view tools/samtools_idxstats/samtools_idxstats.py @ 1:8945bad80f4a draft

v0.0.4; internal changes for packaging

#!/usr/bin/env python
"""Wrapper for "samtools idxstats" for use in Galaxy.

This script takes exactly three command line arguments:
 * Input BAM filename
 * Input BAI filename (via Galaxy metadata)
 * Output tabular filename

This messes about with the filenames to make samtools happy, then
runs "samtools idxstats" and captures the output to the desired
tabular file.
"""
import sys
import os
import subprocess
import tempfile

if "-v" in sys.argv or "--version" in sys.argv:
    #Galaxy seems to invert the order of the two lines
    print "(Galaxy wrapper v0.0.2)"
    cmd = "samtools 2>&1 | grep -i ^Version"
    sys.exit(os.system(cmd))

def sys_exit(msg, error_level=1):
   """Print error message to stdout and quit with given error level."""
   sys.stderr.write("%s\n" % msg)
   sys.exit(error_level)

if len(sys.argv) != 4:
   sys_exit("Require three arguments: BAM, BAI, tabular filenames")

bam_filename, bai_filename, tabular_filename = sys.argv[1:]

if not os.path.isfile(bam_filename):
    sys_exit("Input BAM file not found: %s" % bam_filename)
if not os.path.isfile(bai_filename):
    if bai_filename == "None":
        sys_exit("Error: Galaxy did not index your BAM file")
    sys_exit("Input BAI file not found: %s" % bai_filename)

#Assign sensible names with real extensions, and setup symlinks:
tmp_dir = tempfile.mkdtemp()
bam_file = os.path.join(tmp_dir, "temp.bam")
bai_file = os.path.join(tmp_dir, "temp.bam.bai")
os.symlink(os.path.abspath(bam_filename), bam_file)
os.symlink(os.path.abspath(bai_filename), bai_file)
assert os.path.isfile(bam_file), bam_file
assert os.path.isfile(bai_file), bai_file
assert os.path.isfile(bam_file + ".bai"), bam_file

#Run samtools idxstats:
cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
return_code = os.system(cmd)

#Remove the temp symlinks:
os.remove(bam_file)
os.remove(bai_file)
os.rmdir(tmp_dir)

if return_code:
    sys_exit("Return code %i from command:\n%s" % (return_code, cmd))