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cdbyank - Online in the Cloud

Run cdbyank in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command cdbyank that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


cdbyank - Query an index file created with cdbfasta.

DESCRIPTION


Usage:
cdbyank <index_file> [-d <fasta_file>] [-a <key>|-n|-l|-s]

[-o <outfile>] [-q <char>|-Q][-F] [-R] [-P] [-x] [-w] [-z <dbfasta.cdbz>

<index_file> is the index file created previously with cdbfasta

(usually having a ".cidx" suffix)

-a <key> the sequence name (accession) for a fasta record to be

retrieved; if not given, a list of accessions is expected at stdin

-d <fasta_file> is the fasta file to pull records from;

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

-o the records found are written to file <outfile> instead of stdout

-x allows retrieval of multiple records per key, if the indexed

database had records with the same key (non-unique keys); (without -x only one
record for a given key is retrieved)

-i case insensitive query (expects the <index_file> to have been

created with cdbfasta -i option)

-Q output the query key surrounded by character '%' before the

corresponding record

-q same as -Q but use character <char> instead of '%'

-w enable warnings (sent to stderr) when a key is not found

-F pulls only the defline for each record (discard the sequence)

-P only displays the position(s) (file offset) within the

database file, for the requested record(s)

-R sequence range extraction: expects the input <key(s)> to have

the format: '<seq_name> <start> <end>' and pulls only the specified sequence range

-z decompress the entire file <dbfasta.cdbz>

(assumes it was built using cdbfasta with '-z' option)

-v show version number and exit

Index file statistics (no database file needed): -n display the number of records
indexed -l list all keys stored in <index_file> -s display indexing summary info

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