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SearchIO::infernal.pm: parser->next_result deliveres only one result from mulit-CM infernal report #119

Open cjfields opened 9 years ago

cjfields commented 9 years ago

Author Name: Nadine Tatto (Nadine Tatto) Original Redmine Issue: 3279, https://redmine.open-bio.org/issues/3279 Original Date: 2011-08-10 Original Assignee: Bioperl Guts

I have an infernal report containing about 2000 CMs from an infernal run against Rfam.cm. To parse this report I wanted to use Bio::SearchIO::infernal.pm. Unfortunately this turned out to be a problem for me, because “$parser->next_result” only delivers the result for the first CM in the report and nothing more.

The script is called this way: ./infernalParser.pl infernal.output

Output: 5S_rRNA

Expected Output: 5S_rRNA 5_8S_rRNA U1 … (names of all CM’s contained in the report)

cjfields commented 9 years ago

Original Redmine Comment Author Name: Nadine Tatto Original Date: 2011-08-10T08:40:56Z

added shorter infernal report, original report seems to be to big in file size for upload