hyfi-lookup

Description: Finds the locations of k-mers in a sequence file using a pre-computed index.

Usage: hyfi-lookup [options] <FASTA filename> <index filename>

Input:

• <FASTA filename>: a FASTA file containing k-mers to be located. If a '-' is given, then standard input is read. The header line for each k-mer is expected to be space-delimited, and contain the following information.
  

> kmer id <space> qid:query id <space> qs:query sequence

• <index filename>: a precomputed index on a sequence file, made with the program hyfi-index.

Output: A FASTA file with k-mer locations. The sequences are just the input kmers, and for each occurence of each k-mer in the sequence file, the k-mer is reported along with a header line specifying the location as follows:

>sequence id:start-stop:strand <space> query id <space> query sequence Output is written to standard output.

Options:

• --kmer: Interpret the first argument after the options as a k-mer, and report locations for the k-mer only. The output headers will have no content in the last two fields.
• -o <output filename>: write the program output to an output file, rather than the standard out.
• --dump-index: Print the index file in a text format.
• -v <number>: verbosity level. The verbosity is controlled by <number>; 0 means no extra output, and 5 means extreme verbosity. The default is 0.

Bugs: None reported yet.