fix: remove the option to override the default tab output delimiter (#12

)

BREAKING CHANGE: This removes the `--delimiter` commandline arg

ngsderive/__main__.py

@@ -43,9 +43,6 @@ class SaneFormatter(
         help="Write to filename rather than standard out.",
         default="stdout",
     )
-    common.add_argument(
-        "--delimiter", default="<tab>", 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 == "<tab>":
-        args.delimiter = "\t"
-
 
 def run():
     args = get_args()
@@ -277,23 +270,20 @@ def run():
         readlen.main(
             args.ngsfiles,
             outfile=args.outfile,
-            delimiter=args.delimiter,
             n_samples=args.n_samples,
             majority_vote_cutoff=args.majority_vote_cutoff,
         )
     if args.subcommand == "instrument":
         instrument.main(
             args.ngsfiles,
             outfile=args.outfile,
-            delimiter=args.delimiter,
             n_samples=args.n_samples,
         )
     if args.subcommand == "strandedness":
         strandedness.main(
             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,
@@ -305,15 +295,13 @@ def run():
         encoding.main(
             args.ngsfiles,
             outfile=args.outfile,
-            delimiter=args.delimiter,
             n_samples=args.n_samples,
         )
     if args.subcommand == "junction-annotation":
         junction_annotation.main(
             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,

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()

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()

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()
 

ngsderive/commands/readlen.py

@@ -13,15 +13,14 @@
 def main(
     ngsfiles,
     outfile=sys.stdout,
-    delimiter="\t",
     n_samples=100000,
     majority_vote_cutoff=0.7,
 ):
 
     writer = csv.DictWriter(
         outfile,
         fieldnames=["File", "Evidence", "MajorityPctDetected", "ConsensusReadLength"],
-        delimiter=delimiter,
+        delimiter="\t",
     )
     writer.writeheader()
     outfile.flush()

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()