.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CDBYANK "1" "January 2021" "cdbyank version 1.00" "User Commands"
.SH NAME
cdbyank \- Query an index file created with cdbfasta.
.SH DESCRIPTION
.SS "Usage:"
.IP
cdbyank <index_file> [\-d <fasta_file>] [\-a <key>|\-n|\-l|\-s]
.IP
[\-o <outfile>] [\-q <char>|\-Q][\-F] [\-R] [\-P] [\-x] [\-w]
[\-z <dbfasta.cdbz>
.IP
<index_file> is the index file created previously with cdbfasta
.IP
(usually having a ".cidx" suffix)
.HP
\fB\-a\fR <key> the sequence name (accession) for a fasta record to be
.IP
retrieved; if not given, a list of accessions is expected
at stdin
.HP
\fB\-d\fR <fasta_file> is the fasta file to pull records from;
.IP
if not specified, cdbyank will look in the same directory
where <index_file> resides, for a file with the same name
but without the ".cidx" suffix
.HP
\fB\-o\fR the records found are written to file <outfile> instead of stdout
.HP
\fB\-x\fR allows retrieval of multiple records per key, if the indexed
.IP
database had records with the same key (non\-unique keys);
(without \fB\-x\fR only one record for a given key is retrieved)
.HP
\fB\-i\fR case insensitive query (expects the <index_file> to have been
.IP
created with cdbfasta \fB\-i\fR option)
.HP
\fB\-Q\fR output the query key surrounded by character '%' before the
.IP
corresponding record
.HP
\fB\-q\fR same as \fB\-Q\fR but use character <char> instead of '%'
.HP
\fB\-w\fR enable warnings (sent to stderr) when a key is not found
.HP
\fB\-F\fR pulls only the defline for each record (discard the sequence)
.HP
\fB\-P\fR only displays the position(s) (file offset) within the
.IP
database file, for the requested record(s)
.HP
\fB\-R\fR sequence range extraction: expects the input <key(s)> to have
.IP
the format: '<seq_name> <start> <end>'
and pulls only the specified sequence range
.HP
\fB\-z\fR decompress the entire file <dbfasta.cdbz>
.IP
(assumes it was built using cdbfasta with '\-z' option)
.HP
\fB\-v\fR show version number and exit
.IP
Index file statistics (no database file needed):
\fB\-n\fR display the number of records indexed
\fB\-l\fR list all keys stored in <index_file>
\fB\-s\fR display indexing summary info
.IP