BP_SEARCH2GFF(1p)

💖 BP_SEARCH2GFF 💖

okay bestie, so this is bp_search2gff, a User Contributed Perl Documentation page (section 1p of the manual, iykyk). Sit down, grab a boba, because we're turning search reports into GFF and it's gonna be so satisfying. ✨

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🌸 NAME 🌸

bp_search2gff — turn a SearchIO report into GFF

no cap, that's literally the whole job description and she does it flawlessly 💅

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🦋 SYNOPSIS 🦋

Usage:

bp_search2gff [-o outputfile] [-f reportformat] [-i inputfilename]  OR file1 file2 ..

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✨ DESCRIPTION ✨

This script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF. That's it, that's the serve. 🎀

The options are:

• -i infilename — (optional) inputfilename, will read either ARGV files or from STDIN
• -o filename — the output filename [default STDOUT]
• -f format — search result format (blast, fasta,waba,axt) (ssearch is fasta format). default is blast.
• -t/--type seqtype — if you want to see query or hit information in the GFF report
• -s/--source — specify the source (will be algorithm name otherwise like BLASTN)
• --method — the method tag (primary_tag) of the features (default is similarity)
• --scorefunc — a string or a file that when parsed evaluates to a closure which will be passed a feature object and that returns the score to be printed
• --locfunc — a string or a file that when parsed evaluates to a closure which will be passed two features, query and hit, and returns the location (Bio::LocationI compliant) for the GFF3 feature created for each HSP; the closure may use the clone_loc() and create_loc() functions for convenience, see their PODs
• --onehsp — only print the first HSP feature for each hit
• -p/--parent — the parent to which HSP features should refer if not the name of the hit or query (depending on --type)
• --target/--notarget — whether to always add the Target tag or not
• -h — this help menu
• --version — GFF version to use (put a 3 here to use gff 3)
• --component — generate GFF component fields (chromosome)
• -m/--match — generate a 'match' line which is a container of all the similarity HSPs
• --addid — add ID tag in the absence of --match
• -c/--cutoff — specify an evalue cutoff

Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You specify this by doing: bp_search2gff < file1 file2 file3

🫶 reminder bestie: no files on the command line means she's reading from STDIN, and you tell her with that lil redirect right there.

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👑 AUTHOR 👑

Jason Stajich, jason-at-bioperl-dot-org

💜 Contributors 💜

Hilmar Lapp, hlapp-at-gmx-dot-net

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🧚 clone_loc

• Title : clone_loc
• Usage : my $l = clone_loc($feature->location);
• Function: Helper function to simplify the task of cloning locations for --locfunc closures.

Presently simply implemented using Storable::dclone().

• Example :
• Returns : A Bio::LocationI object of the same type and with the same properties as the argument, but physically different. All structured properties will be cloned as well.
• Args : A Bio::LocationI compliant object

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🌈 create_loc

• Title : create_loc
• Usage : my $l = create_loc("10..12");
• Function: Helper function to simplify the task of creating locations for --locfunc closures. Creates a location from a feature-table formatted string.
• Example :
• Returns : A Bio::LocationI object representing the location given as formatted string.
• Args : A GenBank feature-table formatted string.

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and that's the whole page, bestie!! go forth and GFF-ify everything 💖✨

this icon was brought to you by perl v5.32.1, dated 2021-08-15 — yeah she's an old queen but she still eats 🎀👑