Bio::T...iteScan(3pm)

💖 NAME 💖

Bio::Tools::PrositeScan — bestie, it's a parser for ps_scan result. That's the whole vibe. ✨

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🎀 SYNOPSIS 🎀

okay so here's how you actually use her:

use Bio::Tools::PrositeScan;

my $factory = Bio::Tools::PrositeScan->new(
    -file   => 'out.PrositeScan',
    -format => 'fasta'
);

while(my $match = $factory->next_prediction){
    #  $match is a Bio::SeqFeature::FeaturePair

    # Sequence ID
    my $seq_id = $match->seq_id;

    # PROSITE accession number
    my $psac = $match->hseq_id;

    # Coordinates
    my @coords = ( $match->start, $match->end );

    # Subsequence
    my $seq = $match->feature1->seq;
}

like… look at her go. she ate. 💅

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🌸 DESCRIPTION 🌸

so basically this is a parser for the output of the ps_scan program. you hand her either a file handle or a file name — she's not picky, she's flexible — and she hands you back a Bio::SeqFeature::FeaturePair object. iconic behavior, honestly. 🦋

⚠️ heads up bestie: the current implementation parses the entire file at once. no streaming, no nibbling, she's eating the whole plate in one sitting. plan accordingly. 😭

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👑 AUTHOR 👑

Juguang Xiao, juguang@tll.org.sg — the legend who wrote her. we stan. 🫶

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✨ SEE ALSO ✨

• ps_scan software <ftp://ftp.expasy.org/databases/prosite/ps_scan>
• PROSITE User Manual <http://prosite.expasy.org/prosuser.html>

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💜 new 💜

• Title — new
• Usage —

Bio::Tools::PrositeScan->new(-file => 'out.PrositeScan');
Bio::Tools::PrositeScan->new(-fh => \*FH);

• Returns — L<Bio::Tools::PrositeScan>
• Args — -format => string representing the format type for the ps_scan output, REQUIRED

the -format argument has to be set to "fasta" right now, because that is literally the only parser implemented. fr fr. and that lines up with using the ps_scan arguments -o fasta. 🎀

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🦋 next_prediction 🦋

• Title — new

🙈 yes bestie, it really does say new up there in the original. not my typo. i am merely the messenger. 💀

• Usage —

while($result = $factory->next_prediction){
    ;
}

• Returns — a Bio::SeqFeature::FeaturePair object where feature1 is the matched subsequence and feature2 is the PROSITE accession number. See <http://prosite.expasy.org/prosuser.html#conv_ac>.

like, feature1 is the actual sequence bit she matched, feature2 is the PROSITE accession number — that's the pair, that's the whole point, that's the main character energy. ⭐

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and that's the page, bestie!! this lil manual came from perl v5.32.1, dated 2021-08-15, and it lives in the Bio::T...iteScan(3pm) manpage. go forth and parse some PROSITE hits 💖✨🎀