fixed cli

docs/usage.rst

@@ -31,7 +31,7 @@ You can also iterate over STRFinder object to get exact tandem repeat (ETR) obje
 	>>> for ssr in pytrf.STRFinder(name, seq):
 	>>> 	print(ssr.chrom)
 	>>> 	print(ssr.motif)
-	>>> 	print(ssr.repeats)
+	>>> 	print(ssr.repeat)
 
 You can define the minimum number of repeats required to determine a SSR.
 
@@ -70,21 +70,21 @@ Iterate over GTRFinder object to get ETR object
 	>>> for gtr in pytrf.GTRMiner(name, seq):
 	>>> 	print(gtr.chrom)
 	>>> 	print(gtr.motif)
-	>>> 	print(gtr.repeats)
+	>>> 	print(gtr.repeat)
 
 You can customize the motif size, minimum repeat and minimum length.
 
 .. code:: python
 
-	>>> gtrs = pytrf.GTRFinder(name, seq, max_motif=100, min_repeat=3, min_length=10)
+	>>> gtrs = pytrf.GTRFinder(name, seq, min_motif=20, max_motif=100, min_repeat=3, min_length=10)
 
 A complete example, get all gtrs and output csv format
 
 .. code:: python
 
 	>>> fa = pyfastx.Fastx('tests/data/test.fa', uppercase=True):
 	>>> for name, seq in fa:
-	>>> 	for gtr in pytrf.GTRFinder(name, seq, 100, 2, 10):
+	>>> 	for gtr in pytrf.GTRFinder(name, seq, 30, 100, 2, 10):
 	>>> 		print(vntr.as_string(','))
 
 Exact tandem repeat
@@ -113,7 +113,7 @@ ETR is a readonly object and allows you to access the attributes and convert to
 	>>> ssr.motif
 
 	>>> # get number of repeats
-	>>> ssr.repeats
+	>>> ssr.repeat
 
 	>>> # get repeat length
 	>>> ssr.length
@@ -279,7 +279,7 @@ Find exact generic tandem repeats (GTRs) from fasta/q file.
 
 	pytrf gtrfinder -h
 
-	usage: pytrf findgtr [-h] [-o] [-f] [-m] [-r] [-l] fastx
+	usage: pytrf findgtr [-h] [-o] [-f] [-m] [-M] [-r] [-l] fastx
 
 	positional arguments:
 	  fastx               input fasta or fastq file (gzip support)
@@ -288,7 +288,8 @@ Find exact generic tandem repeats (GTRs) from fasta/q file.
 	  -h, --help          show this help message and exit
 	  -o , --out-file     output file (default: stdout)
 	  -f , --out-format   output format, tsv, csv or gff (default: tsv)
-	  -m , --max-motif    maximum motif length (default: 30)
+	  -m , --min-motif    minimum motif length (default: 10)
+	  -M , --max-motif    maximum motif length (default: 100)
 	  -r , --min-repeat   minimum repeat number (default: 3)
 	  -l , --min-length   minimum repeat length (default: 10)
 
@@ -298,7 +299,7 @@ Find imperfect or approximate tandem repeats (ATRs)
 
 	pytrf atrfinder -h
 
-	usage: pytrf findatr [-h] [-o] [-f] [-m] [-r] [-l] [-e] [-p] [-x] fastx
+	usage: pytrf findatr [-h] [-o] [-f] [-m] [-M] [-r] [-l] [-e] [-p] [-x] fastx
 
 	positional arguments:
 	  fastx                 input fasta or fastq file (gzip support)
@@ -307,15 +308,17 @@ Find imperfect or approximate tandem repeats (ATRs)
 	  -h, --help            show this help message and exit
 	  -o , --out-file       output file (default: stdout)
 	  -f , --out-format     output format, tsv, csv or gff (default: tsv)
-	  -m , --max-motif-size
+	  -m , --min-motif-size
+	                        minimum motif length (default: 1)
+	  -M , --max-motif-size
 	                        maximum motif length (default: 6)
 	  -r , --min-seed-repeat
 	                        minimum repeat number for seed (default: 3)
 	  -l , --min-seed-length
 	                        minimum length for seed (default: 10)
 	  -e , --max-continuous-error
 	                        maximum number of continuous alignment errors (default: 3)
-	  -p , --min-identity   minimum identity from 0 to 100 (default: 70)
+	  -p , --min-identity   minimum identity from 0 to 1 (default: 0.7)
 	  -x , --max-extend-length
 	                        maximum length allowed to extend (default: 2000)
 

pytrfcli.py

@@ -23,12 +23,12 @@ def str_finder(seq, minrep, outfmt, outfw):
 	ssrs = pytrf.STRFinder(seq[0], seq[1], *minrep)
 	get_format_result(ssrs, outfmt, outfw)
 
-def gtr_finder(seq, maxmotif, minrep, minlen, outfmt, outfw):
-	gtrs = pytrf.GTRFinder(seq[0], seq[1], maxmotif, minrep, minlen)
+def gtr_finder(seq, minmotif, maxmotif, minrep, minlen, outfmt, outfw):
+	gtrs = pytrf.GTRFinder(seq[0], seq[1], minmotif, maxmotif, minrep, minlen)
 	get_format_result(gtrs, outfmt, outfw)
 
-def atr_finder(seq, maxmotif, seedrep, seedlen, maxerror, minscore, maxextend, outfmt, outfw):
-	atrs = pytrf.ATRFinder(seq[0], seq[1], maxmotif, seedrep, seedlen, maxerror, minscore, maxextend)
+def atr_finder(seq, minmotif, maxmotif, seedrep, seedlen, maxerror, minscore, maxextend, outfmt, outfw):
+	atrs = pytrf.ATRFinder(seq[0], seq[1], minmotif, maxmotif, seedrep, seedlen, maxerror, minscore, maxextend)
 	get_format_result(atrs, outfmt, outfw)
 
 def tandem_repeat_finder(args):
@@ -41,6 +41,7 @@ def tandem_repeat_finder(args):
 
 	elif args.cmd == 'gtr':
 		return functools.partial(gtr_finder,
+			minmotif = args.min_motif,
 			maxmotif = args.max_motif,
 			minrep = args.min_repeat,
 			minlen = args.min_length,
@@ -50,6 +51,7 @@ def tandem_repeat_finder(args):
 
 	elif args.cmd == 'atr':
 		return functools.partial(atr_finder,
+			minmotif = args.min_motif_size,
 			maxmotif = args.max_motif_size,
 			seedrep = args.min_seed_repeat,
 			seedlen = args.min_seed_length,
@@ -161,11 +163,18 @@ def main():
 	)
 	parser_gtrfinder.set_defaults(cmd='gtr')
 
-	parser_gtrfinder.add_argument('-m', '--max-motif',
+	parser_gtrfinder.add_argument('-m', '--min-motif',
+		default = 10,
+		metavar = '',
+		type = int,
+		help = "minimum motif length (default: 10)"
+	)
+
+	parser_gtrfinder.add_argument('-M', '--max-motif',
 		default = 30,
 		metavar = '',
 		type = int,
-		help = "maximum motif length (default: 30)"
+		help = "maximum motif length (default: 100)"
 	)
 
 	parser_gtrfinder.add_argument('-r', '--min-repeat',
@@ -189,7 +198,14 @@ def main():
 	)
 	parser_atrfinder.set_defaults(cmd='atr')
 
-	parser_atrfinder.add_argument('-m', '--max-motif-size',
+	parser_atrfinder.add_argument('-m', '--min-motif-size',
+		default = 1,
+		metavar = '',
+		type = int,
+		help = "minimum motif length (default: 1)"
+	)
+
+	parser_atrfinder.add_argument('-M', '--max-motif-size',
 		default = 6,
 		metavar = '',
 		type = int,