This is the command gmod_extract_dbxref_from_gff.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_extract_dbxref_from_gff.pl - Extracts Dbxrefs from GFF3 lines that have Target
attributes
SYNOPSIS
% gmod_extract_dbxref_from_gff.pl gff_file_name > output_file
DESCRIPTION
For GFF3 lines of the form:
chr1 CDNA cDNA_match 69388 69593 0 - . Dbxref=Sorghum_CDNA:Contig_448;Target=Contig_448 75 295 +
that is, that have both Target and Dbxref attributes, this script extracts the Dbxref
value and prints out a list of the database and accession parts of the Dbxref value. This
functionality depends on a standard format for the Dbxref value, one where the name of the
database preceeds the accession and are separated by a colon.
Rationale
Another script, gmod_make_gff_from_dbxref.pl, takes a list of databases and accessions
(like this script provides) and a directory of FASTA files and builds a GFF3 file that
corresponds to those targets. The use for these files is to load them into Chado before
that compuational analysis results are loaded to ensure that the database has a complete
picture of the analysis performed.
COMMAND-LINE OPTIONS
None.
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