hyfi-fetch

Description: Retrieve sequences from a sequence file by position.

Usage: hyfi-fetch [options] <FASTA file> <sequence file>

Input:

• <FASTA file>: A FASTA file containing k-mer sequences and their locations in the sequence headers. If a '-' is given instead of a filename, then standard input is read instead. Each header is assumed to have the following information in space delimited format after the sequence id:

> seq id:start-stop:strand <space> qid:query id <space> qs:query sequence

• <sequence file>: a FASTA format sequence file with one sequence entry.

Output: A FASTA file with every window containing each input kmer. In addition to the sequence embedding the k-mers, the sequence headers are identical to the input headers, except that the location of the sequence is modified to reflect the new starting position. All output is written to standard output.

Options:

• -w <window size>: for each position, return a subsequence including <window size> bases; defaults to 30.
• -c: include only the window centered on the k-mer, rather than all windows including the k-mer
• -o <output filename>: write the program output to an output file, rather than the standard out.
• -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: The FASTA sequence file can only have one sequence entry.