blast2gff.pl - Convert a BLAST result file into a GFF file
% blast2gff.pl --blast_result_file [blast result file] --reference_sequence_file [file with reference sequences (optional)] --gff_output_file [gff file name (optional)]
This script takes a blast result file and a set of reference sequences and generates a GFF file from it, with the following form:
GroupUn.1786 tblastn drosophila_HSP 880 1035 . + . Drosophila_Match P91685
It also adds entries for reference sequences, if the --reference_sequence_file flag is used:
Group1.2 sequence sequence 1 265115 . + . Sequence Group1.2
If the --make_dumpable flag is used, it adds information to the 9th column ("Class name") to make the alignments dumpable, e.g. Target EST:actg5.3 5 300 the query start and end sites
This code should be considered beta. Be especially skeptical of the --make_dumpable feature, as it is it untested. Please report all bugs to the gmod-gbrowse mailing list.
--blast_result_file <blast result file>
(Mandatory) File with BLAST output
--reference_sequence_file <file with reference sequences>
(Optional) FASTA formatted file with reference ("database") sequences that BLAST was run against. If specified, GFF entries for the reference sequences are created.
--gff_output_file <gff file name>
(Optional) Name for GFF output file. If not supplied, we will write to STDOUT.
(Optional) Add information to the 9th column to make the alignments dumpable, e.g. Target EST:actg5.3 5 300 (where 5 and 300 are the query start and end sites)
Bioperl also provides BLAST to GFF capability with its scripts//utilities/search2gff.PLS script.
jtr4v at nospam alumni.zerospam.virginia.edu
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.