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

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

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

perl v5.32.1                                       2021-08-15                          BP_FIND-BLAST-MATCHES(1p)

       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.

       2014-08-04 - Gabriel Abud
           First features added

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

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

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