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

CDBFASTA(1) User Commands CDBFASTA(1)

NAME

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

DESCRIPTION

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>] [-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.
<fastafile> is the multi-fasta file to index; -o the index file will be named <index_file>; if not given,
the index filename is database name plus the suffix '.cidx'
-r <record_delimiter> a string of characters at the beginning of line
marking the start of a record (default: '>')
-Q treat input as fastq format, i.e. with '@' as record delimiter
and with records expected to have at least 4 lines
-z database is compressed into the file <compressed_db>
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
tokens, for the multikey options below (-m,-n,-f); Default <stripendchars> set is: '",`.(){}/[]!:;~|><+-
-m ("multi-key" option) create hash entries pointing to
the same record for all tokens found in the defline
-n <numkeys> same as -m, but only takes the first <numkeys>
tokens from the defline
-f indexes *space* delimited tokens (fields) in the defline as given
by LIST of fields or fields ranges (the same syntax as UNIX 'cut')
-w <stopwordslist> exclude 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
-c for deflines in the format: db1|accession1|db2|accession2|...,
only the first db-accession pair ('db1|accession1') is taken as key
-C like -c, but also subsequent db|accession constructs are 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)
-a accession mode: like -C option, but indexes the 'accession'
part for all 'db|accession' constructs found
-A like -a and -C together (both accessions and 'db|accession'
constructs are used as keys
-v show program version and exit
 
January 2017 cdbfasta version 0.99