changeset 0:746e286edff0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exseq_multi.py	Wed Sep 26 08:26:17 2018 -0400
@@ -0,0 +1,56 @@
+#!/usr/bin/python
+#-*- coding: utf-8 -*-
+
+"""
+
+Scripts ayant pour rôle l'extraction de tous les noms de segment contenus dans un fichier genbank.
+Réalisé par Pierrick Lucas.
+Usage : python Extract_all_segment.py --input_files sequences.gb
+
+"""
+
+# Importation des librairies.
+import os, sys, argparse, re
+from Bio import SeqIO
+
+
+##### MAIN
+def __main__():
+  # Options :
+  parser = argparse.ArgumentParser(description='''Extract sequence of multifasta file from position start/end.''', epilog='''This script need few options, use -h to see it.''')
+  parser.add_argument('-i', '--input_file', dest='infile', help='Multifasta file.')
+  parser.add_argument('-s', '--start_position', dest='start', help='Start position to extract.')
+  parser.add_argument('-e', '--end_position', dest='end', help='End position to extract.')
+  parser.add_argument('-o', '--output_file', dest='outfile', help='Output file.')
+
+  # Error :
+  if len(sys.argv)==1 or len(sys.argv)>9 or len(sys.argv)<7 :
+    parser.print_help()
+    sys.exit(1)
+
+  # Get options :
+  options = parser.parse_args()
+  infile = options.infile
+  spos = options.start
+  epos = options.end
+  outfile = options.outfile
+
+  # Variables :
+  if outfile is None:
+    withoutext, justext = os.path.splitext(infile)
+    outputfile = open(withoutext+"_extract_subseq_"+spos+"_to_"+epos+".fasta","w")
+  else:
+    outputfile = open(outfile,"w")
+    
+  # Ouputs :
+  with open(infile, "rU") as inf:
+    # Input treatment :
+    for rec in SeqIO.parse(inf, "fasta"):
+      outputfile.write(rec.id+'\n')
+      outputfile.write(str(rec.seq[int(spos):int(epos)])+'\n')    
+
+  # Fermeture des fichiers.               
+  outputfile.close()
+
+#### MAIN END
+if __name__ == "__main__": __main__()