,4 @@ +0 35 0 35 0 0 23 0 29 29 11 29 12 32 11 +48 26 14 0 102 0 65 71 0 39 53 0 48 34 28 +47 13 88 56 0 102 0 31 73 34 25 73 27 16 63 +7 28 0 11 0 0 14 0 0 0 13 0 15 20 0 diff --git a/data/motifs/jaspar_insects/MA0536.1.pnr.pwm b/data/motifs/jaspar_insects/MA0536.1.pnr.pwm new file mode 100644 index 000000000..9874d66f4 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0536.1.pnr.pwm @@ -0,0 +1,4 @@ +82 802 0 0 0 869 0 580 123 58 91 +180 0 32 869 0 0 0 0 0 278 273 +5 0 1 0 869 0 0 87 530 194 110 +602 67 836 0 0 0 869 202 216 339 395 diff --git a/data/motifs/jaspar_insects/MA0915.1.dve.pwm b/data/motifs/jaspar_insects/MA0915.1.dve.pwm new file mode 100644 index 000000000..6c35ad31d --- /dev/null +++ b/data/motifs/jaspar_insects/MA0915.1.dve.pwm @@ -0,0 +1,4 @@ +276 0 999 999 0 0 0 348 +379 0 0 0 0 999 971 217 +138 0 0 0 0 0 0 348 +207 999 0 0 999 0 29 87 diff --git a/data/motifs/jaspar_insects/MA0916.1.Ets21C.pwm b/data/motifs/jaspar_insects/MA0916.1.Ets21C.pwm new file mode 100644 index 000000000..7754cffa6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0916.1.Ets21C.pwm @@ -0,0 +1,4 @@ +1 1 1 1 997 897 333 1 +996 997 1 1 1 1 1 286 +1 1 997 997 1 1 665 1 +1 1 1 1 1 101 1 712 diff --git a/data/motifs/jaspar_insects/MA0917.1.gcm2.pwm b/data/motifs/jaspar_insects/MA0917.1.gcm2.pwm new file mode 100644 index 000000000..7c16cc0e7 --- /dev/null +++ b/data/motifs/jaspar_insects/MA0917.1.gcm2.pwm @@ -0,0 +1,4 @@ +730 0 235 47 71 0 0 56 +111 12 24 800 0 0 0 352 +159 0 741 141 753 1000 1000 93 +0 988 0 12 177 0 0 500 diff --git a/data/motifs/jaspar_insects/MA1455.1.dmrt99B.pwm b/data/motifs/jaspar_insects/MA1455.1.dmrt99B.pwm new file mode 100644 index 000000000..1797b4e5d --- /dev/null +++ b/data/motifs/jaspar_insects/MA1455.1.dmrt99B.pwm @@ -0,0 +1,4 @@ +289 224 92 341 348 979 10 856 934 137 41 3 618 356 63 479 529 +150 201 38 288 85 4 955 8 26 21 12 4 35 11 825 155 117 +115 142 808 9 39 8 10 10 39 11 933 2 66 260 27 200 128 +445 431 60 360 526 7 23 124 0 829 12 989 279 371 82 164 224 diff --git a/data/motifs/jaspar_insects/MA1456.1.Dref.pwm b/data/motifs/jaspar_insects/MA1456.1.Dref.pwm new file mode 100644 index 000000000..b8d0d3c65 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1456.1.Dref.pwm @@ -0,0 +1,4 @@ +814 791 0 3112 0 0 0 3112 367 1825 +612 1028 0 0 0 3112 0 0 166 188 +1095 357 0 0 0 0 3112 0 122 459 +591 936 3112 0 3112 0 0 0 2457 640 diff --git a/data/motifs/jaspar_insects/MA1457.1.grh.pwm b/data/motifs/jaspar_insects/MA1457.1.grh.pwm new file mode 100644 index 000000000..dfbe71c97 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1457.1.grh.pwm @@ -0,0 +1,4 @@ +1170 1915 3090 3211 29 187 1914 20 49 58 358 546 754 +730 477 27 20 3265 2825 194 57 34 96 569 786 933 +883 535 89 57 18 199 838 3221 23 23 407 818 783 +549 405 126 44 20 121 386 34 3226 3155 1998 1182 862 diff --git a/data/motifs/jaspar_insects/MA1458.1.Hsf.pwm b/data/motifs/jaspar_insects/MA1458.1.Hsf.pwm new file mode 100644 index 000000000..e43ab7de5 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1458.1.Hsf.pwm @@ -0,0 +1,4 @@ +647 533 74 43 11 54 1981 33 1996 1936 668 658 +366 444 57 38 2070 1297 51 37 66 41 449 443 +423 421 43 49 22 279 49 2036 29 50 469 384 +686 724 1948 1992 19 492 41 16 31 95 536 637 diff --git a/data/motifs/jaspar_insects/MA1459.1.M1BP.pwm b/data/motifs/jaspar_insects/MA1459.1.M1BP.pwm new file mode 100644 index 000000000..5a26c5c79 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1459.1.M1BP.pwm @@ -0,0 +1,4 @@ +372 451 342 678 54 36 6 2 69 1382 1 1308 1 58 291 380 365 368 +417 441 323 346 827 5 3 165 1372 29 1384 15 1393 130 72 481 392 458 +438 433 207 310 54 1412 1429 61 5 17 4 18 2 12 939 299 282 305 +234 136 589 127 526 8 23 1233 15 33 72 120 65 1261 159 301 422 330 diff --git a/data/motifs/jaspar_insects/MA1460.1.pho.pwm b/data/motifs/jaspar_insects/MA1460.1.pho.pwm new file mode 100644 index 000000000..31c075044 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1460.1.pho.pwm @@ -0,0 +1,4 @@ +2293 2256 6191 104 143 116 299 340 498 1866 1325 +1738 1182 297 154 318 150 6080 5236 179 2406 2511 +1276 2050 268 124 6303 6516 274 923 5995 1235 1500 +1644 1463 195 6569 187 169 298 452 279 1444 1615 diff --git a/data/motifs/jaspar_insects/MA1461.1.sv.pwm b/data/motifs/jaspar_insects/MA1461.1.sv.pwm new file mode 100644 index 000000000..daf30a7d2 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1461.1.sv.pwm @@ -0,0 +1,4 @@ +187 2 58 644 152 1 2 934 375 1 1 106 4 128 945 25 71 +314 273 734 15 284 323 640 2 29 129 982 1 2 1 2 971 213 +238 444 4 312 383 5 356 59 68 868 3 890 8 868 13 2 669 +259 279 202 26 179 669 1 4 526 1 12 1 983 1 38 1 45 diff --git a/data/motifs/jaspar_insects/MA1462.1.vfl.pwm b/data/motifs/jaspar_insects/MA1462.1.vfl.pwm new file mode 100644 index 000000000..f0b881ba6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1462.1.vfl.pwm @@ -0,0 +1,4 @@ +2978 2925 2283 52 11435 43 91 93 11460 2143 3270 3157 +3107 2757 1953 10668 28 58 53 689 125 1746 2868 3169 +2712 2740 5193 180 163 11602 11545 37 94 6863 3309 2364 +2934 3309 2302 831 105 28 42 10912 52 979 2284 3041 diff --git a/data/motifs/jaspar_insects/MA1700.1.Clamp.pwm b/data/motifs/jaspar_insects/MA1700.1.Clamp.pwm new file mode 100644 index 000000000..e96b04bf6 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1700.1.Clamp.pwm @@ -0,0 +1,4 @@ +332 1071 189 713 74 2510 62 325 31 2451 71 2038 234 1251 +250 455 175 1322 29 32 11 1998 12 28 36 332 502 327 +1888 378 2178 354 2532 43 2562 174 2600 155 2517 118 1515 960 +181 747 109 262 16 66 16 154 8 17 27 163 400 113 diff --git a/data/motifs/jaspar_insects/MA1702.1.Pdp1.pwm b/data/motifs/jaspar_insects/MA1702.1.Pdp1.pwm new file mode 100644 index 000000000..cbaac02c0 --- /dev/null +++ b/data/motifs/jaspar_insects/MA1702.1.Pdp1.pwm @@ -0,0 +1,4 @@ +1468 1848 126 110 4468 109 331 154 4598 4606 914 1407 +759 765 46 49 35 340 76 3282 88 60 1263 1183 +1141 1362 64 119 218 74 4221 79 71 68 694 802 +1448 841 4580 4538 95 4293 188 1301 59 82 1945 1424 diff --git a/data/motifs/make_annotation.sh b/data/motifs/make_annotation.sh index dc2740a0a..db5adbf5f 100755 --- a/data/motifs/make_annotation.sh +++ b/data/motifs/make_annotation.sh @@ -6,81 +6,84 @@ echo $1 # check parameters # JASPAR: source=1, HOCOMOCO: source=2, both : source=0 source=0 -if [ $# -eq 1 ] - then - if [ $1 == "-j" ] - then - source=1 - elif [ $1 == "-h" ] - then - source=2 - fi +if [ $# -eq 1 ]; then + if [ $1 == "-j" ]; then + source=1 + elif [ $1 == "-h" ]; then + source=2 + fi fi -if [ ${source} -eq 0 ] || [ ${source} -eq 1 ] - then - echo "### Jaspar (2020) Annotation ###" +if [ ${source} -eq 0 ] || [ ${source} -eq 1 ]; then + echo "### Jaspar (2020) Annotation ###" - echo "Downloading SQL dump.." + echo "Downloading SQL dump.." - wget -c http://jaspar.genereg.net/download/database/JASPAR2020.sql.tar.gz --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" + wget -c http://jaspar.genereg.net/download/database/JASPAR2020.sql.tar.gz --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" - echo "Un-tarring it (it isn't actually gzipped).." - tar xvf JASPAR2020.sql.tar.gz || { echo "failed extracting archive"; exit 1; } + echo "Un-tarring it (it isn't actually gzipped).." + tar xvf JASPAR2020.sql.tar.gz || { + echo "failed extracting archive" + exit 1 + } - echo "Converting to SQLite3.." + echo "Converting to SQLite3.." - chmod 755 mysql2sqlite - ./mysql2sqlite JASPAR2020.sql | sqlite3 jaspar.db || { echo "failed converting DB to SQLite3"; exit 1; } + chmod 755 mysql2sqlite + ./mysql2sqlite JASPAR2020.sql | sqlite3 jaspar.db || { + echo "failed converting DB to SQLite3" + exit 1 + } - echo "Exporting annotation.." + echo "Exporting annotation.." - sqlite3 jaspar.db '.read jaspar_anno_query.sql' | sed -e 's/"//g' > jaspar_anno.csv || { echo "failed exporting sql table"; exit 1; } + sqlite3 jaspar.db '.read jaspar_anno_query.sql' | sed -e 's/"//g' >jaspar_anno.csv || { + echo "failed exporting sql table" + exit 1 + } - echo "Cleaning up.." - rm JASPAR2020.sql jaspar.db JASPAR2020.sql.tar.gz + echo "Cleaning up.." + rm JASPAR2020.sql jaspar.db JASPAR2020.sql.tar.gz - echo "Done" + echo "Done" - echo + echo - echo "Re-creating Mtf file.." - python createMtf.py --jv --jp + echo "Re-creating Mtf file.." + python3 createMtf.py --jv --jp --ji fi -if [ ${source} -eq 0 ] - then - echo +if [ ${source} -eq 0 ]; then + echo fi -if [ ${source} -eq 0 ] || [ ${source} -eq 2 ] - then - echo "### Hocomoco Full v11 Annotation ###" - echo - echo "Downloading.." - echo - echo "Human" - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv +if [ ${source} -eq 0 ] || [ ${source} -eq 2 ]; then + echo "### Hocomoco Full v11 Annotation ###" + echo + echo "Downloading.." + echo + echo "Human" + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv - echo "Mouse" - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_annotation_MOUSE_mono.tsv + echo "Mouse" + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_annotation_MOUSE_mono.tsv - echo "Converting to CSV.." + echo "Converting to CSV.." - echo "TfName,GeneName,Family,UniProt,Source,TaxGroup,Species" > hocomoco_anno.csv - tail -n+2 HOCOMOCOv11_full_annotation_HUMAN_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Homo sapiens"}' | sed -e 's/{.*}//g' >> hocomoco_anno.csv - tail -n+2 HOCOMOCOv11_full_annotation_MOUSE_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Mus musculus"}' | sed -e 's/{.*}//g' >> hocomoco_anno.csv + echo "TfName,GeneName,Family,UniProt,Source,TaxGroup,Species" >hocomoco_anno.csv + tail -n+2 HOCOMOCOv11_full_annotation_HUMAN_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Homo sapiens"}' | sed -e 's/{.*}//g' >>hocomoco_anno.csv + tail -n+2 HOCOMOCOv11_full_annotation_MOUSE_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Mus musculus"}' | sed -e 's/{.*}//g' >>hocomoco_anno.csv - echo - echo "Cleaning up.." - rm HOCOMOCOv11_full_annotation_HUMAN_mono.tsv - rm HOCOMOCOv11_full_annotation_MOUSE_mono.tsv + echo + echo "Cleaning up.." + rm HOCOMOCOv11_full_annotation_HUMAN_mono.tsv + rm HOCOMOCOv11_full_annotation_MOUSE_mono.tsv - echo - echo "Done" + echo + echo "Done" - echo + echo - echo "Re-creating Mtf file.." - python createMtf.py --hoc + echo "Re-creating Mtf file.." + python3 createMtf.py --hoc fi diff --git a/data/motifs/script.sh b/data/motifs/script.sh index 2b6201a25..a32b25606 100755 --- a/data/motifs/script.sh +++ b/data/motifs/script.sh @@ -3,126 +3,121 @@ # check parameters -if [ $# -eq 0 ] - then - read -p "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source -elif [ $# -eq 1 ] - then - if [ $1 == "-h" ] || [ $1 == "-j" ] || [ $1 == "-all" ] - then - source=$1 - else - read -rp "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source - fi -elif [ $# -eq 2 ] - then - if [ $1 == "-h" ] && [ $2 == "-j" ] - then - source="-all" - elif [ $1 == "-j" ] && [ $2 == "-h" ] - then - source="-all" - else - read -rp "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source - fi -else +if [ $# -eq 0 ]; then + read -p "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source +elif [ $# -eq 1 ]; then + if [ $1 == "-h" ] || [ $1 == "-j" ] || [ $1 == "-all" ]; then + source=$1 + else + read -rp "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source + fi +elif [ $# -eq 2 ]; then + if [ $1 == "-h" ] && [ $2 == "-j" ]; then + source="-all" + elif [ $1 == "-j" ] && [ $2 == "-h" ]; then + source="-all" + else read -rp "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source + fi +else + read -rp "Type -h to use HOCOMOCO, -j to use JASPAR and -all to use all " source fi # if $source is set correctly, start creating all desired files(Pwm, Mtf) -if [ "${source}" == "-h" ] - then - echo - echo "HOCOMOCO" - echo - echo "Create Pwm files..." - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_pcms_HUMAN_mono.txt - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_pcms_MOUSE_mono.txt - python createPwm.py -i HOCOMOCOv11_full_pcms_HUMAN_mono.txt -f hocomoco-pcm -o hocomoco - python createPwm.py -i HOCOMOCOv11_full_pcms_MOUSE_mono.txt -f hocomoco-pcm -o hocomoco - echo - echo "Create Mtf file..." - ./make_annotation.sh -h - echo - - # clean up - rm HOCOMOCOv11_full_pcms_HUMAN_mono.txt - rm HOCOMOCOv11_full_pcms_MOUSE_mono.txt - - - -elif [ "${source}" == "-j" ] - then - echo - echo "JASPAR" - echo - echo "Create Pwm files.." - wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt - wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt - python createPwm.py -i JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_vertebrates - python createPwm.py -i JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_plants - echo - echo "Create Mtf file..." - echo - ./make_annotation.sh -j - echo - - # clean up - rm JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt - rm JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt - -elif [ "${source}" == "-all" ] - then - echo - echo "HOCOMOCO" - echo - echo "Create Pwm files..." - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_pcms_HUMAN_mono.txt - wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_pcms_MOUSE_mono.txt - python createPwm.py -i HOCOMOCOv11_full_pcms_HUMAN_mono.txt -f hocomoco-pcm -o hocomoco - python createPwm.py -i HOCOMOCOv11_full_pcms_MOUSE_mono.txt -f hocomoco-pcm -o hocomoco - echo - echo "Create Mtf file..." - echo - ./make_annotation.sh -h - echo - - # clean up - rm HOCOMOCOv11_full_pcms_HUMAN_mono.txt - rm HOCOMOCOv11_full_pcms_MOUSE_mono.txt - - echo - echo "JASPAR" - echo - echo "Create Pwm files.." - wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt - wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt - python createPwm.py -i JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_vertebrates - python createPwm.py -i JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_plants - echo - echo "Create Mtf file..." - ./make_annotation.sh -j - echo - - # clean up - rm JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt - rm JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt - - echo - echo "TRANSFAC" - echo - echo "Create Mtf file..." - python createMtf.py --t - echo - - echo - echo "UniProbe" - echo - echo "Create Mtf file..." - python createMtf.py --up --us - echo +if [ "${source}" == "-h" ]; then + echo + echo "HOCOMOCO" + echo + echo "Create Pwm files..." + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_pcms_HUMAN_mono.txt + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_pcms_MOUSE_mono.txt + python3 createPwm.py -i HOCOMOCOv11_full_pcms_HUMAN_mono.txt -f hocomoco-pcm -o hocomoco + python3 createPwm.py -i HOCOMOCOv11_full_pcms_MOUSE_mono.txt -f hocomoco-pcm -o hocomoco + echo + echo "Create Mtf file..." + ./make_annotation.sh -h + echo + + # clean up + rm HOCOMOCOv11_full_pcms_HUMAN_mono.txt + rm HOCOMOCOv11_full_pcms_MOUSE_mono.txt + +elif [ "${source}" == "-j" ]; then + echo + echo "JASPAR" + echo + echo "Create Pwm files.." + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt + python3 createPwm.py -i JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_vertebrates + python3 createPwm.py -i JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_plants + python3 createPwm.py -i JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_insects + echo + echo "Create Mtf file..." + echo + ./make_annotation.sh -j + echo + + # clean up + rm JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt + rm JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt + rm JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt + +elif [ "${source}" == "-all" ]; then + echo + echo "HOCOMOCO" + echo + echo "Create Pwm files..." + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_pcms_HUMAN_mono.txt + wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_pcms_MOUSE_mono.txt + python3 createPwm.py -i HOCOMOCOv11_full_pcms_HUMAN_mono.txt -f hocomoco-pcm -o hocomoco + python3 createPwm.py -i HOCOMOCOv11_full_pcms_MOUSE_mono.txt -f hocomoco-pcm -o hocomoco + echo + echo "Create Mtf file..." + echo + ./make_annotation.sh -h + echo + + # clean up + rm HOCOMOCOv11_full_pcms_HUMAN_mono.txt + rm HOCOMOCOv11_full_pcms_MOUSE_mono.txt + + echo + echo "JASPAR" + echo + echo "Create Pwm files.." + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt + wget -c --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6" http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt + python3 createPwm.py -i JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_vertebrates + python3 createPwm.py -i JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_plants + python3 createPwm.py -i JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt -f jaspar-2016 -o jaspar_insects + echo + echo "Create Mtf file..." + ./make_annotation.sh -j + echo + + # clean up + rm JASPAR2020_CORE_vertebrates_non-redundant_pfms_jaspar.txt + rm JASPAR2020_CORE_plants_non-redundant_pfms_jaspar.txt + rm JASPAR2020_CORE_insects_non-redundant_pfms_jaspar.txt + + echo + echo "TRANSFAC" + echo + echo "Create Mtf file..." + python3 createMtf.py --t + echo + + echo + echo "UniProbe" + echo + echo "Create Mtf file..." + python3 createMtf.py --up --us + echo else - echo "ERROR" + echo "ERROR" fi diff --git a/data/setupGenomicData.py b/data/setupGenomicData.py index e6cc2cc4a..45ea135e8 100644 --- a/data/setupGenomicData.py +++ b/data/setupGenomicData.py @@ -166,12 +166,12 @@ def download(url, prefix, output=None): system("ln -s " + args.hg38_genome_path + " " + output_genome_file_name) print("OK") else: - gen_root_url = gencode_url + "Gencode_human/release_24/GRCh38.primary_assembly.genome.fa.gz" + gen_root_url = gencode_url + "Gencode_human/release_21/GRCh38.genome.fa.gz" # chr_list = ["chr"+str(e) for e in range(1,23)+["X","Y","M"]] output_genome_file = open(output_genome_file_name, "w") # for chr_name in chr_list: print("Downloading hg38 genome") - gz_file_name = path.join(output_location, "GRCh38.primary_assembly.genome.fa.gz") + gz_file_name = path.join(output_location, "GRCh38.genome.fa.gz") # if(path.isfile(gz_file_name)): remove(gz_file_name) download(gen_root_url, output_location) gz_file = gzip.open(gz_file_name, 'rb') @@ -182,14 +182,14 @@ def download(url, prefix, output=None): output_genome_file.close() # Fetching GTF - gtf_output_file_name = path.join(output_location, "gencode.v24.annotation.gtf") + gtf_output_file_name = path.join(output_location, "gencode.v21.annotation.gtf") if args.hg38_gtf_path: print("Creating symbolic link to HG38 GTF") system("ln -s " + args.hg38_gtf_path + " " + gtf_output_file_name) print("OK") else: - gtf_url = gencode_url + "Gencode_human/release_24/gencode.v24.annotation.gtf.gz" - gtf_output_file_name_gz = path.join(output_location, "gencode.v24.annotation.gtf.gz") + gtf_url = gencode_url + "Gencode_human/release_21/gencode.v21.annotation.gtf.gz" + gtf_output_file_name_gz = path.join(output_location, "gencode.v21.annotation.gtf.gz") if path.isfile(gtf_output_file_name_gz): remove(gtf_output_file_name_gz) print("Downloading hg19 GTF (gene annotation) from genode") download(gtf_url, output_location) @@ -275,7 +275,7 @@ def download(url, prefix, output=None): system("ln -s " + args.mm10_genome_path + " " + output_genome_file_name) print("OK") else: - gen_root_url = gencode_url + "Gencode_mouse/release_M11/GRCm38.primary_assembly.genome.fa.gz" + gen_root_url = gencode_url + "Gencode_mouse/release_M25/GRCm38.primary_assembly.genome.fa.gz" output_genome_file = open(output_genome_file_name, "w") print("Downloading mm10 genome") gz_file_name = path.join(output_location, "GRCm38.primary_assembly.genome.fa.gz") @@ -288,14 +288,14 @@ def download(url, prefix, output=None): output_genome_file.close() # Fetching GTF - gtf_output_file_name = path.join(output_location, "gencode.vM20.annotation.gtf") + gtf_output_file_name = path.join(output_location, "gencode.vM25.annotation.gtf") if args.mm10_gtf_path: print("Creating symbolic link to MM10 GTF") system("ln -s " + args.mm10_gtf_path + " " + gtf_output_file_name) print("OK") else: - gtf_url = gencode_url + "Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz" - gtf_output_file_name_gz = path.join(output_location, "gencode.vM20.annotation.gtf.gz") + gtf_url = gencode_url + "Gencode_mouse/release_M25/gencode.vM25.annotation.gtf.gz" + gtf_output_file_name_gz = path.join(output_location, "gencode.vM25.annotation.gtf.gz") if path.isfile(gtf_output_file_name_gz): remove(gtf_output_file_name_gz) print("Downloading MM10 GTF (gene annotation)") download(gtf_url, output_location) diff --git a/rgt/AnnotationSet.py b/rgt/AnnotationSet.py index 917b95896..a1764cc40 100644 --- a/rgt/AnnotationSet.py +++ b/rgt/AnnotationSet.py @@ -163,6 +163,8 @@ def __init__(self, gene_source, tf_source=None, alias_source=None, protein_coding=protein_coding, known_only=known_only) else: # The string may represent an organism which points to a gtf file within data.config. + # TODO Gencode doesn't use anymore gene_status and transcript_status, so known_only becomes useless + known_only = False genome_data = GenomeData(gene_source) self.load_gene_list(genome_data.get_annotation(), filter_havana=filter_havana, @@ -304,15 +306,16 @@ def load_alias_dict(self, file_name): # Iterating over alias file entries for line in alias_file: ll = line.strip().split("\t") - ensembl_id = ll[0] - official_name = ll[1] - alias_vec = ll[2].split("&") - self.symbol_dict[ensembl_id] = official_name - for e in alias_vec: - try: - self.alias_dict[e].append(ensembl_id) - except Exception: - self.alias_dict[e] = [ensembl_id] + if len(ll) > 2: + ensembl_id = ll[0] + official_name = ll[1] + alias_vec = ll[2].split("&") + self.symbol_dict[ensembl_id] = official_name + for e in alias_vec: + try: + self.alias_dict[e].append(ensembl_id) + except Exception: + self.alias_dict[e] = [ensembl_id] # Termination alias_file.close() diff --git a/rgt/HINT/DifferentialAnalysis.py b/rgt/HINT/DifferentialAnalysis.py index fc23f0940..648c2f100 100644 --- a/rgt/HINT/DifferentialAnalysis.py +++ b/rgt/HINT/DifferentialAnalysis.py @@ -97,9 +97,9 @@ def diff_analysis_run(args): "#1b9e77", "#d95f02", "#7570b3", "#e7298a", "#66a61e", "#e6ab02", "#a6761d", "#666666", "#7fc97f", "#beaed4", "#fdc086", "#ffff99", "#386cb0", "#f0027f", "#bf5b17", "#666666"] - assert len(mpbs_files) == len(reads_files) == len(conditions), \ - "Number of motif, read and condition names are not same: {}, {}, {}".format(len(mpbs_files), len(reads_files), - len(conditions)) + assert len(reads_files) == len(conditions), \ + "Number of bam file and condition names are not same: {}, {}, {}".format(len(reads_files), + len(conditions)) # Check if the index file exists for reads_file in reads_files: @@ -273,7 +273,7 @@ def get_raw_signal(arguments): if p1 <= cut_site < p2: signal[cut_site - p1] += 1.0 - signal = smooth(signal) + # signal = smooth(signal) return signal @@ -302,7 +302,7 @@ def get_bc_signal(arguments): # smooth the signal signal = np.add(signal, np.array(_signal)) - signal = smooth(signal) + # signal = smooth(signal) return signal @@ -464,7 +464,8 @@ def get_pwm(fasta, regions, window_size): def compute_factors(signals): signals = np.sum(signals, axis=2) - signals_log = np.log(signals) + # avoid to get a NA value + signals_log = np.log(signals + 0.01) signals_log = signals_log[:, ~np.isnan(signals_log).any(axis=0)] signals_log = signals_log - np.mean(signals_log, axis=0, keepdims=True) factors = np.exp(np.median(signals_log, axis=1)) diff --git a/rgt/__version__.py b/rgt/__version__.py index 7e0dc0e84..83ce76fbb 100644 --- a/rgt/__version__.py +++ b/rgt/__version__.py @@ -1 +1 @@ -__version__ = "0.13.1" +__version__ = "0.13.2" diff --git a/rgt/motifanalysis/Match.py b/rgt/motifanalysis/Match.py index bfed72586..e2dc9904e 100644 --- a/rgt/motifanalysis/Match.py +++ b/rgt/motifanalysis/Match.py @@ -197,8 +197,7 @@ def main(args): # TODO: should be more clever, allow precomputed regions etc if args.target_genes_filename: print(">> creating target promoter file..") - annotation = AnnotationSet(args.organism, alias_source=args.organism, - protein_coding=True, known_only=True) + annotation = AnnotationSet(args.organism, alias_source=args.organism, protein_coding=True) target_genes = GeneSet("target_genes") target_genes.read(args.target_genes_filename) @@ -220,8 +219,7 @@ def main(args): if args.promoter_make_background or (args.promoters_only and not args.target_genes_filename): print(">> creating background promoter file..") if not annotation: - annotation = AnnotationSet(args.organism, alias_source=args.organism, - protein_coding=True, known_only=True) + annotation = AnnotationSet(args.organism, alias_source=args.organism, protein_coding=True) # background is made of all known genes minus the target genes (if any) background_genes = GeneSet("background_genes") diff --git a/setup.py b/setup.py index 68e8dd1e4..05264a684 100644 --- a/setup.py +++ b/setup.py @@ -250,7 +250,7 @@ def recursive_chown_chmod(path_to_walk, uid, gid, file_permission, path_permissi data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.mm10\n")) data_config_file.write("gene_regions: " + path.join(genome, "genes_Gencode_mm10.bed\n")) data_config_file.write("# gene_regions: " + path.join(genome, "genes_RefSeq_mm10.bed # alternative to Gencode\n")) -data_config_file.write("annotation: " + path.join(genome, "gencode.vM20.annotation.gtf\n")) +data_config_file.write("annotation: " + path.join(genome, "gencode.vM25.annotation.gtf\n")) data_config_file.write("gene_alias: " + path.join(genome, "alias_mouse.txt\n\n")) genome = "hg19" data_config_file.write("[" + genome + "]\n") @@ -267,7 +267,7 @@ def recursive_chown_chmod(path_to_walk, uid, gid, file_permission, path_permissi data_config_file.write("chromosome_sizes: " + path.join(genome, "chrom.sizes.hg38\n")) data_config_file.write("gene_regions: " + path.join(genome, "genes_Gencode_hg38.bed\n")) data_config_file.write("# gene_regions: " + path.join(genome, "genes_RefSeq_hg38.bed # alternative to Gencode\n")) -data_config_file.write("annotation: " + path.join(genome, "gencode.v24.annotation.gtf\n")) +data_config_file.write("annotation: " + path.join(genome, "gencode.v21.annotation.gtf\n")) data_config_file.write("gene_alias: " + path.join(genome, "alias_human.txt\n\n")) data_config_file.write("repeat_maskers: " + path.join(genome, "repeat_maskers\n\n")) genome = "zv9" @@ -331,6 +331,13 @@ def recursive_chown_chmod(path_to_walk, uid, gid, file_permission, path_permissi user_config_file.write("#annotation: undefined\n") user_config_file.write("#gene_alias: undefined\n\n") + user_config_file.write("# Here you can change your motif database preset. Use the parameter --filter\n" + "# in the 'rgt-motifanalysis matching' tool to subset only certain species, \n" + "# for specific experiments.\n" + "# Uncomment the following section and modify the list at will.\n") + user_config_file.write("#[MotifData]\n") + user_config_file.write("#repositories: jaspar_vertebrates, jaspar_plants, jaspar_insects\n\n") + script_dir = path.dirname(path.abspath(__file__)) # Copying data from package folder to installation folder @@ -355,8 +362,8 @@ def recursive_chown_chmod(path_to_walk, uid, gid, file_permission, path_permissi "double_hit_bias_table_F.txt", "double_hit_bias_table_R.txt", "H3K4me3_proximal.hmm", "LearnDependencyModel.jar", "SlimDimontPredictor.jar", "test.fa"], "motifs": ["createMtf.py", "createPwm.py", - "jaspar_vertebrates", "jaspar_plants", "uniprobe_primary", "uniprobe_secondary", "hocomoco", - "jaspar_vertebrates.mtf", "jaspar_plants.mtf", "uniprobe_primary.mtf", "uniprobe_secondary.mtf", "hocomoco.mtf"], + "jaspar_vertebrates", "jaspar_plants", "jaspar_insects", "uniprobe_primary", "uniprobe_secondary", "hocomoco", + "jaspar_vertebrates.mtf", "jaspar_plants.mtf", "jaspar_insects.mtf", "uniprobe_primary.mtf", "uniprobe_secondary.mtf", "hocomoco.mtf"], "fig": ["rgt_logo.gif", "style.css", "default_motif_logo.png", "jquery-1.11.1.js", "jquery.tablesorter.min.js", "tdf_logo.png", "viz_logo.png"], } diff --git a/test/tdf.sh b/test/tdf.sh index 7b3beb7a4..3bb441ede 100755 --- a/test/tdf.sh +++ b/test/tdf.sh @@ -24,7 +24,7 @@ fi # Run test script cd ${DIR}/TDF_examples/FENDRR_mm9/ -rgt-TDF promotertest -r FENDRR.fasta -de fendrr_gene_list_fold_change.txt -score -organism mm9 -rn FENDRR -o promoter_test -t FENDRR_FC/ -l 20 +rgt-TDF promotertest -r FENDRR.fasta -de fendrr_gene_list_fold_change.txt -score -organism mm9 -rn FENDRR -o promoter_test -t FENDRR_FC/ -l 15 rgt-TDF integrate -path promoter_test cd ${DIR}/TDF_examples/MEG3_hg38/ diff --git a/tools/rgt-tools.py b/tools/rgt-tools.py index eb83a6061..2ecc1f463 100755 --- a/tools/rgt-tools.py +++ b/tools/rgt-tools.py @@ -13,7 +13,6 @@ import natsort from operator import attrgetter import matplotlib -matplotlib.use('Agg', warn=False) import matplotlib.pyplot as plt from os.path import expanduser home = expanduser("~") @@ -67,8 +66,8 @@ def get_sequence(sequence, ch, ss, es, reverse=False, complement=False, rna=Fals version_message = "rgt-tools - Regulatory Analysis Toolbox (RGT). Version: " + str(__version__) parser = argparse.ArgumentParser(description='RGT-tools is for converting various data format in bioinformatic research\ Author: Joseph Chao-Chung Kuo', - formatter_class=argparse.ArgumentDefaultsHelpFormatter, version=version_message) - + formatter_class=argparse.ArgumentDefaultsHelpFormatter) + parser.add_argument('--version', action='version', version=version_message) subparsers = parser.add_subparsers(help='sub-command help', dest='mode') ############### GTF add transcripts ######################################