Man page - bp_seqret(1)
Packages contas this manual
- bp_process_sgd(1)
- bp_genbank2gff3(1)
- bp_make_mrna_protein(1)
- bp_search2alnblocks(1)
- bp_seqret(1)
- bp_fetch(1)
- bp_seqretsplit(1)
- bp_mrtrans(1)
- bp_index(1)
- bp_extract_feature_seq(1)
- bp_seqcut(1)
- bp_nexus2nh(1)
- bp_aacomp(1)
- bp_gccalc(1)
- bp_unflatten_seq(1)
- bp_local_taxonomydb_query(1)
- bp_dbsplit(1)
- bp_process_gadfly(1)
- bp_oligo_count(1)
- bp_nrdb(1)
- bp_seqpart(1)
- bp_tree2pag(1)
- bp_taxonomy2tree(1)
- bp_filter_search(1)
- bp_bioflat_index(1)
- bp_taxid4species(1)
- bp_split_seq(1)
- bp_find-blast-matches(1)
- bp_mask_by_search(1)
- bp_mutate(1)
- bp_seqconvert(1)
- bp_search2gff(1)
- bp_fastam9_to_table(1)
- bp_seq_length(1)
- bp_biogetseq(1)
- bp_translate_seq(1)
- bp_search2table(1)
- bp_sreformat(1)
- bp_revtrans-motif(1)
- bp_search2tribe(1)
Package: bioperl
apt-get install bioperl
apt-get install bioperl
Manuals in package:
Documentations in package:
Manual
| BP_SEQRET(1p) | User Contributed Perl Documentation | BP_SEQRET(1p) |
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
| 2021-08-15 | perl v5.32.1 |