Input Formats

Input formats

Auto-detect reads the first header line, in this order (loqculate/io/readers.py):

1. EncyclopeDIA: numFragments present.
2. Skyline: Total Area Fragment, Peptide Sequence, and File Name all present.
3. DIA-NN report: Stripped.Sequence and Precursor.Quantity both present.
4. DIA-NN precursor matrix: Stripped.Sequence present without that report pair. Stderr warns to prefer diann_report.tsv.
5. Spectronaut: PEP.StrippedSequence present.
6. Generic: fallback. Requires columns peptide, concentration, area after lower-casing names.

--format / fmt=: auto, encyclopedia, skyline, diann_report, diann_matrix, spectronaut, generic.

Concentration map

CLI always takes the path. Columns filename, concentration. Use basenames.

Join behavior differs:

• Skyline: keep rows whose File Name is in the map, outer-merge, drop missing concentration.
• DIA-NN report: inner-merge on File.Name.
• EncyclopeDIA, DIA-NN matrix, Spectronaut: wide tables. Filename columns are renamed to concentrations; rows whose concentration is not in the map are dropped.
• Generic: no join. Concentration comes from the data file. The map path is still opened (validate_concentration_map); a missing file is a warning, not a raise.

Blank concentration cells in the map warn on stderr.

Multiplier

--multiplier_file: peptide, multiplier. Applied after the reader. Inner join.

Demo

• data/demo/one_protein.csv
• data/demo/filename2samplegroup_map.csv
• data/demo/multiplier_file.csv