a tool for creating a gff3 file given


 % --fasta_dir <directory> --tmp_dir <directory> \


  --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: .)


This tool takes a list of tab separated db identifiers and accessions on the command line (like 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: [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.


Scott Cain <[email protected]>.

Copyright (c) 2007,2008

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