GMOD_M..._DBXREF(1p)

💖 GMOD_M..._DBXREF(1p) 💖

okay bestie, welcome to gmod_make_gff_from_dbxref.pl — she's a User Contributed Perl script and she's here to serve 💅

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✨ NAME ✨

gmod_make_gff_from_dbxref.pl — a tool for creating a gff3 file given a list of dbxrefs and fasta files. that's it, that's the whole job 🫶

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🌸 SYNOPSYS 🌸

(yes she spells it like that, we respect her choices)

 % gmod_make_gff_from_dbxref.pl --fasta_dir <directory> --tmp_dir <directory> \
                                <dbxref_list

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🎀 COMMAND-LINE OPTIONS 🎀

• --fasta_dir — the directory holding your fasta files. required, no cap, you literally cannot skip this one 💀
• --tmp_dir — where she keeps her lil temporary files (default: /tmp)
• --type — the SO term she stamps on the features she creates (default: region)
• --source — what goes in column 2 of the GFF file (default: .)

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🦋 DESCRIPTION 🦋

so here's the vibe: you hand her a list of tab-separated db identifiers and accessions right on the command line (the exact kind of thing gmod_extract_dbxref_from_gff.pl would hand you), plus a directory full of fasta files, and she builds you a GFF file. iconic behavior honestly 👑

the way she works is that she tries several different options for sniffing out the accession in the fasta description line. here's what she currently attempts:

>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 (i.e. the entire line — that's the last resort, the "fine, I'll do it myself" option 😭)

🚨 bestie listen: if your description line looks different from all of the above and you want a hand modifying this script so it plays nice with your data, please email the schema mailing list: gmod-schema@lists.sourceforge.net. and if you go ahead and 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. sharing is caring fr fr 💜

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👑 AUTHOR 👑

Scott Cain <cain@cshl.edu>.

Copyright (c) 2007,2008

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. slay, and also legally binding 💅

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and that's the whole page!! 🌈 this lil beauty comes to you from perl v5.30.0, dated 2019-12-05, filed under GMOD_M..._DBXREF(1p) — drink water, read your manpages, mwah 💖✨🎀