Bio::SeqIO::tab(3pm)

💖 Bio::SeqIO::tab 💖

okay bestie, welcome to Bio::SeqIO::tab(3pm) — it's from the User Contributed Perl Documentation, and it's genuinely one of those little modules that ate and left no crumbs 🫶

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✨ NAME ✨

Bio::SeqIO::tab — nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"

like. that's it. that's the whole vibe. an id, a tab, the sequence, a newline. so simple it's iconic 💅

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🌸 SYNOPSIS 🌸

Do not use this module directly. Use it via the Bio::SeqIO class.

fr fr. this is a backstage module, not a main character you call by name. go through Bio::SeqIO, that's the move 👑

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🦋 DESCRIPTION 🦋

so this object can transform Bio::Seq objects to and from tabbed flat file databases. glow up in both directions ✨

it is very useful when you're doing large scale stuff using the Unix command line utilities — grep, sort, awk, sed, split, you name it. literally the whole squad 🤝

imagine you have a format converter seqconvert along the following lines:

my $in  = Bio::SeqIO->newFh(-fh => \*STDIN , '-format' => $from);
my $out = Bio::SeqIO->newFh(-fh=> \*STDOUT, '-format' => $to);
print $out $_ while <$in>;

then you can very easily filter sequence files for duplicates as:

$ seqconvert < foo.fa -from fasta -to tab | sort -u |\
     seqconvert -from tab -to fasta > foo-unique.fa

or grep [-v] for certain sequences with:

$ seqconvert < foo.fa -from fasta -to tab | grep -v '^S[a-z]*control' |\
     seqconvert -from tab -to fasta > foo-without-controls.fa

or chop up a huge file with sequences into smaller chunks with:

$ seqconvert < all.fa -from fasta -to tab | split -l 10 - chunk-
$ for i in chunk-*; do seqconvert -from tab -to fasta < $i > $i.fa; done
# (this creates files chunk-aa.fa, chunk-ab.fa, ..., each containing 10
# sequences)

no cap, this is the pipeline dream 🧚

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💌 FEEDBACK 💌

📬 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated 🥺

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. many experienced and reponsive experts will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible 🙏

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

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👑 AUTHORS 👑

Philip Lijnzaad, p.lijnzaad@med.uu.nl

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _

🍓 next_seq

Title   : next_seq
Usage   : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args    :

🍓 write_seq

Title   : write_seq
Usage   : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args    : Bio::Seq object

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and that's the whole page, bestie 🎀 this was Bio::SeqIO::tab(3pm), shipped as part of perl v5.32.1, dated 2021-08-15. slay, go read a sequence, ily 💜