BP_SEQRET

NAME

bp_seqret − bioperl implementation of sequence fetch from local db (like EMBOSS seqret)

USAGE

bp_seqret [−f/−−format outputformat] [−o/−−out/−−outfile outfile] [−d/−−db dbname] [−i/−−id/−s/−−seqname seqname1]

Example usage:

   bp_seqret −f fasta −db db.fa −i seq1 −i seq2 > output.fas
   bp_seqret db.fa:seq1 output.fas
   bp_seqret db.fa:seq1 −o output.fas
   bp_seqret −db db.fa −o output.fas seq1 seq2 seq3
   bp_seqret −db db.fa seq1 seq2 seq3 output.fas
   bp_seqret −db db.fa seq1 seq2 seq3 − > output.fas

The DB is expected to be a Fasta formatted sequence file with multiple sequences.

Output format is Fasta by default.

If no output filename is provided then output is written to STDOUT. Providing ’−’ as the output filename will accomplish the same thing.

AUTHOR

Jason Stajich jason_AT_bioperl−dot−org