initial commit trying to use scikit

bitk3/keepSeqByOrgId.py

@@ -0,0 +1,55 @@
+#!/usr/bin/python3.5
+import argparse
+import skbio
+
+
+def main(sampleFile, pos, sep=''):
+    """ script to split a MSA by the organisms id """
+    seqInfo = bitk3.fastaReader(sampleFile)
+    if sep == '':
+        countsDict = bitk3.countFeaturesInHeaders(seqInfo[0], pos)
+    else:
+        countsDict = bitk3.countFeaturesInHeaders(seqInfo[0], pos, sep)
+
+    keys = list(countsDict.keys())
+    keys.sort()
+
+    for key in keys:
+        print('{} : {}'.format(key, countsDict[key]))
+
+    return countsDict
+
+if __name__ == "__main__":
+    import bitk3
+    parser = argparse.ArgumentParser(prog='countFeatureInTag',
+                                     usage='%(prog)s fasta_file.fa position',
+                                     description='Count features in headers of \
+                                                  fasta formated files')
+
+    parser.add_argument('sampleFile',
+                        metavar='fasta_file.fa',
+                        type=str,
+                        help='Valid fasta formated file')
+
+    parser.add_argument('pos',
+                        metavar='position',
+                        type=int,
+                        help='Integer of the position of the information \
+                              to be counted. Positions are divided by default \
+                              using "|" as separator')
+    parser.add_argument('--sep',
+                        metavar='sep',
+                        type=str,
+                        help='Change the character that separates the \
+                              fields in header',
+                        default='')
+
+    args = parser.parse_args()
+
+    sampleFile = args.sampleFile
+    pos = args.pos
+    sep = args.sep
+
+    main(sampleFile, pos, sep)
+else:
+    from bitk3 import bitk3