umgap bestof
Selects the best read of every fixed size group.
The umgap bestof command takes groups of taxon IDs as input and outputs for each group the
taxon ID with the most non-root identifications.
Usage
The input is given in FASTA format on standard input. Per FASTA header, there should be multiple numbers (taxon IDs). Per 6 FASTA records (or whichever number you specify with -f), the best record is selected and written to standard output. If the input is a series of identified taxon IDs for each of the 6 translations of a read, the output will most likely come from the actual coding frame.
$ cat dna.fa >header1 CGCAGAGACGGGTAGAACCTCAGTAATCCGAAAAGCCGGGATCGACCGCCCCTTGCTTGCAGCCGGGCACTACAGGACCC $ umgap translate -n -a < dna.fa | umgap prot2kmer2lca 9mer.index | tee input.fa >header1|1 9606 9606 2759 9606 9606 9606 9606 9606 9606 9606 8287 >header1|2 2026807 888268 186802 1598 1883 >header1|3 1883 >header1|1R 27342 2759 155619 1133106 38033 2 >header1|2R >header1|3R 2951 $ umgap bestof < input.fa >header1|1 9606 9606 2759 9606 9606 9606 9606 9606 9606 9606 8287
Taxon IDs are separated by newlines in the actual output, but are separated by spaces in this example.
- -h / --help
- Prints help information
- -V / --version
- Prints version information
- -f / --frames f
- The number of frames of which to pick the best [default: 6]