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#!/usr/bin/env python | |
import sys | |
i = 0 | |
ovlpstr = '' | |
ovlpln = 10 #20 , 2 for test | |
chnkln = 100 #200, 5 for test | |
start = 0 | |
end = 0 | |
chr = '' | |
dna = '' | |
filenum = 0 | |
chr_num = 1; | |
# This module can handle multiple files | |
for arg in sys.argv[1:] : | |
filename = arg | |
print filename | |
fa_in = open( filename, 'r' ) | |
#fa_out = open( filename, 'r' ) | |
fa_out = open( filename + '.ppd', 'w' ) # in case of T.v, there'll too many files | |
ovlpstr = '' | |
dna = '' | |
start = 0 | |
end = 0 | |
i = 0 | |
for line in fa_in : # read hg19.fa, multi chromosomes in one file | |
if i in range(chnkln) : | |
if line[0] == '>': # new chromosome | |
if i != 0 : # there is a previous chromosome | |
fa_out.write(chr + ':' + str(start) + '-' + str(end) + '>\t' + dna +'\n') | |
#fa_out.write("(1)") | |
else : | |
#fa_out.write("(2)") | |
pass | |
ovlpstr = '' | |
dna = '' | |
start = 0 | |
end = 0 | |
i = 0 | |
chr = line.split()[0].split('|')[0].strip('>').lstrip('chr') | |
if chr.isdigit() == True or chr == "X" or chr == "Y" : | |
chr = 'chr' + chr | |
else : | |
if ( "MT" in line ) or ( "mito" in line ) : | |
chr = 'chrMT' | |
elif ( "chr" in line ) or ( "CHR" in line ) : | |
#print chr | |
chr = 'chr' + chr | |
#chr = 'chr' + str(chr_num) | |
#chr_num = chr_num + 1 | |
elif "|" in line : | |
print line.split("|")[1] | |
print "T. vaginalis case" | |
else : | |
chr = filename.split('/')[len(filename.split('/'))-1].split(".")[0] | |
fa_out.close() | |
fa_out = open( chr + '.fna.ppd', 'w' ) | |
print str(chr+'.fna.ppd'), "is being processed" | |
#fa_out.write("(3)") | |
else : | |
if i >= (chnkln - ovlpln) : | |
ovlpstr = ovlpstr + line.strip() | |
#fa_out.write("(4)") | |
elif i == 0 : | |
if ovlpstr == '' : # The first line | |
start = 1 | |
end = 0 | |
#fa_out.write("(5)") | |
else : # From second line, consider overlap | |
dna = ovlpstr | |
start = end - len(ovlpstr) + 1 | |
i = ovlpln | |
ovlpstr = '' | |
#fa_out.write("(6)") | |
else : | |
#fa_out.write("(7)") | |
pass | |
#fa_out.write("(8)") | |
dna = dna + line.strip() | |
#fa_out.write(line) | |
end = end + len(line.strip()) | |
if i == (chnkln - 1) : | |
fa_out.write(chr + ':' + str(start) + '-' + str(end) + '>\t' + dna +'\n') | |
i = 0 | |
else : | |
i = i + 1 | |
#flush buffer | |
fa_out.write(chr + ':' + str(start) + '-' + str(end) + '>\t' + dna +'\n') | |
# clean up | |
fa_out.close() | |
fa_in.close() |
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