bioperl/bioperl-live — pull request #79 by Buuntu (2014-08-05 22:12:59+00:00)
Title: Added script to extract DNA sequences (as well as 5' or 3' regions if specified) from a FASTA file using a BLAST output file

Added a personal script to extract a DNA sequence from a FASTA file using a BLAST output file.
Expects at least two arguments, the BLAST file and the FASTA file. There are a number of optional arguments that are explained in the script.

This script is especially useful when trying to extract sequences with variance (hence the BLAST search beforehand) from FASTA files.
For example, say that you are trying to extract a given gene and 2000 base pairs 5' to it from 20 different genomes. All you have is one gene sequence, however. By doing a BLAST search between each of the genomes and the gene and then using this script, you can extract the sequences that you are interested in.

The script also has options to extract a specified 3' or 5' sequence from the FASTA file, as well as an e-value cut off. The final output is the extracted sequence in FASTA format.

Is this useful/generic enough to be included in the scripts directory? The script is well tested and takes command-line arguments.