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Merge pull request #11365 from bernt-matthias/ccedmendoza_patch-1

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Make filter work with file containing header
This commit is contained in:
Nicola Soranzo
2021-02-14 11:35:38 +00:00
committed by GitHub
parent 6fe522494a 610e31147a
commit d857d55a4f
2 changed files with 18 additions and 13 deletions
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tools/filters/gff/gtf_filter_by_attribute_values_list.py
+9 -7
View File
@@ -53,13 +53,15 @@ def gff_filter(gff_file, attribute_name, ids_file, output_file):
ids_dict[line.split('\t')[0].strip()] = True
# Filter GFF file using ids.
output = open(output_file, 'w')
for line in open(gff_file):
fields = line.split('\t')
attributes = parse_gff_attributes(fields[8])
if (attribute_name in attributes) and (attributes[attribute_name] in ids_dict):
output.write(line)
output.close()
with open(output_file, 'w') as output, open(gff_file) as ingff:
for line in ingff:
if not line or line.startswith('#'):
output.write(line)
continue
fields = line.split('\t')
attributes = parse_gff_attributes(fields[8])
if attribute_name in attributes and attributes[attribute_name] in ids_dict:
output.write(line)
if __name__ == "__main__":
tools/filters/gff/gtf_filter_by_attribute_values_list.xml
+9 -6
View File
@@ -1,8 +1,11 @@
<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.1">
<tool id="gtf_filter_by_attribute_values_list" name="Filter GTF data by attribute values_list" version="0.2">
<description></description>
<command interpreter="python">
gtf_filter_by_attribute_values_list.py $input $attribute_name $ids $output
</command>
<requirements>
<requirement type="package" version="3.6">python</requirement>
</requirements>
<command><![CDATA[
python '$__tool_directory__/gtf_filter_by_attribute_values_list.py' '$input' $attribute_name '$ids' '$output'
]]></command>
<inputs>
<param format="gtf" name="input" type="data" label="Filter"/>
<param name="attribute_name" type="select" label="Using attribute name">
@@ -19,10 +22,10 @@
<tests>
<!-- Test filtering with a simple list of values. -->
<test>
<param name="input" value="gops_subtract_in1.gff"/>
<param name="input" value="gops_subtract_in1_wcomment.gff"/>
<param name="attribute_name" value="gene_id"/>
<param name="ids" value="gtf_filter_by_attribute_values_list_in1.txt"/>
<output name="output" file="gtf_filter_by_attribute_values_list_out1.gtf"/>
<output name="output" file="gtf_filter_by_attribute_values_list_out1_wcomment.gtf"/>
</test>
<!-- Test filtering with a more complex tabular file. -->
<test>