Provided by: chado-utils_1.31-4_all
gmod_make_gff_from_dbxref.pl - a tool for creating a gff3 file given a list of dbxrefs and fasta files.
% gmod_make_gff_from_dbxref.pl --fasta_dir <directory> --tmp_dir <directory> \ <dbxref_list
--fasta_dir Directory containing fasta files (required) --tmp_dir Temporary directory (default: /tmp) --type SO term to use for created features (default: region) --source Column 2 of the GFF file (default: .)
This tool takes a list of tab separated db identifiers and accessions on the command line (like gmod_extract_dbxref_from_gff.pl would produce) along with a directory containing fasta files and creates a GFF file. The script tries several options for identifying the accession in the fasta description line. These are the types of things it currently tries: >mi|5419616|mn|TC130707| to get TC130707 >gi|34072055|gb|CG180994.1|CG180994 to get CG180994.1 >mi|12821100|mn|2_11498(1330441)| to get 2_11498. >123456 to get 123456 (ie, the entire line, which is the last resort). If you have a description line that is different from this and would like help modifying this script to work with your data, please email the schema mailing list: email@example.com. If you modify the script yourself to work with your data, please also mail the schema mailing list to report your changes so they can be included.
Scott Cain <firstname.lastname@example.org>. Copyright (c) 2007,2008 This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.