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14_postProcessing_of_pairwise_v3.0.py
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14_postProcessing_of_pairwise_v3.0.py
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#!/usr/bin/python
MINIMUM_LENGTH = 1
############################
##### DEF1 : Get Pairs #####
############################
def get_pairs(fasta_file_path):
F2 = open(fasta_file_path, "r")
list_pairwises = []
while 1:
next2 = F2.readline()
if not next2:
break
if next2[0] == ">":
fasta_name_query = next2[:-1]
next3 = F2.readline()
fasta_seq_query = next3[:-1]
next3 = F2.readline() ## jump one empty line (if any after the sequence)
#next3 = F2.readline()
fasta_name_match = next3[:-1]
next3 = F2.readline()
fasta_seq_match = next3[:-1]
pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
## ADD pairwise with condition
list_pairwises.append(pairwise)
F2.close()
#print list_pairwises
return(list_pairwises)
##############################################
#################################
##### DEF2 : Extract length #####
#################################
def extract_length(length_string): # format length string = 57...902
l3 = string.split(length_string, "...")
n1 = string.atoi(l3[0])
n2 = string.atoi(l3[1])
length = n2-n1
return(length)
##############################################
####################################
##### DEF3 : Remove Redondancy #####
####################################
def filter_redondancy(list_paireu, MIN_LENGTH):
bash1 = {}
list_pairout = []
for pair in list_paireu:
query_name = pair[0]
#print query_name
query_seq = pair[1]
match_name = pair[2]
match_seq = pair[3]
l1 = string.split(query_name, "||")
short_query_name = l1[0][1:]
length_matched = extract_length(l1[1]) ### DEF2 ###
l2 = string.split(match_name, "||")
short_match_name = l2[0][1:]
binom = "%s_%s" %(short_query_name, short_match_name)
#print binom
if binom not in bash1.keys():
bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
else:
old_length = bash1[binom][-1]
if length_matched > old_length:
bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
#else:
# print "shorter!"
for bino in bash1.keys():
print bino
length = bash1[bino][-1]
#print length
if length > MIN_LENGTH:
print "\t %d bp" %(length)
list_pairout.append(bash1[bino])
else:
print "\t%s have been removed due to length (%d bp)" %(bino, length)
#print bash1.keys()
return(list_pairout)
##############################################
################################
###### DEF3: filter lengh ######
################################
# def filter_length(list_pairs, MIN_LENGTH):
# list_pairs2 = []
# for pair in list_pairs:
# #print pair[0]
# seq = pair[1]
# #print seq
# ln = len(seq)
# #print ln
# if ln > MIN_LENGTH:
# list_pairs2.append(pair)
# print list_pairs2
# return(list_pairs2)
##############################################
#######################
##### RUN RUN RUN #####
#######################
import string, os, time, re, sys
#MINIMUM_LENGTH = string.atoi(sys.argv[1])
WORK_DIR = sys.argv[1]
F_IN = "%s/13_PairwiseMatch.fasta" %WORK_DIR
F_OUT = "%s/15_PairwiseMatch_filtered.fasta" %WORK_DIR
File_OUT = open(F_OUT, "w")
F_OUT2 = "%s/15_onlyMatch_filtered.fasta" %WORK_DIR
File_OUT2 = open(F_OUT2, "w")
F_OUT3 = "%s/15_PairwiseNames_longName_filtered.csv" %WORK_DIR
File_OUT3 = open(F_OUT3, "w")
list_pairwises = get_pairs(F_IN) ### DEF1 ###
#for paireu in list_pairwises:
# print paireu[0]
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])
## Write only "matches" [AND UNGAP THEM: needed before the 2nd run of blast]
File_OUT2.write("%s\n" %pair[2])
seq_match = pair[3]
seq_match_ungapped = string.replace(seq_match, "-", "")
File_OUT2.write("%s\n" %seq_match_ungapped)
## Write the name of the pair [required to test for reciprocal best hit]
File_OUT3.write("%s,%s\n" %(pair[0][1:],pair[2][1:]))
File_OUT.close()
File_OUT2.close()
File_OUT3.close()
##############################################