[−][src]Module umgap::args

Argument parsing for the UMGAP

Structs

BestOf	Pick the frame with the most none-root hits.
Error	The Error type.
FastqToFasta	Interleaves a number of FASTQ files into a single FASTA output.
Filter	Filter peptides in a FASTA format based on specific criteria.
JsonTree	Aggregates taxa to a JSON tree for usage in the unipept visualisations.
PeptToLca	Looks up each line of input in a given FST index and outputs the result. Lines starting with a '>' are copied. Lines for which no mapping is found are ignored.
PrintIndex	Print the values in an FST index to stdout.
ProtToKmer	Splits each protein sequence in a FASTA format into a list of kmers.
ProtToKmerToLca	Reads all the records in a specified FASTA file and queries the k-mers in an FST for the LCA's.
ProtToPept	Splits each protein sequence in a FASTA format into a list of (tryptic) peptides.
ProtToTrypToLca	Reads all the records in a specified FASTA file and queries the tryptic peptides in an FST for the LCA's.
Report	Count and report on a list of taxon ids.
SeedExtend	Seed and extend.
SnapTaxon	Snap taxa to a specified rank or one of the specified taxa.
TaxaToAgg	Aggregates taxa to a single taxon.
Taxonomy	Show the id, name, and rank of the given taxon ids in a CSV format
Translate	Translates DNA into Amino Acid Sequences.
Uniq	Concatenates the data strings of all consecutive FASTA entries with the same header.

ErrorKind	The kind of an error.
Frame	A reading frame
Method	An aggregation method
Opt	The Options enum for UMGAP arguments
Strategy	An aggregation strategy

Additional methods for Result, for easy interaction with this crate.

Convenient wrapper around std::Result.