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

v0.0.4; internal changes for packaging

0:d4412c04d7b1

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 v0.0.1)"
    cmd = "samtools 2>&1 | grep -i ^Version"
    sys.exit(os.system(cmd))

def stop_err(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:
   stop_err("Require three arguments: BAM, BAI, tabular filenames")

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

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

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

1:8945bad80f4a

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")

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))