mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
72 lines
2.4 KiB
Python
72 lines
2.4 KiB
Python
#!/usr/bin/env python
|
|
#Guruprasad Ananda
|
|
"""
|
|
This tool provides the UNIX "join" functionality.
|
|
"""
|
|
import sys, os, tempfile, subprocess
|
|
|
|
def stop_err(msg):
|
|
sys.stderr.write(msg)
|
|
sys.exit()
|
|
|
|
def main():
|
|
infile1 = sys.argv[1]
|
|
infile2 = sys.argv[2]
|
|
field1 = int(sys.argv[3])
|
|
field2 = int(sys.argv[4])
|
|
mode =sys.argv[5]
|
|
outfile = sys.argv[6]
|
|
|
|
tmpfile1 = tempfile.NamedTemporaryFile()
|
|
tmpfile2 = tempfile.NamedTemporaryFile()
|
|
|
|
try:
|
|
#Sort the two files based on specified fields
|
|
os.system("sort -t ' ' -k %d,%d -o %s %s" %(field1, field1, tmpfile1.name, infile1))
|
|
os.system("sort -t ' ' -k %d,%d -o %s %s" %(field2, field2, tmpfile2.name, infile2))
|
|
except Exception, exc:
|
|
stop_err( 'Initialization error -> %s' %str(exc) )
|
|
|
|
option = ""
|
|
for line in file(tmpfile1.name):
|
|
line = line.strip()
|
|
if line:
|
|
elems = line.split('\t')
|
|
for j in range(1,len(elems)+1):
|
|
if j == 1:
|
|
option = "1.1"
|
|
else:
|
|
option = option + ",1." + str(j)
|
|
break
|
|
|
|
#check if join has --version option. BSD join doens't have this option, while GNU join does.
|
|
#The return value in the latter case will be 0, and non-zero in the latter case.
|
|
ret = subprocess.call('join --version 2>/dev/null', shell=True)
|
|
# check if we are a version later than 7 of join. If so, we want to skip
|
|
# checking the order since join will raise an error with duplicated items in
|
|
# the two files being joined.
|
|
if ret == 0:
|
|
cl = subprocess.Popen(["join", "--version"], stdout=subprocess.PIPE)
|
|
(stdout, _) = cl.communicate()
|
|
version_line = stdout.split("\n")[0]
|
|
(version, _) = version_line.split()[-1].split(".")
|
|
if int(version) >= 7:
|
|
flags = "--nocheck-order"
|
|
else:
|
|
flags = ""
|
|
else:
|
|
flags = ""
|
|
|
|
if mode == "V":
|
|
cmdline = "join %s -t ' ' -v 1 -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
|
|
else:
|
|
cmdline = "join %s -t ' ' -o %s -1 %d -2 %d %s %s > %s" %(flags, option, field1, field2, tmpfile1.name, tmpfile2.name, outfile)
|
|
|
|
try:
|
|
os.system(cmdline)
|
|
except Exception, exj:
|
|
stop_err('Error joining the two datasets -> %s' %str(exj))
|
|
|
|
if __name__ == "__main__":
|
|
main()
|