umgap prot2tryp2lca
Digests a FASTA stream of peptides and maps all tryptic peptides to taxon IDs.

The input is given in a FASTA format on standard input with a single peptide per FASTA header, which may be hardwrapped with newlines. The command prints the lowest common ancestors for each tryptic peptide found in each given peptide to standard output.

$ cat input.fa
>header1
AYKKAGVSGHVWQSDGITNCLLRGLTRVKEAVANRDSGNGYINKVYYWTVDKRATTRDALDAGVDGIMTNYPDVITDVLN
$ umgap prot2tryp2lca tryptic-lca.index < input.fa
>header1
571525
1
571525
6920

-m / --in-memory

Load index in memory instead of memory mapping the file contents. This makes querying significantly faster, but requires some initialization time.

-h / --help

Prints help information

-o / --one-on-one

Map unknown sequences to 0 instead of ignoring them

-V / --version

Prints version information

-c / --chunksize c

Number of reads grouped into one chunk. Bigger chunks decrease the overhead caused by multithreading. Because the output order is not necessarily the same as the input order, having a chunk size which is a multiple of 12 (all 6 translations multiplied by the two paired-end reads) will keep FASTA records that originate from the same reads together [default: 240]

-k / --keep k

Amino acid symbols that a peptide must contain to be processed [none by default]

-d / --drop d

Amino acid symbols that a peptide may not contain to be processed [none by default]

-L / --maxlen L

Maximum length allowed [default: 50]

-l / --minlen l

Minimum length required [default: 5]

-p / --pattern p

The cleavage-pattern (regex), i.e. the pattern after which the next peptide will be cleaved for tryptic peptides) [default: ([KR])([^P])]