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bioperl / bioperl-live-redmine

Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
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blast2sam #130

Open cjfields opened 8 years ago

cjfields commented 8 years ago

Author Name: Albert Vilella (Albert Vilella) Original Redmine Issue: 3324, https://redmine.open-bio.org/issues/3324 Original Date: 2012-02-10 Original Assignee: Bioperl Guts

blast2sam takes any of the given flavors of blast output, instantiates the right bioperl object for them, then writes them into sam format.

cjfields commented 8 years ago

Original Redmine Comment Author Name: Peter Cock Original Date: 2012-02-10T14:51:13Z

Are you asking for SAM output in BioPerl’s AlignIO or SearchIO? That would probably let you do BLAST to SAM

cjfields commented 8 years ago

Original Redmine Comment Author Name: Albert Vilella Original Date: 2012-02-15T11:28:27Z

Peter Cock wrote:

Are you asking for SAM output in BioPerl’s AlignIO or SearchIO? That would probably let you do BLAST to SAM

Since it seems there is a sam module under Bio::Assembly::IO sam with a write_assembly method, it may be a matter of converting SearchIO objects coming from blast into it.

cjfields commented 7 years ago

@avilella would you be interested in implementing this?