From ae0c97f1bb1a1c2f225e9da8b0d51a67de0d7626 Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Thu, 14 Sep 2023 01:04:03 +0300 Subject: [PATCH] rename option + man --- README.md | 3 +++ isoquant.py | 2 +- src/graph_based_model_construction.py | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 7008fdd7..ade10951 100644 --- a/README.md +++ b/README.md @@ -421,6 +421,9 @@ We recommend to not modify these options unless you are clearly aware of their e `--no_secondary` Ignore secondary alignments. +`--report_unstranded` + Report transcripts for which the strand cannot be detected using canonical splice sites. + `--aligner` Force to use this alignment method, can be `starlong` or `minimap2`; `minimap2` is currently used as default. Make sure the specified aligner is in the `$PATH` variable. diff --git a/isoquant.py b/isoquant.py index c50c51c6..d49630c7 100755 --- a/isoquant.py +++ b/isoquant.py @@ -140,7 +140,7 @@ def add_hidden_option(*args, **kwargs): # show command only with --full-help parser.add_argument('--check_canonical', action='store_true', default=False, help="report whether splice junctions are canonical") - add_additional_option("--keep_noncanonical", help="report transcripts for which the strand cannot be detected " + add_additional_option("--report_unstranded", help="report transcripts for which the strand cannot be detected " "using canonical splice sites", action='store_true', default=False) parser.add_argument("--sqanti_output", help="produce SQANTI-like TSV output", diff --git a/src/graph_based_model_construction.py b/src/graph_based_model_construction.py index b0251a04..1401b46b 100644 --- a/src/graph_based_model_construction.py +++ b/src/graph_based_model_construction.py @@ -379,7 +379,7 @@ def construct_fl_isoforms(self): elif len(novel_exons) == 2 and (not polya_site or transcript_ss_strand == '.'): # logger.debug("uuu Avoiding single intron %s isoform: %d\t%s" % (new_transcript_id, count, str(path))) pass - elif transcript_strand == '.' and not self.params.keep_noncanonical: + elif transcript_strand == '.' and not self.params.report_unstranded: logger.info("Avoiding unreliable transcript with %d exons" % len(novel_exons)) pass else: