CDBYANK(1)

💖 CDBYANK(1) 💖

okay bestie, gather round, because today we're talking about cdbyank, a lil tool from the User Commands corner of your manual that goes and fetches stuff out of an index file. think of it as the ✨main character✨ of fasta lookup. no cap. 🦋

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🌸 NAME 🌸

cdbyank — query an index file created with cdbfasta. that's it. that's the whole vibe check. 🎀

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✨ DESCRIPTION ✨

💫 Usage 💫

cdbyank <index_file> [-d <fasta_file>] [-a <key>|-n|-l|-s]
[-o <outfile>] [-q <char>|-Q][-F] [-R] [-P] [-x] [-w] [-z <dbfasta.cdbz>

so <index_file> is the index file you (or someone iconic) already made with cdbfasta earlier — it's usually chillin' with a .cidx suffix, iykyk. 🍓

and then here's every single flag, laid out, don't skip a single one because they all matter:

• -a <key> — this is the sequence name (aka the accession) of the fasta record you want pulled up. and if you don't pass it? bestie, then cdbyank expects a whole list of accessions coming in at stdin. 💅
• -d <fasta_file> — tells it which fasta file to pull records from. if you leave this out, cdbyank will go snooping in the same directory where <index_file> lives, looking for a file with the same name but without the .cidx suffix. it finds it itself, she's independent like that. 👑
• -o — the records that got found are written to the file <outfile> instead of stdout. bye bye terminal spam. 🫶
• -x — this one allows retrieval of multiple records per key, but only if the indexed database actually had records sharing the same key (we call those non-unique keys). and just so we're clear: without -x, only one record for a given key gets retrieved. periodt. ⭐
• -i — case insensitive query. heads up though: it expects the <index_file> to have been created with the cdbfasta -i option. don't come for her if you didn't do that part. 🙈
• -Q — outputs the query key surrounded by the character '%', right before the corresponding record. cute lil label moment. 🎀
• -q — literally the same as -Q but you get to use the character <char> instead of '%'. customizable slay. 💖
• -w — enable warnings when a key is not found. those warnings get sent to stderr. lowkey helpful, highkey honest. 😭
• -F — pulls only the defline for each record, discarding the sequence entirely.
• -P — only displays the position(s) (that's the file offset) within the database file, for the requested record(s). no sequence, just coordinates. 🌈
• -R — sequence range extraction! it expects your input <key(s)> to have the format '<seq_name> <start> <end>' and it pulls only that specified sequence range. slice it, diva. ✨
• -z — decompresses the entire file <dbfasta.cdbz>. this one assumes it was built using cdbfasta with the '-z' option, so don't just assume, okay? 🔥
• -v — show version number and exit. quick lil hey-hello. 👋

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🧚 index file statistics (no database file needed!!) 🧚

bestie the way these don't even need a database file?? iconic:

• -n — display the number of records indexed.
• -l — list all keys stored in <index_file>.
• -s — display indexing summary info. 🌸

real talk: -a <key>, -n, -l and -s live in the same slot in the synopsis, so it's one of those vibes — pick your path. 💅

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and that's the whole page, you ate it. 💜 this was cdbyank version 1.00, dated December 2025 — from the User Commands fam, written up for you with love. go query something iconic. 🦋✨