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


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


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

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