Parser to extract meta information from mzML mass spectrometry files and parse relevant information to a ISA-Tab structure
Overview
mzml2isa is a Python3 program that can automatically generate ISA-Tab document structure metadata files from raw XML metabolomics data files (mzML open access data format). The mzml2ISA tool provides the backbone of ISA-Tab metabolomics study which can then be edited with an ISA editing tool, ISAcreator (see MetaboLights pre-packaged ISA Creator)
- Currently the program does the following:
Extract meta information from mzML files and stores it as either python dictionary or JSON format
Creates an ISA-Tab file structure with relevant meta information filled in.
Add additional metadata that cannot be parsed from mzML files to the ISA-Tab files through a JSON formatted dictionnary.
Install
See the Installation page of the online documentation.
Usage
CLI
mzml2isa -i /path/to/mzml_files/ -o /path/to/out_folder/ -s name_of_studyPython Module
See the Usage page and the Examples page for more information.
Metabolights
To download some real data from MetaboLights studies to test the converter with, run
python scripts/metabolights-dl.py <size>from inside the repository, where size is the maximum size in GiB you can allocate to download files. The script will download the files to the example_files/metabolights folder and then run mzml2isa on those files..
If you use a *NIX machine with curlftpfs and bash available, you can also run
scripts/metabolights.shto mount the database to the example directory and start converting mzML studies.
Workflow
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file mzml2isa-0.4.24.zip.
File metadata
- Download URL: mzml2isa-0.4.24.zip
- Upload date:
- Size: 139.6 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
28407331e6c6b5534af3fe89184b36a65d44908c374b2f8f92d51a2e24414fc6
|
|
| MD5 |
b1e79fb9c53cddcfdfbabedf2330c8ad
|
|
| BLAKE2b-256 |
bdbd1b1e9842eceb80d71d33d65c0b540457f8bcd264f283e81dd7c2d4cb3a30
|
File details
Details for the file mzml2isa-0.4.24.tar.gz.
File metadata
- Download URL: mzml2isa-0.4.24.tar.gz
- Upload date:
- Size: 128.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
5733f9cf314e21bbe3cacdcb32c9a1088ab08b8b2986dbc5a3e5a02397dda5e4
|
|
| MD5 |
6675978ee2f74aaff3d44e032b59851e
|
|
| BLAKE2b-256 |
fb3b4d96b977f61fbb6426e53a9e975e1d73b82389f3f5153b93a2cadf0b1a11
|
File details
Details for the file mzml2isa-0.4.24.tar.bz2.
File metadata
- Download URL: mzml2isa-0.4.24.tar.bz2
- Upload date:
- Size: 101.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
eb5fbbceec2f2cc0daf94b4041277b1b73f1abf5b363144748bdd8aa14e98a1d
|
|
| MD5 |
01c71fae82689807f0126c2b7bcf986f
|
|
| BLAKE2b-256 |
dd03bea5554f2cba1a52f26fc497a775e3c078d5efff0f489e5d948a5b6c24b6
|
File details
Details for the file mzml2isa-0.4.24-py3-none-any.whl.
File metadata
- Download URL: mzml2isa-0.4.24-py3-none-any.whl
- Upload date:
- Size: 146.1 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
93ab77a0128270bf95e66cac7403e5e18797f37e3d65574d5258beed761d293c
|
|
| MD5 |
07bfffea043a01fc51d84561ff7ead83
|
|
| BLAKE2b-256 |
19eb40f43bea5dd8ca1ba6082ce1373450b8f76ac366027329260166c578c01a
|
