Man page - bp_fastam9_to_table(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)
apt-get install bioperl
Manual
| BP_FASTAM9_TO_TABLE(1p) | User Contributed Perl Documentation | BP_FASTAM9_TO_TABLE(1p) |
NAME
fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
SYNOPSIS
fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
DESCRIPTION
Command line options:
-e/--evalue evalue -- filter by evalue
-b/--bitscore bitscore -- filter by bitscore
--header -- boolean flag to print column header
-o/--out -- optional outputfile to write data,
otherwise will write to STDOUT
-h/--help -- show this documentation
Not technically a SearchIO script as this doesn't use any Bioperl components but is a useful and fast. The output is tabular output with the standard NCBI -m9 columns.
queryname hit name percent identity alignment length number mismatches number gaps query start (if on rev-strand start > end) query end hit start (if on rev-strand start > end) hit end evalue bit score
Additionally 3 more columns are provided
fasta score
sw-score
percent similar
query length
hit length
query gaps
hit gaps
AUTHOR - Jason Stajich
Jason Stajich jason_at_bioperl-dot-org
| 2021-08-15 | perl v5.32.1 |