.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH CDBFASTA "1" "October 2018" "cdbfasta version 0.99" "User Commands"
.SH NAME
cdbfasta \- Creates an index file for records from a multi-fasta file.
.SH DESCRIPTION
.SS "Usage:"
.IP
cdbfasta <fastafile> [\-o <index_file>] [\-r <record_delimiter>]
.IP
[\-z <compressed_db>] [\-i] [\-m|\-n <numkeys>|\-f<LIST>]|\-c|\-C]
.IP
[\-w <stopwords_list>] [\-s <stripendchars>] [\-v]
.IP
Creates an index file for records from a multi\-fasta file.
By default (without \fB\-m\fR/\-n/\-c/\-C option), only the first
space\-delimited token from the defline is used as a key.
.IP
<fastafile> is the multi\-fasta file to index;
\fB\-o\fR the index file will be named <index_file>; if not given,
.IP
the index filename is database name plus the suffix '.cidx'
.HP
\fB\-r\fR <record_delimiter> a string of characters at the beginning of line
.IP
marking the start of a record (default: '>')
.HP
\fB\-Q\fR treat input as fastq format, i.e. with '@' as record delimiter
.IP
and with records expected to have at least 4 lines
.HP
\fB\-z\fR database is compressed into the file <compressed_db>
.IP
before indexing (<fastafile> can be "\-" or "stdin"
in order to get the input records from stdin)
.HP
\fB\-s\fR strip extraneous characters from *around* the space delimited
.IP
tokens, for the multikey options below (\fB\-m\fR,\-n,\-f);
Default <stripendchars> set is: '",`.(){}/[]!:;~|><+\-
.HP
\fB\-m\fR ("multi\-key" option) create hash entries pointing to
.IP
the same record for all tokens found in
the defline
.HP
\fB\-n\fR <numkeys> same as \fB\-m\fR, but only takes the first <numkeys>
.IP
tokens from the defline
.HP
\fB\-f\fR indexes *space* delimited tokens (fields) in the defline as given
.IP
by LIST of fields or fields ranges (the same syntax as UNIX 'cut')
.HP
\fB\-w\fR <stopwordslist> exclude from indexing all the words found
.IP
in the file <stopwordslist> (for options \fB\-m\fR, \fB\-n\fR and \fB\-k\fR)
.HP
\fB\-i\fR do case insensitive indexing (i.e. create additional keys for
.IP
all\-lowercase tokens used for indexing from the defline
.HP
\fB\-c\fR for deflines in the format: db1|accession1|db2|accession2|...,
.IP
only the first db\-accession pair ('db1|accession1') is taken as key
.HP
\fB\-C\fR like \fB\-c\fR, but also subsequent db|accession constructs are indexed,
.IP
along with the full (default) token; additionally,
all nrdb concatenated accessions found in the defline
are parsed and stored (assuming 0x01 or '^|^' as separators)
.HP
\fB\-a\fR accession mode: like \fB\-C\fR option, but indexes the 'accession'
.IP
part for all 'db|accession' constructs found
.HP
\fB\-A\fR like \fB\-a\fR and \fB\-C\fR together (both accessions and 'db|accession'
.IP
constructs are used as keys
.HP
\fB\-v\fR show program version and exit
.IP