def pseudoalign(fqs, sample, paired, reference, outdir, temp, threads, keep_files, partial=False): '''Calls Kallisto to pseudoalign reads.''' file_list = [] # Get read length stats reads_file = ''.join([temp, sample, '.reads.txt']) num, avg, std = analyze_reads(fqs, paired, reads_file, keep_files) # Kallisto fails if std used for single-end is 0 if std == 0: std = .00001 temp2 = check_path(''.join([temp, sample])) command = ['kallisto pseudo -i', reference, '-t', threads, '-o', temp2] if paired: command.extend([fqs[0], fqs[1]]) else: fq = fqs[0] command.extend(['--single -l', str(avg), '-s', str(std), fq]) run_command(command, '[alignment] Pseudoaligning with Kallisto: ') # Move and rename Kallisto output file_in = ''.join([temp2, 'pseudoalignments.tsv']) count_file = ''.join([temp, sample, '.counts.tsv']) file_list.append(file_in) run_command(['mv', file_in, count_file]) file_in = ''.join([temp2, 'pseudoalignments.ec']) eq_file = ''.join([temp, sample, '.eq.tsv']) file_list.append(file_in) run_command(['mv', file_in, eq_file]) run_command(['rm -rf', temp2]) remove_files(file_list, keep_files) return count_file, eq_file, num, avg, std
help='keep intermediate files\n\n', default=False) parser.add_argument('-t', '--threads', type = str, default='1') parser.add_argument('-v', '--verbose', action = 'count', default=False) args = parser.parse_args() temp, outdir = [check_path(path) for path in [args.temp,args.outdir]] sample = os.path.basename(args.bam).split('.')[0] if args.log: log_file = args.log else: log_file = ''.join([outdir,sample,'.extract.log']) with open(log_file, 'w'): pass if args.verbose: handlers = [log.FileHandler(log_file), log.StreamHandler()] log.basicConfig(level=log.DEBUG,
type=str, help='run name\n\n', default='', metavar='') parser.add_argument('-v', '--verbose', action = 'count', default=False) args = parser.parse_args() if args.run: args.run += '.' indir, outdir = [check_path(path) for path in [args.indir, args.outdir]] (genotype_files, partial_files, gene_count_files, quant_files) = get_paths(indir) if genotype_files: process_json(genotype_files, indir, outdir, args.run, 'genotypes') if partial_files: process_json(partial_files, indir, outdir, args.run, 'partial_genotypes') if gene_count_files: process_json(gene_count_files, indir, outdir, args.run, 'genes')
'--verbose', action = 'count', default=False) args = parser.parse_args() if args.verbose: log.basicConfig(level = log.DEBUG, format = '%(message)s') else: handlers = [log.StreamHandler()] log.basicConfig(format = '%(message)s') log.info('') hline() check_path('dat/ref') if args.update: log.info('[reference] Updating HLA reference') checkout_version('origin') build_fasta() elif args.rebuild: build_fasta() elif args.version: if args.version not in versions: sys.exit('[reference] Error: invalid version.') checkout_version(versions[args.version]) build_fasta()
metavar = '') parser.add_argument('--output_nomenclature', type = str, help = 'input nomenclature (current, polysolver)', default = 'current', metavar = '') parser.add_argument('-v', '--verbose', action = 'count', default=False) args = parser.parse_args() outdir = check_path(args.outdir) if os.path.isdir(args.input): # add convert polysolver output indir = check_path(args.input) genotype_files, partial_files, count_files, quant_files = get_paths(indir) if genotype_files: process_json(genotype_files, indir, outdir, args.run, 'genotypes.json')
) parser.add_argument('-v', '--verbose', action='count', default=False) args = parser.parse_args() if args.verbose: log.basicConfig(level=log.DEBUG, format='%(message)s') else: handlers = [log.StreamHandler()] log.basicConfig(format='%(message)s') log.info('') hline() check_path(rootDir + 'dat/ref') if args.update: log.info('[reference] Updating HLA reference') checkout_version('origin') build_fasta() elif args.rebuild: build_fasta() elif args.version: if args.version not in versions: sys.exit('[reference] Error: invalid version.') checkout_version(versions[args.version]) build_fasta()
parser.add_argument('--keep_files', action='count', help='keep intermediate files\n\n', default=False) parser.add_argument('-t', '--threads', type=str, default='1', metavar='') parser.add_argument('-v', '--verbose', action='count', default=False) args = parser.parse_args() if len(args.file) == 0: sys.exit('[genotype] Error: FASTQ or alignment.p file required') sample = os.path.basename(args.file[0]).split('.')[0] temp, outdir = [check_path(path) for path in [args.temp, args.outdir]] if args.log: log_file = args.log else: log_file = ''.join([outdir, sample, '.genotype.log']) with open(log_file, 'w'): pass if args.verbose: handlers = [log.FileHandler(log_file), log.StreamHandler()] log.basicConfig(level=log.DEBUG, format='%(message)s', handlers=handlers)