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.

perl v5.26.0                                       2017-09-14                      GMOD_MAKE_GFF_FROM_DBXREF(1p)