comparison tools/mira4/mira4_make_bam.py @ 9:302d13490b23 draft

Uploaded v0.0.2 preview 1, BAM output

9:302d13490b23

#!/usr/bin/env python
"""Wrapper script using miraconvert & samtools to get BAM from MIRA.
"""
import os
import sys
import shutil
import subprocess
import tempfile

def stop_err(msg, err=1):
    sys.stderr.write(msg+"\n")
    sys.exit(err)

def run(cmd, log_handle):
    try:
        child = subprocess.Popen(cmd, shell=True,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.STDOUT)
    except Exception, err:
        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
        #TODO - call clean up?
        log_handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
        sys.exit(1)
    #Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    assert not stderr #Should be empty as sent to stdout
    if len(stdout) > 10000:
        #miraconvert can be very verbose (is holding stdout in RAM a problem?)
        stdout = stdout.split("\n")
        stdout = stdout[:10] + ["...", "<snip>", "..."] + stdout[-10:]
        stdout = "\n".join(stdout)
    log_handle.write(stdout)
    return child.returncode

def make_bam(mira_convert, maf_file, fasta_file, bam_file, log_handle):
    if not os.path.isfile(mira_convert):
        return "Missing binary %r" % mira_convert
    if not os.path.isfile(maf_file):
        return "Missing input MIRA file: %r" % maf_file
    if not os.path.isfile(fasta_file):
        return "Missing padded FASTA file: %r" % fasta_file

    log_handle.write("\n====================== Converting MIRA assembly to SAM =======================\n")
    tmp_dir = tempfile.mkdtemp()
    sam_file = os.path.join(tmp_dir, "x.sam")

    # Note add nbb to the template name, possible MIRA 4.0 RC4 bug
    cmd = '"%s" -f maf -t samnbb "%s" "%snbb"' % (mira_convert, maf_file, sam_file)
    return_code = run(cmd, log_handle)
    if return_code:
        return "Error %i from command:\n%s" % (return_code, cmd)
    if not os.path.isfile(sam_file):
        return "Conversion from MIRA to SAM failed"

    log_handle.write("\n================= Converting MIRA assembly from SAM to BAM ===================\n")
    #Also doing SAM to (uncompressed) BAM during depad
    bam_stem = bam_file + ".tmp" # Have write permissions and want final file in this folder
    cmd = 'samtools depad -S -u -T "%s" "%s" | samtools sort - "%s"' % (fasta_file, sam_file, bam_stem)
    return_code = run(cmd, log_handle)
    if return_code:
        return "Error %i from command:\n%s" % (return_code, cmd)
    if not os.path.isfile(bam_stem + ".bam"):
        return "samtools depad or sort failed to produce BAM file"

    os.remove(sam_file)
    os.rmdir(tmp_dir)

    log_handle.write("\n====================== Indexing MIRA assembly BAM file =======================\n")
    cmd = 'samtools index "%s.bam"' % bam_stem
    return_code = run(cmd, log_handle)
    if return_code:
        return "Error %i from command:\n%s" % (return_code, cmd)
    if not os.path.isfile(bam_stem + ".bam.bai"):
        return "samtools indexing of BAM file failed to produce BAI file"

    shutil.move(bam_stem + ".bam", bam_file)
    os.remove(bam_stem + ".bam.bai") #Let Galaxy handle that...

    return None #Good :)

if __name__ == "__main__":
    mira_convert, maf_file, fasta_file, bam_file = sys.argv[1:]
    msg = make_bam(mira_convert, maf_file, fasta_file, bam_file, sys.stdout)
    if msg:
        stop_err(msg)