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stxmjh / interproscan

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Convert mode misbehaves for nucleic acid sequences #29

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Run InterProScan in CONVERT mode against an XML input file, which contains 
nucleic acid sequence annotations
2. Specify GFF3 as output format
3. Here is the command:
./interproscan.sh -mode convert -i test_nt_seqs.fasta.xml -f gff3

What is the expected output?
##gff-version 3
##feature-ontology 
http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
##sequence-region reverse 1 384
reverse provided_by_user    nucleic_acid    1   384 .   +   .   Name=reverse;md5=51884b55e9f02
5009d1b4682889bab2c;ID=reverse
reverse getorf  ORF 1   384 .   +   .   Name=reverse_6;Target=pep_reverse_1_384 1 
128;md5=51884b55e9f025009d1b4682889bab2c;ID=orf_reverse_1_384
reverse getorf  polypeptide 1   128 .   +   .   md5=d1b6cbf29dde9e5220196f3f6114a1c3;ID=p
ep_reverse_1_384
reverse PRINTS  protein_match   78  87  .   +   .   Name=PR00003;signature_desc=4-disulphid
e core signature;Target=null 78 87;status=T;ID=match$1_78_87;date=20-09-2013
reverse PRINTS  protein_match   107 116 .   +   .   Name=PR00003;signature_desc=4-disulph
ide core signature;Target=null 107 
116;status=T;ID=match$1_107_116;date=20-09-2013

What do you see instead?
##gff-version 3
##feature-ontology 
http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
null    Pfam    protein_match   432 579 2.0E-68 +   .   Name=PF08144;signature_desc=CPL 
(NUC119) domain;Target=null 432 
579;status=T;ID=match$1_432_579;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR012959"
null    Gene3D  protein_match   136 487 2.5E-65 +   .   Name=G3DSA:1.25.10.10;Target=null 
136 487;status=T;ID=match$2_136_487;date=20-09-2013;Dbxref="InterPro:IPR011989"
null    ProSiteProfiles protein_match   492 530 .   +   .   Name=PS50302;signature_desc=Pum
ilio RNA-binding repeat profile.;Target=null 492 
530;status=T;ID=match$3_492_530;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR001313"
null    ProSiteProfiles protein_match   200 235 .   +   .   Name=PS50302;signature_desc=Pum
ilio RNA-binding repeat profile.;Target=null 200 
235;status=T;ID=match$3_200_235;Ontology_term="GO:0003723";date=20-09-2013;Dbxre
f="InterPro:IPR001313"

Original issue reported on code.google.com by Maxim.Sc...@gmail.com on 20 Sep 2013 at 10:58

GoogleCodeExporter commented 9 years ago 
This bug is now fixed and committed, but needs further testing. The fix will be 
part of the official release, which will be out soon.

Best,
Maxim

Original comment by Maxim.Sc...@gmail.com on 20 Sep 2013 at 3:46