Support InterProScan 5.74 output and non-spec GFF attributes#9
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Updates to keep ipr_to_gff and prot_to_genome working with recent InterProScan releases and common third-party GFF3 files. ipr_to_gff: - Handle the new XML schema namespace introduced in recent InterProScan versions (https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas, previously http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5). get_tag now strips any leading "{...}" namespace rather than asserting on a fixed URI, so it is robust to future namespace changes, and --namespace defaults to auto-detect. - Support the funfamhmmer3-match type (CATH-Gene3D FunFam), which newer InterProScan versions emit. process_hmmer3 is parameterised by the match and location tag names and reused for funfam matches. gff: - Tolerate unescaped ';' inside GFF3 attribute values (invalid per spec but emitted by tools such as funannotate, e.g. gene names like "SULTR3;4"). A ';'-separated piece without '=' is treated as a continuation of the previous value instead of raising ValueError. data: - Replace the deprecated pkg_resources.resource_filename with an importlib.resources-based shim. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Keeps
ipr_to_gffandprot_to_genomeworking with recent InterProScanreleases and common third-party GFF3 files. Verified end-to-end on a real
~4 GB InterProScan 5.74 XML and a funannotate genome GFF.
ipr_to_gff
(
https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/schemas, previouslyhttp://www.ebi.ac.uk/interpro/resources/schemas/interproscan5).get_tagnow strips any leading{...}namespace instead of asserting afixed URI, so it is robust to future changes;
--namespacedefaults toauto-detect.
funfamhmmer3-matchtype (CATH-Gene3D FunFam) emitted by newerInterProScan.
process_hmmer3is parameterised by match/location tag namesand reused for funfam.
gff
;inside attribute values (invalid per spec but emittedby tools such as funannotate, e.g. gene names like
SULTR3;4). A piecewithout
=is treated as a continuation of the previous value instead ofraising
ValueError, and is re-escaped correctly on output.data
pkg_resources.resource_filenamewith animportlib.resourcesshim.