FASTA(1)

💖 FASTA(1) 💖

okay bestie, welcome to FASTA(1) — yes, the page is called FASTA, and it lives in the User Commands section of the manual, but the actual star of the show is a little program called famap. don't ask, it's giving family drama. sit down, hydrate, let's go 🫶

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✨ NAME ✨

famap — prepare Fasta sequence database for re-PCR searches

like, it literally gets your FASTA files ready so re-PCR can do its lil searches. iconic behavior. 👑

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🌸 SYNOPSIS 🌸

famap [-hV] -b mmapped-file [-t cvt] [fafile ...]

famap [-hV] -d mmapped-file [ord ...]

famap [-hV] -l mmapped-file [ord ...]

three whole modes, three whole vibes. pick your fighter 💅

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🦋 DESCRIPTION 🦋

so the program famap is part of the e-PCR suite, and its whole job — its entire main character arc — is building mmapped-file out of FASTA files so that reverse e-PCR searches can happen. that's it. that's the plot. ✨

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🎀 OPTIONS 🎀

first up, the flags hanging out in the synopsis:

• -hV — they show up together in every synopsis line, like a little duo 🫶
• -b mmapped-file — you're naming the mmapped file right there in the call
• -t cvt — hand it a conversion table (more on that in a sec 👇)
• [fafile ...] — and then as many FASTA files as your heart desires
• -d mmapped-file [ord ...] — mmapped file plus optional ord args
• -l mmapped-file [ord ...] — same shape, mmapped file plus optional ord args

and where cvt (the conversion table) is one of these cuties:

• off — as is (this is the default, no notes) 🙈
• n — nucleotide [acgtnACGTN] allowed
• N — nucleotide uppercase allowed [ACGTN]
• nx — nucleotide with ambiguity codes allowed
• NX — nucleotide with ambiguity codes uppercase

lowercase besties, notice that n and nx let lowercase through, while N and NX are strict uppercase-only situations. read the brackets, they never lie 💀

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🌈 EXAMPLE 🌈

here's the whole lil pipeline in one place, exactly as written:

famap -tN -b genome.famap org/chr_*.fa

fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap

re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200

see famap(1) and re-pcr(1) 💜

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🔥 SEE ALSO 🔥

• /usr/share/doc/ncbi-epcr/README.txt
• bioperl(1), e-pcr(1), famap(1) and re-pcr(1)

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👑 AUTHORS 👑

this manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others, so generous 💖). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation.

on Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

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and that's the whole page, bestie!! 🎀 this one's from the Fasta converter for e-PCR source, version whatever the "versi..." got cut off at because terminals have no chill, and it's dated April 2008 — vintage, honestly, we stan a classic 💅✨ no cap, you now know famap better than it knows itself. mwah 🫶💖