Mercurial > repos > p.lucas > extract_fasta_subsequence

comparison exseq_multi.py @ 0:746e286edff0 draft

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author p.lucas
date Wed, 26 Sep 2018 08:26:17 -0400
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1 #!/usr/bin/python
2 #-*- coding: utf-8 -*-
3
4 """
5
6 Scripts ayant pour rôle l'extraction de tous les noms de segment contenus dans un fichier genbank.
7 Réalisé par Pierrick Lucas.
8 Usage : python Extract_all_segment.py --input_files sequences.gb
9
10 """
11
12 # Importation des librairies.
13 import os, sys, argparse, re
14 from Bio import SeqIO
15
16
17 ##### MAIN
18 def __main__():
19 # Options :
20 parser = argparse.ArgumentParser(description='''Extract sequence of multifasta file from position start/end.''', epilog='''This script need few options, use -h to see it.''')
21 parser.add_argument('-i', '--input_file', dest='infile', help='Multifasta file.')
22 parser.add_argument('-s', '--start_position', dest='start', help='Start position to extract.')
23 parser.add_argument('-e', '--end_position', dest='end', help='End position to extract.')
24 parser.add_argument('-o', '--output_file', dest='outfile', help='Output file.')
25
26 # Error :
27 if len(sys.argv)==1 or len(sys.argv)>9 or len(sys.argv)<7 :
28 parser.print_help()
29 sys.exit(1)
30
31 # Get options :
32 options = parser.parse_args()
33 infile = options.infile
34 spos = options.start
35 epos = options.end
36 outfile = options.outfile
37
38 # Variables :
39 if outfile is None:
40 withoutext, justext = os.path.splitext(infile)
41 outputfile = open(withoutext+"_extract_subseq_"+spos+"_to_"+epos+".fasta","w")
42 else:
43 outputfile = open(outfile,"w")
44
45 # Ouputs :
46 with open(infile, "rU") as inf:
47 # Input treatment :
48 for rec in SeqIO.parse(inf, "fasta"):
49 outputfile.write(rec.id+'\n')
50 outputfile.write(str(rec.seq[int(spos):int(epos)])+'\n')
51
52 # Fermeture des fichiers.
53 outputfile.close()
54
55 #### MAIN END
56 if __name__ == "__main__": __main__()