Merge pull request #189 from CostaLab/develop

Develop

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 <http://www.regulatory-genomics.org/rgt/download-installation>`__.

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
 ###################################################################################################

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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