Bio::A...emboss(3pm)

💖 Bio::AlignIO::emboss — the perl manual page, but make it make sense 💖

okay bestie, so this is the user-contributed Perl documentation for Bio::A...emboss(3pm) — yes the title's literally abbreviated like that, it's giving mysterious. Anyway. It's a Perl module page, it lives in the Bioperl docs, and it's about parsing EMBOSS pairwise alignment output. Let's go. 🦋

---

✨ NAME ✨

Bio::AlignIO::emboss — parse EMBOSS alignment output (the stuff coming out of the applications water and needle).

---

✨ SYNOPSIS ✨

not me telling you this but like, do not use the object directly. fr. go through Bio::AlignIO.

# do not use the object directly
use Bio::AlignIO;
# read in an alignment from the EMBOSS program water
my $in = Bio::AlignIO->new(-format => 'emboss',
                          -file   => 'seq.water');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}

---

✨ DESCRIPTION ✨

so this object handles the parsing and the writing of pairwise sequence alignments from the EMBOSS suite. that's it, that's the job. she's a specialist 💅

---

✨ FEEDBACK ✨

🌸 Mailing Lists 🌸

user feedback is, like, an integral part of the evolution of this and other Bioperl modules — no cap. send your comments and suggestions preferably to the Bioperl mailing list. 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 responsive 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. (yes bestie, code and data examples — help them help you 💖)

🌸 Reporting Bugs 🌸

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

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

---

✨ AUTHOR - Jason Stajich ✨

Email jason@bioperl.org

---

✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — iykyk, that underscore is the "backstage, don't touch" sign.

---

🎀 next_aln 🎀

• Title : next_aln
• Usage : $aln = $stream->next_aln()
• Function: returns the next alignment in the stream.
• Returns : L<Bio::Align::AlignI> object — returns 0 on end of file or on error
• Args : NONE

---

🎀 write_aln 🎀

• Title : write_aln
• Usage : $stream->write_aln(@aln)
• Function: writes the $aln object into the stream in emboss format
• Returns : 1 for success and 0 for error
• Args : L<Bio::Align::AlignI> object

---

and that's the whole page, periodt 💜 this lil doc is perl v5.32.1, dated 2021-08-15 — iconic, vintage, still serving. bye bestie, go align something 🌈✨