Provided by: chado-utils_1.31-5_all bug

NAME

       gmod_make_gff_from_dbxref.pl - a tool for creating a gff3 file given a list of dbxrefs and
       fasta files.

SYNOPSYS

        % gmod_make_gff_from_dbxref.pl --fasta_dir <directory> --tmp_dir <directory> \
                                       <dbxref_list

COMMAND-LINE OPTIONS

         --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:

       >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:
       gmod-schema@lists.sourceforge.net.  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 <cain@cshl.edu>.

       Copyright (c) 2007,2008

       This library is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.