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)
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)
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)