diff --git a/ngsderive/__main__.py b/ngsderive/__main__.py index 8479976..1aad328 100755 --- a/ngsderive/__main__.py +++ b/ngsderive/__main__.py @@ -43,9 +43,6 @@ class SaneFormatter( help="Write to filename rather than standard out.", default="stdout", ) - common.add_argument( - "--delimiter", default="", help="Delimiter for the outfile." - ) common.add_argument( "--debug", default=False, action="store_true", help="Enable DEBUG log level." ) @@ -264,10 +261,6 @@ def process_args(args): else: args.outfile = open(args.outfile, "w") - # set delimiter - if args.delimiter == "": - args.delimiter = "\t" - def run(): args = get_args() @@ -277,7 +270,6 @@ def run(): readlen.main( args.ngsfiles, outfile=args.outfile, - delimiter=args.delimiter, n_samples=args.n_samples, majority_vote_cutoff=args.majority_vote_cutoff, ) @@ -285,7 +277,6 @@ def run(): instrument.main( args.ngsfiles, outfile=args.outfile, - delimiter=args.delimiter, n_samples=args.n_samples, ) if args.subcommand == "strandedness": @@ -293,7 +284,6 @@ def run(): args.ngsfiles, args.gene_model, outfile=args.outfile, - delimiter=args.delimiter, n_genes=args.n_genes, minimum_reads_per_gene=args.minimum_reads_per_gene, only_protein_coding_genes=args.only_protein_coding_genes, @@ -305,7 +295,6 @@ def run(): encoding.main( args.ngsfiles, outfile=args.outfile, - delimiter=args.delimiter, n_samples=args.n_samples, ) if args.subcommand == "junction-annotation": @@ -313,7 +302,6 @@ def run(): args.ngsfiles, args.gene_model, outfile=args.outfile, - delimiter=args.delimiter, min_intron=args.min_intron, min_mapq=args.min_mapq, min_reads=args.min_reads, diff --git a/ngsderive/commands/encoding.py b/ngsderive/commands/encoding.py index f178b77..bdf0a77 100644 --- a/ngsderive/commands/encoding.py +++ b/ngsderive/commands/encoding.py @@ -17,12 +17,12 @@ ILLUMINA_1_3_SET = set([i for i in range(31, 93)]) -def main(ngsfiles, outfile=sys.stdout, delimiter="\t", n_samples=1000000): +def main(ngsfiles, outfile=sys.stdout, n_samples=1000000): writer = csv.DictWriter( outfile, fieldnames=["File", "Evidence", "ProbableEncoding"], - delimiter=delimiter, + delimiter="\t", ) writer.writeheader() outfile.flush() diff --git a/ngsderive/commands/instrument.py b/ngsderive/commands/instrument.py index d5b7d85..59c9117 100755 --- a/ngsderive/commands/instrument.py +++ b/ngsderive/commands/instrument.py @@ -184,11 +184,11 @@ def resolve_instrument( ) -def main(ngsfiles, outfile=sys.stdout, delimiter="\t", n_samples=10000): +def main(ngsfiles, outfile=sys.stdout, n_samples=10000): writer = csv.DictWriter( outfile, fieldnames=["File", "Instrument", "Confidence", "Basis"], - delimiter=delimiter, + delimiter="\t", ) writer.writeheader() outfile.flush() diff --git a/ngsderive/commands/junction_annotation.py b/ngsderive/commands/junction_annotation.py index 3f9ccb5..4a3112f 100644 --- a/ngsderive/commands/junction_annotation.py +++ b/ngsderive/commands/junction_annotation.py @@ -251,7 +251,6 @@ def main( ngsfiles, gene_model_file, outfile=sys.stdout, - delimiter="\t", min_intron=50, min_mapq=30, min_reads=1, @@ -287,7 +286,7 @@ def main( "complete_novel_spliced_reads", ] - writer = csv.DictWriter(outfile, fieldnames=fieldnames, delimiter=delimiter) + writer = csv.DictWriter(outfile, fieldnames=fieldnames, delimiter="\t") writer.writeheader() outfile.flush() diff --git a/ngsderive/commands/readlen.py b/ngsderive/commands/readlen.py index 299218a..47dfb8d 100755 --- a/ngsderive/commands/readlen.py +++ b/ngsderive/commands/readlen.py @@ -13,7 +13,6 @@ def main( ngsfiles, outfile=sys.stdout, - delimiter="\t", n_samples=100000, majority_vote_cutoff=0.7, ): @@ -21,7 +20,7 @@ def main( writer = csv.DictWriter( outfile, fieldnames=["File", "Evidence", "MajorityPctDetected", "ConsensusReadLength"], - delimiter=delimiter, + delimiter="\t", ) writer.writeheader() outfile.flush() diff --git a/ngsderive/commands/strandedness.py b/ngsderive/commands/strandedness.py index 0aaae56..d92df56 100755 --- a/ngsderive/commands/strandedness.py +++ b/ngsderive/commands/strandedness.py @@ -288,7 +288,6 @@ def main( ngsfiles, gene_model_file, outfile=sys.stdout, - delimiter="\t", n_genes=100, minimum_reads_per_gene=10, only_protein_coding_genes=True, @@ -329,7 +328,7 @@ def main( fieldnames = ["ReadGroup"] + fieldnames fieldnames = ["File"] + fieldnames - writer = csv.DictWriter(outfile, fieldnames=fieldnames, delimiter=delimiter) + writer = csv.DictWriter(outfile, fieldnames=fieldnames, delimiter="\t") writer.writeheader() outfile.flush()