Man page - bp_search2tribe(1)

Packages contains this manual

Package:  bioperl
apt-get install bioperl

Manuals in package:
• bp_extract_feature_seq(1)
• bp_index(1)
• bp_taxid4species(1)
• bp_aacomp(1)
• bp_seqpart(1)
• bp_search2tribe(1)
• bp_dbsplit(1)
• bp_taxonomy2tree(1)
• bp_mutate(1)
• bp_process_gadfly(1)
• bp_find-blast-matches(1)
• bp_nexus2nh(1)
• bp_search2alnblocks(1)
• bp_biogetseq(1)
• bp_unflatten_seq(1)
• bp_fastam9_to_table(1)
• bp_tree2pag(1)
• bp_gccalc(1)
• bp_sreformat(1)
• bp_split_seq(1)
• bp_seqretsplit(1)
• bp_process_sgd(1)
• bp_make_mrna_protein(1)
• bp_revtrans-motif(1)
• bp_mask_by_search(1)
• bp_seqcut(1)
• bp_mrtrans(1)
• bp_seqret(1)
• bp_filter_search(1)
• bp_nrdb(1)
• bp_seqconvert(1)
• bp_search2gff(1)
• bp_bioflat_index(1)
• bp_oligo_count(1)
• bp_search2table(1)
• bp_genbank2gff3(1)
• bp_translate_seq(1)
• bp_local_taxonomydb_query(1)
• bp_fetch(1)
• bp_seq_length(1)
Documentations in package:
• bioperl

Manual

BP_SEARCH2TRIBE

NAME
SYNOPSIS
DESCRIPTION
AUTHOR

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NAME

bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

Usage:
bp_search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

This script is probably too slow for most people’s uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output from BLAST, or the blast2table from the BLAST O ’Reilly book to get a tabular output from these programs and then feed the table into MCL with the mcxdeblast script and the --m9 option.

This script will turn a protein Search report ( BLASTP, FASTP, SSEARCH ) into a Markov Matrix for TribeMCL clustering.

The options are:

-o filename - the output filename [default STDOUT]
-f format - search result format (blast, fasta)
(ssearch is fasta format). default is blast.
-w or --weight VALUE - Change the default weight for E(0.0) hits
to VALUE (default=200 (i.e. 1e-200) )
-h - this help menu

Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You specify this by doing: bp_search2tribe < file1 file2 file3

AUTHOR

Jason Stajich, jason-at-bioperl-dot-org

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