Command line interface

mzspeclib

A collection of utilities for inspecting and manipulating spectral libraries.

mzspeclib [OPTIONS] COMMAND [ARGS]...

Options

-d, --debug-logging

Enable debug logging

-l, --log-file <log_file>

Write log messages to this file as well as STDERR

convert

Convert a spectral library from one format to another. If outpath is -, instead of writing to file, data will instead be sent to STDOUT.

mzspeclib convert [OPTIONS] INPATH OUTPATH

Options

-i, --input-format <input_format>

The file format of the input file. If omitted, will attempt to infer automatically.

Options:

bibliospec | blib | dia-nn.tsv | dlib | encyclopedia | json | msp | mzSpecLib.json | mzSpecLib.txt | mzlb.json | mzlb.txt | mzlib.json | mzlib.txt | mzspeclib.json | mzspeclib.txt | spectronaut.tsv | sptxt | text

-f, --format <format>

Options:

text | json | msp

-k, --library-attribute <library_attributes>

Specify an attribute to add to the library metadata section. May be repeated.

-K, --header-file <header_file>

Specify a file to read name-value pairs from. May be JSON or TAB-separated

Arguments

INPATH

Required argument

OUTPATH

Required argument

describe

Produce a minimal textual description of a spectral library.

mzspeclib describe [OPTIONS] PATH

Options

-i, --input-format <input_format>

The file format of the input file. If omitted, will attempt to infer automatically.

Options:

bibliospec | blib | dia-nn.tsv | dlib | encyclopedia | json | msp | mzSpecLib.json | mzSpecLib.txt | mzlb.json | mzlb.txt | mzlib.json | mzlib.txt | mzspeclib.json | mzspeclib.txt | spectronaut.tsv | sptxt | text

Arguments

PATH

Required argument

index

Build an external on-disk SQL-based index for the spectral library

mzspeclib index [OPTIONS] INPATH

Options

-i, --input-format <input_format>

The file format of the input file. If omitted, will attempt to infer automatically.

Options:

bibliospec | blib | dia-nn.tsv | dlib | encyclopedia | json | msp | mzSpecLib.json | mzSpecLib.txt | mzlb.json | mzlb.txt | mzlib.json | mzlib.txt | mzspeclib.json | mzspeclib.txt | spectronaut.tsv | sptxt | text

Arguments

INPATH

Required argument

validate

Semantically and structurally validate a spectral library.

mzspeclib validate [OPTIONS] INPATH

Options

-p, --profile <profiles>

Options:

consensus | single | silver | peptide | gold

-i, --input-format <input_format>

The file format of the input file. If omitted, will attempt to infer automatically.

Options:

bibliospec | blib | dia-nn.tsv | dlib | encyclopedia | json | msp | mzSpecLib.json | mzSpecLib.txt | mzlb.json | mzlb.txt | mzlib.json | mzlib.txt | mzspeclib.json | mzspeclib.txt | spectronaut.tsv | sptxt | text

Arguments

INPATH

Required argument