comparison tools/mira4_0/mira4_make_bam.py @ 32:56b421d59805 draft

planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit fd979d17340cde155de176604744831d9597c6b6

31:fd95aaef8818

#!/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 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 depad(fasta_file, sam_file, bam_file, log_handle):
    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 "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...


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 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"

    #Also doing SAM to (uncompressed) BAM during depad
    msg = depad(fasta_file, sam_file, bam_file, log_handle)
    if msg:
        return msg

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

    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:

32:56b421d59805

#!/usr/bin/env python
"""Wrapper script using miraconvert & samtools to get BAM from MIRA.
"""

import os
import shutil
import subprocess
import sys
import tempfile


def run(cmd, log_handle):
    try:
        child = subprocess.Popen(cmd, shell=True,
                                 stdout=subprocess.PIPE,
                                 stderr=subprocess.STDOUT)
    except Exception as 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 depad(fasta_file, sam_file, bam_file, log_handle):
    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 "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...


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 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"

    # Also doing SAM to (uncompressed) BAM during depad
    msg = depad(fasta_file, sam_file, bam_file, log_handle)
    if msg:
        return msg

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

    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: