.\" Automatically generated by Pod::Man 4.07 (Pod::Simple 3.32)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
.    ds C`
.    ds C'
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is >0, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.\"
.\" Avoid warning from groff about undefined register 'F'.
.de IX
..
.if !\nF .nr F 0
.if \nF>0 \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    if !\nF==2 \{\
.        nr % 0
.        nr F 2
.    \}
.\}
.\" ========================================================================
.\"
.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
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.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.