Python exec_in_row Examples

Example #1

File: run-trimmomatic.py Project: qfma/ohnolog-dc

def run_trimmomatic(fastq_files):

    pairs = get_fastq_pairs(fastq_files)
    trimmomatic_commands = []

    for pair in pairs:
        trimmomatic_commands.append(trimmomatic_call(pair[0], pair[1]))

    print "Starting to run trimmomatic commands..."
    exec_in_row(trimmomatic_commands)

Example #2

File: run-tophat.py Project: qfma/ohnolog-dc

def run_liver(fastq_files):

    pairs = get_fastq_pairs(fastq_files)
    tophat_commands = []

    for pair in pairs:
        mate0 = pair[0]
        mate1 = pair[1]
        basename = mate0.split(".")[0]
        output = basename
        # if not os.path.isdir(output):
        #     os.mkdir(output)
        tophat_commands.append(tophat_call(output, mate0, mate1))

    print "Starting to run tophat2 commands..."
    print tophat_commands
    exec_in_row(tophat_commands)

Example #3

File: namesort-bam.py Project: qfma/ohnolog-dc

def run_samtools_sort(all_alns):
    samtools_commands = []
    for aln in all_alns:
        samtools_commands.append(get_samtools_params(aln))
    
    exec_in_row(samtools_commands)