35 lines
1017 B
Python
35 lines
1017 B
Python
#!/usr/bin/python
|
|
import sys
|
|
input_file = sys.argv[1]
|
|
file_index = 1
|
|
|
|
headerLines = list()
|
|
intervals = open(input_file)
|
|
prevContig = None
|
|
outFile = None
|
|
|
|
def parseContig(line):
|
|
if( line.find("-") > -1 ): ## format is chr:start-stop
|
|
return line.split(":")[0]
|
|
else:
|
|
return line.split("\t")[0]
|
|
|
|
for line in open(input_file).readlines():
|
|
if ( line.startswith("@") ):
|
|
headerLines.append(line)
|
|
else:
|
|
thisContig = parseContig(line)
|
|
if ( thisContig != prevContig ):
|
|
file_index += 1
|
|
try:
|
|
newOutFile = open(sys.argv[file_index],'w')
|
|
if ( outFile != None):
|
|
outFile.close()
|
|
outFile = newOutFile
|
|
for headerline in headerLines:
|
|
outFile.write(headerline)
|
|
except IndexError:
|
|
print("Error: fewer output files than contigs. Writing remainder to final file.")
|
|
prevContig = thisContig
|
|
outFile.write(line)
|