BP_SEARCH2GFF(1)

💅 BP_SEARCH2GFF(1) — bestie's SearchIO-to-GFF era 💅

okay so this page lives in the User Contributed Perl Documentation section, and it's all about bp_search2gff, a script that turns a SearchIO report into GFF. no cap, we're getting every flag. 🫶

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✨ NAME ✨

bp_search2gff — turn a SearchIO report into GFF. literally the whole vibe. 🌸

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🌈 SYNOPSIS 🌈

Usage:

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

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💅 DESCRIPTION 💅

okay so this script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF. iconic. 🧚

The options are:

• -i infilename — (optional) input filename; it 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

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👑 AUTHOR 👑

Jason Stajich, jason-at-bioperl-dot-org. king behavior. 💜

🫶 Contributors 🫶

Hilmar Lapp, hlapp-at-gmx-dot-net. royalty. 🎀

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🌈 clone_loc 🌈

• Title: clone_loc
• Usage: my $l = clone_loc($feature->location);
• Function: helper function that simplifies the task of cloning locations for --locfunc closures. Presently simply implemented using Storable::dclone().
• Example: —
• Returns: a L<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 L<Bio::LocationI> compliant object.

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🍓 create_loc 🍓

• Title: create_loc
• Usage: my $l = create_loc("10..12");
• Function: helper function that simplifies 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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💖 that's the whole page, bestie. this fab little manual shipped with perl v5.42.3, dated 2021-02-03. periodt. 🫶✨