Provided by: bioperl_1.7.2-2_all bug

NAME

       bp_find-blast-matches.pl - extract DNA sequences based on BLAST hits

SYNOPSIS

       bp_find-blast-matches.pl [-h -e -p -5 -n -o -3 -header] -blast <BLAST_FILE> -fasta
       <FASTA_FILE>

OPTIONS

   Mandatory:
       -blast
           BLAST output file to read from. The alignment should use the file specified by
           '-fasta' option ideally

       -fasta
           FASTA file to read from. This is where the sequence will be extracted from

   Optional:
       -h  Displays this help message

       -e  Maximum e-value for matches (0.01 by default)

       -p  Number of base pairs of 5' region to be included with the sequence

       -5  Number of base pairs of 5' region only, excluding the regular sequence

       -3  Number of base pairs of 3' region only, excluding the regular sequence

       -n  Number of top hits to display, starting with the best hit

       -o  Exact match to display (this option can't be used in conjunction with '-n'

       -header
           The FASTA header to display instead of the default

DESCRIPTION

       This script takes a BLAST output file and a FASTA file as arguments, given after the
       '-blast' and '-fasta' options respectively. The BLAST output file should have been
       generated with your sequence of interest and the FASTA file supplied as an argument.
       Example: find-blast-matches.pl -blast BLAST_FILE -fasta FASTA_FILE

       It parses through the BLAST file to check for high quality matches, which are then
       searched for in the FASTA file.  The sequence may vary from you candidate sequence, hence
       the BLAST search prior.

       The sequence from the FASTA file is then displayed to STDOUT.  Optional arguments can be
       used, such as to extract the 5' or 3' region.

AUTHOR

       Gabriel Abud - <gabriel.jabud-at-gmail.com>

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules.
       Send your comments and suggestions preferably to the Bioperl mailing list.  Your
       participation is much appreciated

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via email or the web:

         https://github.com/bioperl/bioperl-live/issues

EDIT HISTORY

       2014-08-04 - Gabriel Abud
           First features added

DEPENDANCIES

       Getopt::long, Pod::Usage, Bio::SearchIO, Bio::Seq, Bio::SeqIO, Bio::Perl, File::Basename