cdbyank − Query an index file created with cdbfasta.
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 |
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−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 ’%’ |
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−w enable warnings (sent to stderr) when a key is not found |
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−F pulls only the defline for each record (discard the sequence) |
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−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