GMOD_EX...ROM_GFF(1p)

🌸 GMOD_EXTRACT_DBXREF_FROM_GFF(1p) — the girlies' guide 🌸

okay so bestie, this is a User Contributed Perl Documentation page, section 1p of the manual, and it's literally about one tiny little script that does one tiny little thing and does it flawlessly. no notes. 💅

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✨ NAME ✨

gmod_extract_dbxref_from_gff.pl — extracts Dbxrefs from GFF3 lines that have Target attributes. that's it. that's the whole job. she's a specialist and she ate. 🎀

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🦋 SYNOPSIS 🦋

% gmod_extract_dbxref_from_gff.pl gff_file_name > output_file

so you hand her a gff file, she yells the results into output_file. redirect or perish, no cap. 💖

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🌈 DESCRIPTION 🌈

bestie. listen. we're talking about GFF3 lines that look like this:

chr1 CDNA  cDNA_match  69388   69593  0  -  .  Dbxref=Sorghum_CDNA:Contig_448;Target=Contig_448 75 295 +

the vibe check here is: this line has both a Target attribute and a Dbxref attribute. when a line passes that check, the script pulls out the Dbxref value and prints a list of the database part and the accession part of that Dbxref value. two parts, separate columns, living their truth.

⚠️ and here's the fine print, bestie, don't skip it: this whole thing depends on the Dbxref value following a standard format — one where the name of the database comes before the accession and they're separated by a colon. that's the format. that's the only format. if your Dbxref is giving ✨chaos✨ instead, she cannot help you. 🫶

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🧚 Rationale 🧚

so there's another script, gmod_make_gff_from_dbxref.pl, and she's the main character of the next episode. she takes a list of databases and accessions (exactly the kind this script provides) plus a directory of FASTA files, and she builds a GFF3 file that corresponds to those targets. iconic behaviour, honestly.

and the why? the reason these files exist at all is to load them into Chado before the computational analysis results get loaded. that way the database has a complete picture of the analysis that was performed. it's giving "do your paperwork before the party" and honestly? slay. no cap. 💖

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💅 COMMAND-LINE OPTIONS 💅

None.

literally. zero. no flags, no --help energy, no secret menu. she takes a gff_file_name argument and that's the whole relationship. periodt. 😭

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👑 AUTHOR 👑

Scott Cain <cain@cshl.org>

Copyright (c) 2007

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

(that's the licensing, bestie — same terms as Perl itself, so go be free, just keep the receipts. 🎀)

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and that's the whole page!! 🌸 written up as perl v5.30.0, dated 2019-12-05, filed under GMOD_EX...ROM_GFF(1p) — mwah, thanks for reading, ily, go extract some Dbxrefs. 🦋✨💜