GMOD_GF...OCESSOR(1p)

💖 NAME

$0 — bestie, this one preps a GFF3 file for bulk loading into a chado database. That's the whole gig. It's giving "backstage crew for the main event" energy. ✨

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✨ SYNOPSIS

% gmod_gff_preprocessor [options] --gfffile <filename>

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🎀 COMMAND-LINE OPTIONS

• --gfffile — the file holding your GFF3. It's optional, so if you don't pass it, she'll just read from stdin like the flexible queen she is. 💅
• --outfile — the name kernel used for naming the result files. (Yes, "kernel." That's what it says. We don't question the lore.) 🫶
• --splitfile — splits the files into more manageable chunks, and you can hand it an argument to control exactly how the splitting goes down.
• --onlysplit — splits the files and then dips. No sorting. Bye! 👋
• --nosplit — no splitting at all, so it just sorts. Sort-only era. 🎀
• --hasrefseq — set this if your file contains a reference sequence line. (Only needed if you're not splitting files.)
• --dbprofile — name your gmod.conf profile here. If you don't, she uses the default one.
• --inheritance_tiers — how many levels of inheritance do you expect this file to have? Default: 3.

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🦋 DESCRIPTION

splitfile — just setting this flag to 1 makes the file split by reference sequence. But if you give it an optional argument, it gets split even further, according to these rules:

• source=1 — splits files according to the value in the source column.
• source=a,b,c — puts lines with sources that match (via regular expression) 'a', 'b', or 'c' into a separate file.
• type=a,b,c — puts lines with types that match 'a', 'b', or 'c' into a separate file.

Say you want all your analysis results living in their own file. You'd say --splitfile type=match, and then all your cDNA_match, EST_match and cross_genome_match features get their own separate files (separated by reference sequence). Main character moves only. 💅✨

inheritence_tiers — the number of levels of inheritance this file has. So if the file has "central dogma" genes in it (gene/mRNA/exon,polypeptide), then it has 3. Up to 4 is supported, but ngl, the higher the number, the more slowly it performs. If you genuinely don't know? 3 is a reasonable guess. 🫶

🌸 FASTA sequence

If your GFF3 file has FASTA sequence hanging out at the end, that sequence gets placed in a separate file with the extension .fasta. 🦋

You can load this fasta file separately after the split and/or sorted GFF3 files are loaded, using this command:

gmod_bulk_load_gff3.pl -g <fasta file name>

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👑 AUTHOR

Scott Cain <cain@cshl.org> 💖

Copyright (c) 2006-2007

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

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okay bestie, that's the whole page, no notes, we ate. 🍓

Signed, sealed, delivered by perl v5.30.0, dated 2019-12-05, from the GMOD_GF...OCESSOR(1p) files — part of the User Contributed Perl Documentation. Iconic. Periodt. 💜✨