From daa544350b6d037470d93e2544191e455367ffa9 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 9 Jul 2024 10:55:38 +0200 Subject: [PATCH] update doc --- ...at_sp_filter_feature_by_attribute_value.pl | 8 +++---- ...at_sp_filter_feature_by_attribute_value.md | 23 ++++++++++++++----- 2 files changed, 21 insertions(+), 10 deletions(-) diff --git a/bin/agat_sp_filter_feature_by_attribute_value.pl b/bin/agat_sp_filter_feature_by_attribute_value.pl index b8631cd8..0f599fdd 100755 --- a/bin/agat_sp_filter_feature_by_attribute_value.pl +++ b/bin/agat_sp_filter_feature_by_attribute_value.pl @@ -387,7 +387,7 @@ =head1 DESCRIPTION /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures. /!\ Removing all children of a feature will automatically remove this feature too (excepted if --keep_parental is activated). /!\ If --keep_parental is not activated and --na_aside is activated, and all level3 features of a record are split between both _na.gff and _discarded.gff, -, then the parental level1 and level2 features are removed and will end up in the _na.gff file only. +then the parental level1 and level2 features are removed and will end up in the _na.gff file only. =head1 SYNOPSIS @@ -426,14 +426,14 @@ =head1 OPTIONS =item B<--na_aside> Bolean. Deactivated by default. By default if the attribute tag on which the filter is based is missing, the feature will be written into . -When activated, such features will be written into a separate file called _na.gff - +When activated, such features will be written into a separate file called _na.gff. =item B<--keep_parental> Bolean. Deactivated by default. When activated even if all child features have been removed, the parental one will be kept. =item B<-t> or B<--test> + Test to apply (> < = ! >= <=). default value "=". If you use one of these two character >, <, please don't forget to quote the parameter like that "<=" otherwise your terminal will complain. @@ -441,7 +441,7 @@ =head1 OPTIONS =item B<-o> or B<--output> -Output GFF file. If no output file is specified, the output will be +Output GFF file. If no output file is specified, the output will be written to STDOUT. =item B<-v> diff --git a/docs/tools/agat_sp_filter_feature_by_attribute_value.md b/docs/tools/agat_sp_filter_feature_by_attribute_value.md index e0d37896..b9fa6e50 100644 --- a/docs/tools/agat_sp_filter_feature_by_attribute_value.md +++ b/docs/tools/agat_sp_filter_feature_by_attribute_value.md @@ -3,11 +3,14 @@ ## DESCRIPTION The script aims to filter features according to attribute value (9th column). -If the attribute tag is missing the feature will not be discarded. -If the attribute exists and the value pass the test, the feature is discarded. -Attribute are stored in the 9th column and have this shape: tag=value -/!\\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and -removing all children of a feature will automatically remove this feature too. +- If the attribute exists and the value do not pass the test, the feature is written into . +- If the attribute exists and the value pass the test, the feature is discarded and written into _discarded.gff. +- If the attribute tag is missing (test cannot be applyed), the feature will be written into by default. If --na_aside parameter is activated then it will be written into _na.gff. + +Attribute are stored in the 9th column and have this shape: tag=value. +/!\\ Removing a level1 or level2 feature will automatically remove all linked subfeatures. +/!\\ Removing all children of a feature will automatically remove this feature too (excepted if --keep_parental is activated). +/!\\ If --keep_parental is not activated and --na_aside is activated, and all level3 features of a record are split between both _na.gff and _discarded.gff, then the parental level1 and level2 features are removed and will end up in the _na.gff file only. ## SYNOPSIS @@ -43,6 +46,14 @@ agat_sp_filter_feature_by_attribute_value.pl --help Bolean. Deactivated by default. When activated the values provided by the --value parameter are handled case insensitive. +- **<--na\_aside** + + Bolean. Deactivated by default. By default if the attribute tag on which the filter is based is missing, the feature will be written into . + When activated, such features will be written into a separate file called _na.gff. + +- **<--keep\_parental>** + + Bolean. Deactivated by default. When activated even if all child features have been removed, the parental one will be kept. - **-t** or **--test** @@ -53,7 +64,7 @@ agat_sp_filter_feature_by_attribute_value.pl --help - **-o** or **--output** - Output GFF file. If no output file is specified, the output will be + Output GFF file. If no output file is specified, the output will be written to STDOUT. - **-v**