Closed unode closed 6 years ago
The GFF3 format specification allows for multiple value attributes if separated with a comma. From the official docs:
Parent=AF2312,AB2812,abc-3
With the current version of NGLess a GFF file:
##gff-version 3 reference protein_coding gene 40 100 . + . gene_id=geneA;gene_name=featA1,featA2 reference protein_coding gene 110 130 . + . gene_id=geneB;gene_name=featA1 reference protein_coding gene 140 200 . + . gene_id=geneC;gene_name=featA2
and a script:
ngless "0.7" input = fastq('reads.fq.gz') mapped = map(input, fafile='ref.fna.gz') union = count(mapped, gff_file='features.gff', features=['gene'], subfeatures=['gene_name'], mode={union}) write(union, ofile='output.txt')
produces:
reads.fq.gz -1 4 featA1 0 featA1,featA2 4 featA2 1
however the expectation is that values are expanded. Additionally, expansion should take into account the content of arguments mode= and multiple= in count():
mode=
multiple=
count()
reads.fq.gz -1 4 featA1 4 featA2 5
This was fixed in 1dda615716d6e3748b07b52d0a63d30bc497b359
The GFF3 format specification allows for multiple value attributes if separated with a comma. From the official docs:
With the current version of NGLess a GFF file:
and a script:
produces:
however the expectation is that values are expanded. Additionally, expansion should take into account the content of arguments
mode=
andmultiple=
incount()
: