CDBFASTA(1)

💖 NAME 💖

cdbfasta — bestie she creates an index file for records from a multi-fasta file. that's the whole job, and she does it flawlessly. ✨

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🦋 DESCRIPTION 🦋

okay so listen. you've got a big ol' multi-fasta file and you want to jump straight to a record instead of scrolling through it like it's a group chat from 2021. cdbfasta makes you an index, and honestly? she ate. 🔥

📋 Usage 📋

cdbfasta <fastafile> [-o <index_file>] [-r <record_delimiter>]
       [-z <compressed_db>] [-i] [-m|-n <numkeys>|-f<LIST>]|-c|-C]
       [-w <stopwords_list>] [-s <stripendchars>] [{-Q|-G}]
       [-v]

Creates an index file for records from a multi-fasta file. By default — like, when you don't pass -m/-n/-c/-C — only the first space-delimited token from the defline is used as a key. one token, one key, no notes. 💅

<fastafile> is the multi-fasta file to index. With -o the index file will be named <index_file>. If you don't give it one, the index filename is the database name plus the suffix .cidx. she names her own files, main character energy.

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🌈 OPTIONS 🌈

• -o <index_file> — names the index file <index_file>. If you don't pass it, the index filename is the database name plus the suffix .cidx.
• -r <record_delimiter> — a string of characters at the beginning of a line marking the start of a record. Default is '>'. 👑
• -Q — treat the input as fastq format, aka with '@' as the record delimiter and with records expected to have at least 4 lines. lowkey a whole different genre of file.
• -z <compressed_db> — the database gets compressed into the file <compressed_db> before indexing. and bestie, <fastafile> can be "-" or "stdin" here, so you can pipe the input records in from stdin. 🫶
• -s <stripendchars> — strips extraneous characters from around the space-delimited tokens, for the multikey options below (-m, -n, -f). Default <stripendchars> set is: '",`.(){}/[]!:;~|><+- — yes there's a backtick in there, she contains multitudes. 🙈
• -m — the "multi-key" option: creates hash entries pointing to the same record for all tokens found in the defline. one record, many doors. 🚪✨
• -n <numkeys> — same as -m, but only takes the first <numkeys> tokens from the defline. And when you use it with the -a option (peep below), it only collects the first <numkeys> accessions from each defline.
• -f LIST — indexes space-delimited tokens (fields) in the defline as given by LIST of fields or field ranges — same syntax as UNIX cut, iykyk. ✂️
• -w <stopwordslist> — excludes from indexing all the words found in the file <stopwordslist> (for options -m, -n and -k). 🚫
• -i — do case insensitive indexing, i.e. create additional keys for all-lowercase tokens used for indexing from the defline. shout it, whisper it, same key. 📢
• -c — for deflines in the format: db1|accession1|db2|accession2|..., only the first db-accession pair ('db1|accession1') is taken as the key.
• -C — like -c, but the subsequent db|accession constructs are also indexed, along with the full (default) token. additionally, all nrdb concatenated accessions found in the defline are parsed and stored — assuming 0x01 or '^|^' as separators. she's thorough!! 💅
• -a — accession mode: like -C but indexes only the 'accession' part for all 'db|accession' constructs found, plus the default first tokens.
• -A — like -a and -C together (both accessions and 'db|accession' constructs are used as keys). why choose when you can have both 💖
• -D — index each pipe ('|') delimited token found in the record identifier, e.g. >key1|key2|key3|..
• -d — same as -D but using a custom key delimiter <kdelim> instead of the pipe character '|'. your delimiter, your rules. 🎀
• -G — FASTA records are treated as large genomic sequences (e.g. full chromosomes/contigs) and their formatting is checked for suitability for fast range queries — that means uniform line length within each record. no raggedy lines allowed bestie, the range queries need consistency. 📏
• -v — show program version and exit. bye!! 👋

⚠️ heads up: -s only strips characters from around the space-delimited tokens, and only matters for the multikey options (-m, -n, -f) — don't expect it to do anything for the plain default key. also -G still checks your formatting; if your records aren't uniform, that's on your file, not on her. 💀

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and that's the whole page, bestie — go index something gorgeous. 🧚💜

signing off from cdbfasta version 1.00, dated December 2025, page CDBFASTA(1) — User Commands, mwah 💋🎀