view scripts/S11_post_processing_of_pairwise.py @ 4:6709645eff5d draft

planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f

#!/usr/bin/env python
## AUTHOR: Eric Fontanillas
## LAST VERSION: 14/08/14 by Julie BAFFARD

MINIMUM_LENGTH = 1

#######################
##### RUN RUN RUN #####
#######################
import string, os, time, re, sys
from functions import get_pairs, extract_length, filter_redondancy

## 1 ## INPUT/OUTPUT
SHORT_FILE = sys.argv[1] ## short-name-query_short-name-db

F_IN = "%s/17_ReciprocalHits_%s.fasta" %(SHORT_FILE, SHORT_FILE)

F_OUT = "%s/19_ReciprocalBestHits_%s.fasta"  %(SHORT_FILE, SHORT_FILE) 
File_OUT = open(F_OUT, "w")

## 2 ## RUN
list_pairwises = get_pairs(F_IN)              ### DEF1 ###

list_pairwises_filtered1 = filter_redondancy(list_pairwises, MINIMUM_LENGTH)          ### DEF3 ###


i = 0
for pair in list_pairwises_filtered1:
     i = i+1

     ## Write pairwise alignment
     File_OUT.write("%s\n" %pair[0])
     File_OUT.write("%s\n" %pair[1])
     File_OUT.write("%s\n" %pair[2])
     File_OUT.write("%s\n" %pair[3])
     
     seq = pair[1]
     ungapped_seq = string.replace(seq, "-", "")

     name = pair[0]
     S1 = string.split(name, "||")
     short_name = S1[0]    
     
File_OUT.close()