This is the command gmod_make_gff_from_dbxref.plp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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:
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.
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