Skip to content

Commit 73473ea

Browse files
author
Nolan Woods
authored
Update README.rst
1 parent 957b295 commit 73473ea

File tree

1 file changed

+12
-12
lines changed

1 file changed

+12
-12
lines changed

README.rst

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -80,17 +80,17 @@ Examples:
8080

8181
[0].[join(' - 1..', [description, to_string(length(seq))]), join(' ', [to_string(length(features[?type=='CDS' && qualifiers.translation])), 'proteins']), join(`"\t"`, ['Location', 'Strand', 'Length', 'PID', 'Gene', 'Synonym', 'Code', 'COG', 'Product']), (features[?type=='CDS' && qualifiers.translation].[join('..', [to_string(sum([location.start, `1`])), to_string(location.end)]), [location.strand][?@==`1`] && '+' || '-', length(qualifiers.translation[0]), (qualifiers.db_xref[?starts_with(@, 'GI')].split(':', @)[1])[0] || '-', qualifiers.gene[0] || '-', qualifiers.locus_tag[0] || '-', '-', '-', qualifiers.product[0] ] | [*].join(`"\t"`, [*].to_string(@)) )] | []
8282

83-
Convert dataset to faa format using fasta output::
84-
85-
[0].let({org: (annotations.organism || annotations.source)}, &(features[?type=='CDS' && qualifiers.translation].{id:
86-
join('|', [
87-
(qualifiers.db_xref[?starts_with(@, 'GI')].['gi', split(':', @)[1]]),
88-
(qualifiers.protein_id[*].['ref', @]),
89-
(qualifiers.locus_tag[*].['locus', @]),
90-
join('', [':', [location][?strand==`-1`] && 'c' || '', to_string(sum([location.start, `1`])), '..', to_string(location.end)])
91-
][][]),
92-
seq: qualifiers.translation[0],
93-
description: (org && join('', [qualifiers.product[0], ' [', org, ']']) || qualifiers.product[0])}))
83+
Convert dataset to faa format using fasta output::
84+
85+
[0].let({org: (annotations.organism || annotations.source)}, &(features[?type=='CDS' && qualifiers.translation].{id:
86+
join('|', [
87+
(qualifiers.db_xref[?starts_with(@, 'GI')].['gi', split(':', @)[1]]),
88+
(qualifiers.protein_id[*].['ref', @]),
89+
(qualifiers.locus_tag[*].['locus', @]),
90+
join('', [':', [location][?strand==`-1`] && 'c' || '', to_string(sum([location.start, `1`])), '..', to_string(location.end)])
91+
][][]),
92+
seq: qualifiers.translation[0],
93+
description: (org && join('', [qualifiers.product[0], ' [', org, ']']) || qualifiers.product[0])}))
9494

9595
See CONTRIBUTING.rst_ for information on contributing to this repo.
9696

@@ -101,4 +101,4 @@ See CONTRIBUTING.rst_ for information on contributing to this repo.
101101
.. _JMESPath playground: https://glenveegee.github.io/jmespath-edit/
102102
.. _split(): https://github.com/jmespath/jmespath.py/issues/159
103103
.. _let(): https://github.com/jmespath/jmespath.site/pull/6
104-
.. _SeqFeature.extract(): https://biopython.org/docs/latest/api/Bio.SeqFeature.html#Bio.SeqFeature.SeqFeature.extract
104+
.. _SeqFeature.extract(): https://biopython.org/docs/latest/api/Bio.SeqFeature.html#Bio.SeqFeature.SeqFeature.extract

0 commit comments

Comments
 (0)