From f928bb4c598c0880def5653f50c87d8c25138e5d Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 5 Mar 2024 10:02:44 +0100 Subject: [PATCH] update doc --- bin/agat_sp_compare_two_annotations.pl | 9 ++++++--- docs/tools/agat_sp_compare_two_annotations.md | 7 +++++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl index 99ca41db..37949627 100755 --- a/bin/agat_sp_compare_two_annotations.pl +++ b/bin/agat_sp_compare_two_annotations.pl @@ -703,7 +703,7 @@ =head1 DESCRIPTION The script aims to compare two annotation of the same assembly. It provided information about split/fusion of genes between the two annotations. -The most common case are: +The most common cases are: 1 => 0 ( gene uniq to file1) 0 => 1 ( gene uniq to file2) 1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2) @@ -713,6 +713,9 @@ =head1 DESCRIPTION Then you can get more complex cases: => ( genes from file 1 overlap genes from file2) +The script output a folder containing a report of number of different cases as well as a file +per case type listing per line the gene feature's ID involved in each case. + =head1 SYNOPSIS agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ] @@ -732,8 +735,8 @@ =head1 OPTIONS =item B<-o> , B<--output> or B<--out> -Output GFF file. If no output file is specified, the output will be -written to STDOUT. +Output folder. It contains a report that resume the type and number of cases, as well as a file per case type +containing one case per line with the list of gene feature's ID (or other type of feature level1) from file1 then file2 separated by a |. =item B<--debug> or B<-d> diff --git a/docs/tools/agat_sp_compare_two_annotations.md b/docs/tools/agat_sp_compare_two_annotations.md index 4a8cb028..d5a2f270 100644 --- a/docs/tools/agat_sp_compare_two_annotations.md +++ b/docs/tools/agat_sp_compare_two_annotations.md @@ -14,6 +14,9 @@ The most common case are: Then you can get more complex cases: <many> => <many> (<many> genes from file 1 overlap <many> genes from file2) +The script output a folder containing a report of number of different cases as well as a file +per case type listing per line the gene feature's ID involved in each case. + ## SYNOPSIS ``` @@ -33,8 +36,8 @@ agat_sp_compare_two_annotations.pl --help - **-o** , **--output** , **--out** or **--outfile** - Output GFF file. If no output file is specified, the output will be - written to STDOUT. + Output folder. It contains a report that resume the type and number of cases, as well as a file per case type + containing one case per line with the list of gene feature's ID (or other type of feature level1) from file1 then file2 separated by a |. - **-v**