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.IX Title "GMOD_EXTRACT_DBXREF_FROM_GFF 1p"
.TH GMOD_EXTRACT_DBXREF_FROM_GFF 1p "2016-12-17" "perl v5.24.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
gmod_extract_dbxref_from_gff.pl \- Extracts Dbxrefs from GFF3 lines that have Target attributes
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  % gmod_extract_dbxref_from_gff.pl gff_file_name > output_file
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
For \s-1GFF3\s0 lines of the form:
.PP
.Vb 1
\& chr1 CDNA  cDNA_match  69388   69593  0  \-  .  Dbxref=Sorghum_CDNA:Contig_448;Target=Contig_448 75 295 +
.Ve
.PP
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.
.SS "Rationale"
.IX Subsection "Rationale"
Another script, gmod_make_gff_from_dbxref.pl, takes a list of databases
and accessions (like this script provides) and a directory of \s-1FASTA\s0 files
and builds a \s-1GFF3\s0 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.
.SH "COMMAND-LINE OPTIONS"
.IX Header "COMMAND-LINE OPTIONS"
None.
.SH "AUTHOR"
.IX Header "AUTHOR"
Scott Cain <cain@cshl.org>
.PP
Copyright (c) 2007
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
