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.IX Title "GMOD_MAKE_GFF_FROM_DBXREF 1p"
.TH GMOD_MAKE_GFF_FROM_DBXREF 1p "2019-12-05" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
gmod_make_gff_from_dbxref.pl \- a tool for creating a gff3 file given
a list of dbxrefs and fasta files.
.SH "SYNOPSYS"
.IX Header "SYNOPSYS"
.Vb 2
\& % gmod_make_gff_from_dbxref.pl \-\-fasta_dir <directory> \-\-tmp_dir <directory> \e
\&                                <dbxref_list
.Ve
.SH "COMMAND-LINE OPTIONS"
.IX Header "COMMAND-LINE OPTIONS"
.Vb 4
\&  \-\-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: .)
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1GFF\s0 file.
The script tries several options for identifying the accession in the
fasta description line.  These are the types of things it currently
tries:
.IP ">mi|5419616|mn|TC130707|" 4
.IX Item ">mi|5419616|mn|TC130707|"
to get \s-1TC130707\s0
.IP ">gi|34072055|gb|CG180994.1|CG180994" 4
.IX Item ">gi|34072055|gb|CG180994.1|CG180994"
to get \s-1CG180994.1\s0
.IP ">mi|12821100|mn|2_11498(1330441)|" 4
.IX Item ">mi|12821100|mn|2_11498(1330441)|"
to get 2_11498.
.IP ">123456" 4
.IX Item ">123456"
to get 123456 (ie, the entire line, which is the last resort).
.PP
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.
.SH "AUTHOR"
.IX Header "AUTHOR"
Scott Cain <cain@cshl.edu>.
.PP
Copyright (c) 2007,2008
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.