---
name: "gmod_make_gff_from_dbxref.pl"
section: "1p"
platform: "linux"
package: "chado-utils"
version: "1.31-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmod_make_gff_from_dbxref.pl"
---

# gmod\_make\_gff\_from\_dbxref.pl(1p)

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

## 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.