GFF3

petlx.gff3.fromgff3(filename, region=None)

Extract feature rows from a GFF3 file.

New in version 0.2.

Changed in version 0.15.

A region query string of the form ‘[seqid]’ or ‘[seqid]:[start]-[end]’ may be given for the region argument. If given, requires the GFF3 file to be bgzipped and tabix indexed.

petlx.gff3.gff3lookup(features, facet='seqid')

Build a GFF3 feature lookup based on interval trees. See also petlx.interval.facetintervallookup().

New in version 0.2.

petlx.gff3.gff3join(table, features, seqid='seqid', start='start', end='end', proximity=1)

Join with a table of GFF3 features. See also petlx.interval.intervaljoin().

New in version 0.2.

petlx.gff3.gff3leftjoin(table, features, seqid='seqid', start='start', end='end', proximity=1)

Left join with a table of GFF3 features. See also petlx.interval.intervalleftjoin().

New in version 0.2.