|GMOD_MAKE_GFF_FROM_DBXREF(1p)||User Contributed Perl Documentation||GMOD_MAKE_GFF_FROM_DBXREF(1p)|
NAME¶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: .)
DESCRIPTION¶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:
- to get TC130707
- to get CG180994.1
- to get 2_11498.
- 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: firstname.lastname@example.org. 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.
AUTHOR¶Scott Cain <email@example.com>.
Copyright (c) 2007,2008
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.