| Subject: | Bug in go-show-assocs-by-node.pl? |
| Date: | Wed, 16 Mar 2011 11:09:35 +0800 (CST) |
| To: | bug-go-perl [...] rt.cpan.org |
| From: | liu [...] qdio.ac.cn |
Dear sir/madam:
I encountered errors with go-show-assocs-by-node.pl from the go-perl. Can you help me with this? I think it is because of the format change in gene_association or gene_ontology.obo. Does this script work with the current format?
my code:
go-show-assocs-by-node.pl -id GO:0008150 gene_ontology.1_0.obo query_vs_uniprot_sprot.gene_association
also:
go-show-assocs-by-node.pl -id GO:0008150 gene_ontology.1_2.obo query_vs_uniprot_sprot.gene_association
my system/environment:
* go-perl-0.13
* perl, v5.8.8 built for x86_64-linux-thread-multi
* Linux localhost.localdomain 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
error message, many lines of them:
<error>
<message>no ID</message>
<file>query_vs_uniprot_sprot.gene_association</file>
<line>UniProtKB Q9Z2K8 IDH1 GO:0055114 GO_REF:0000004 IEA SP_KW:KW-0560 P Isocitrate dehydrogenase [NADP] cytoplasmic IDHC_MICOH|IDP2|IDH1 protein taxon:79684 20110305 UniProtKB</line>
<line_no>13893</line_no>
<parse_class>GO::Parsers::go_ont_parser</parse_class>
</error>
Thank you so much!
Chengzhang Liu