---
name: "cdbfasta"
section: "1"
platform: "linux"
package: "cdbfasta"
version: "1.00+git20230710.da8f5ba+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cdbfasta"
---

# cdbfasta(1)

Creates an index file for records from a multi-fasta file.

## NAME

cdbfasta - Creates an index file for records from a multi-fasta file.

## DESCRIPTION

### Usage:

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  cdbfasta \<fastafile\> \[-o \<index\_file\>\] \[-r \<record\_delimiter\>\]

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  \[-z \<compressed\_db\>\] \[-i\] \[-m\|-n \<numkeys\>\|-f\<LIST\>\]\|-c\|-C\]

- \[-w \<stopwords\_list\>\] \[-s \<stripendchars\>\] \[{-Q\|-G}\]

  \[-v\]

-

  Creates an index file for records from a multi-fasta file. By default (without **-m**/-n/-c/-C option), only the first space-delimited token from the defline is used as a key.

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  \<fastafile\> is the multi-fasta file to index; **-o** the index file will be named \<index\_file\>; if not given,

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  the index filename is database name plus the suffix '.cidx'

**-r** \<record\_delimiter\> a string of characters at the beginning of line

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  marking the start of a record (default: '\>')

**-Q** treat input as fastq format, i.e. with '@' as record delimiter

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  and with records expected to have at least 4 lines

**-z** database is compressed into the file \<compressed\_db\>

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  before indexing (\<fastafile\> can be "-" or "stdin" in order to get the input records from stdin)

**-s** strip extraneous characters from \*around\* the space delimited

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  tokens, for the multikey options below (**-m**,-n,-f); Default \<stripendchars\> set is: '",\`.(){}/\[\]!:;~\|\>\<+-

**-m** ("multi-key" option) create hash entries pointing to

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  the same record for all tokens found in the defline

**-n** \<numkeys\> same as **-m**, but only takes the first \<numkeys\>

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  tokens from the defline; when used with **-a** option (see below), only collects the first \<numkeys\> accessions from each defline

**-f** indexes \*space\* delimited tokens (fields) in the defline as given

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  by LIST of fields or fields ranges (the same syntax as UNIX 'cut')

**-w** \<stopwordslist\> exclude from indexing all the words found

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  in the file \<stopwordslist\> (for options **-m**, **-n** and **-k**)

**-i** do case insensitive indexing (i.e. create additional keys for

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  all-lowercase tokens used for indexing from the defline

**-c** for deflines in the format: db1\|accession1\|db2\|accession2\|...,

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  only the first db-accession pair ('db1\|accession1') is taken as key

**-C** like **-c**, but also subsequent db\|accession constructs are indexed,

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  along with the full (default) token; additionally, all nrdb concatenated accessions found in the defline are parsed and stored (assuming 0x01 or '^\|^' as separators)

**-a** accession mode: like **-C** but indexes only the 'accession' part for all

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  'db\|accession' constructs found, plus the default first tokens

**-A** like **-a** and **-C** together (both accessions and 'db\|accession'

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  constructs are used as keys

**-D** index each pipe ('\|') delimited token found in the record identifier

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  (e.g. \>key1\|key2\|key3\|.. )

**-d** same as **-D** but using a custom key delimiter \<kdelim\> instead of the pipe

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  character '\|'

**-G** FASTA records are treated as large genomic sequences (e.g. full

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  chromosomes/contigs) and their formatting is checked for suitability for fast range queries (i.e. uniform line length within each record)

**-v** show program version and exit

-