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PROGRAM:

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:
[email protected]. 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.

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