Proteomics Converter

A Python package to convert between somadata.Adat and input required by pandora.

Installation

Requires Python>=3.9.

Installation with pip:

pip install proteomics-converter --extra-index-url https://ussd.artifactory.illumina.com/api/pypi/pypi-bioinfo/simple 

Installation with poetry:

# Add ilmn pypi as source
poetry source add --priority=supplemental ilmn https://ussd.artifactory.illumina.com/api/pypi/pypi-bioinfo/simple
# Install package from ilmn pypi
poetry add proteomics-converter --source ilmn

Usage

Converting an adat object to pandora inputs

adat_to_pandora_input converts an adat object to PandoraInput:

• counts dataframe in long format, with three columns count_col, somamer_index_col, sample_index_col
• sample metadata dataframe
• somamer metadata dataframe
• adat header as dictionary

from proteomics_converter.adat_func import adat_to_pandora_input

pandora_input = adat_to_pandora_input(
   adat=adat,
   count_col='Count_Raw',
   somamer_index_col='SeqId',
   sample_index_col='SampleID',
)

Converting pandora inputs to an adat object

pandora_input_to_adat is the reverse of adat_to_pandora_input that converts pandora input to an adat object.

from proteomics_converter.adat_func import pandora_input_to_adat, PandoraInput

adat = pandora_input_to_adat(
    pandora_input=PandoraInput(counts=counts, sample_metadata=sample_metadata, somamer_metadata=somamer_metadata, header_metadata=header_metadata),
    sample_index_col='SampleID',
    somamer_index_col='SeqId',
    count_col='Count',
)