parseet 0.2.0

This package is used to parse ms samplesheet for further analyses.

BULK METABOLOMICS SAMPLESHEET

This folder contains the files necessary for the samplesheet of LC-MS and spatial metabolomics. Samplesheet template (LC-MS_metabolomics_samplesheet.xlsx or spatial_metabolomics_samplesheet.xlsx) should be given to clients to be compiled. Once received back, it should be tested with the parser (LC-MS_parse_samplesheet.py or spatial_parse_samplesheet.py).

Samplesheet template

Samplesheet templates contains 3 sheets:

• input: the one the user should fill. It contains two sections, one with user info and the other with samples metadata.
• example_ok: an example of a good samplesheet
• example_fail: an example of a problematic samplesheet

Parser

The parser will check the samplesheet for its correct compilation and raises warnings and/or errors if any. If no errors are found, the samples metadata section is saved as a csv file (specified as -o). Warnings also prevent file to be saved, but this can be overruled by --ignore-warnings.

Test

In test folder, 3 test samplesheet for each technology are found:

• test_error.xlsx: a test samplesheet with errrors
• test_ok.xlsx: a test samplesheet correctly compiled
• test_warning.xlsx: a test samplesheet with warnings

Several test should be run after changind any file:

• python LC-MS_parse_samplesheet.py (this should result in an error for missing input and output)
• python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok.xlsx -o test.csv --dry-run (this should be ok, with no errors nor warnings, but no file should be saved due to --dry-run)
• python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok.xlsx -o test.csv (this should be ok, with also test.csv file saved)
• python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_error.xlsx -o test.csv (this should raise errors and no test.csv file should be created)
• python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_warning.xlsx -o test.csv (this should raise warnings and no test.csv file should be created)
• python LC-MS_parse_samplesheet.py (this should result in an error for missing input and output)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_ok.xlsx -o test.csv --dry-run (this should be ok, with no errors nor warnings, but no file should be saved due to --dry-run)
• python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok_timecourse.xlsx -o test.csv (this should be ok, with also test.csv file saved)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_ok.xlsx -o test.csv (this should be ok, with also test.csv file saved)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_error.xlsx -o test.csv (this should raise errors and no test.csv file should be created)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv (this should raise warnings and no test.csv file should be created)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv --ignore-warnings (this should raise warnings, but test.csv file should be created)
• python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv --ignore-warnings (this should raise warnings, but test.csv file should be created)