Provided by: cdbfasta_0.99-20100722-1_amd64 bug


       cdbyank - Query an index file created with cdbfasta.


              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