afetch(1)

🎀 afetch(1) · the Biosquid Manual 💅

okay bestie, meet afetch, the alignment-fetching queen 👑 It goes into an alignment database and pulls out the exact alignment you're after. Let's get into it 🫶

✨ NAME ✨

afetch - retrieve an alignment from an alignment database 🦋

🧚 SYNOPSIS 🧚

afetch [options] alignmentdb key

afetch --index alignmentdb

💖 DESCRIPTION 💖

so afetch grabs the alignment named key out of an alignment database that lives in the file alignmentdb 🫶

alignmentdb is a "multiple multiple alignment" file in Stockholm (e.g. native Pfam) format. yes, "multiple multiple," it's giving layers 💀

key can be either the name (ID) of the alignment or its accession number (AC). either one works, no cap ✨

your alignmentdb file should get SSI indexed with afetch --index first for efficient retrieval 🔥

⚠️ an SSI index isn't required, but retrieving without one may be painfully slow 🙈 so yeah, index it first, bestie.

🌸 OPTIONS 🌸

• -h — pull up the brief help 🆘 It shows the version number and a summary of every option, expert options included.

🔮 EXPERT OPTIONS 🔮

• --index — this one's a special command, not a retrieval. Instead of fetching a key, afetch --index alignmentdb builds an SSI index of the names and accessions of the alignments in the file alignmentdb 🧠 Run it once on your alignmentdb file to get it ready for all future afetches. main character energy 👑

🦋 SEE ALSO 🦋

alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), sfetch(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1). 💜

💜 AUTHOR 💜

Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine. It's freely distributed under the GNU General Public License (GPL). See COPYING in the source code distribution for more details, or contact the author 🌈

Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: eddy@genetics.wustl.edu

that's a wrap on afetch 🎀 Biosquid 1.9g, January 2003, afetch(1). stay aligned, bestie 🫶💅✨