BLAST

This is the Title of the Book, eMatter Edition

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309

Appendix E

APPENDIX E

blast2table.pl

It’s often useful to have both the standard report and tabular data for the same

search. This program converts standard WU-BLAST or NCBI-BLAST output to the

NCBI tabular format (

-m 8) described in Appendix A. It supports concatenated

BLAST reports and is more efficient than most full-featured BLAST parsers.

blast2table.pl can be used either on a file or in a pipe:

blast2table.pl my_blast_output > my_table_output

blastp nr query | blast2table.pl > table_from_wu-blast

The Unix tee program can create both the standard output and a table at the same

time:

blastall -p blastp -d nr -i query | tee standard | blast2table.pl > table

blast2table.pl also has a few useful filtering options (see Table E-1). The following

command displays only those with an alignment of over 50 percent identity and with

a bit score greater than 20:

blast2table.pl -p 50 -b 20 blast_output

The complete program is listed next and may be downloaded as blast2table.pl from

this book’s web site.

#!/usr/bin/perl -w

use strict;

use Getopt::Std;

Table E-1. blast2table.pl options

Option Description

-b Minimum number of bits for each alignment

-e Maximum E-value for each alignment or alignment group

-m Minimum coordinate of the query sequence

-n Maximum coordinate of the query sequence

-p Minimum percent ...