from alphastats.loader.MaxQuantLoader import MaxQuantLoader
from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
from alphastats.loader.FragPipeLoader import FragPipeLoader
from alphastats.loader.DIANNLoader import DIANNLoader
from alphastats.loader.SpectronautLoader import SpectronautLoader
from alphastats.loader.GenericLoader import GenericLoader
from alphastats.loader.mzTabLoader import mzTabLoader

software_options = {
    "MaxQuant": {
        "import_file": "Please upload proteinGroups.txt",
        "intensity_column": ["LFQ intensity [sample]", "Intensity [sample]"],
        "index_column": ["Protein IDs", "Gene names", "Majority protein IDs", "Protein names"],
        "loader_function": MaxQuantLoader,
    },
    "AlphaPept": {
        "import_file": "Please upload results_proteins.csv or results.hdf",
        "intensity_column": ["[sample]_LFQ"],
        "index_column": ["Unnamed: 0"],
        "loader_function": AlphaPeptLoader,
    },
    "DIANN": {
        "import_file": "Please upload report.pg_matrix.tsv",
        "intensity_column": ["[sample]"],
        "index_column": ["Protein.Group"],
        "loader_function": DIANNLoader,
    },
    "FragPipe": {
        "import_file": "Please upload combined_protein.tsv file from FragPipe.",
        "intensity_column": ["[sample] MaxLFQ Intensity", "[sample] Intensity"],
        "index_column": ["Protein", "Protein ID"],
        "loader_function": FragPipeLoader,
    },
    "Spectronaut": {
        "import_file": "Please upload spectronaut.tsv",
        "intensity_column": ["PG.Quantity", "F.PeakArea", "PG.Log2Quantity"],
        "index_column": ["PG.ProteinGroups", "PEP.StrippedSequence"],
        "loader_function": SpectronautLoader,
    },
     "Other": {
        "import_file": "Please upload your proteomics file.",
        "intensity_column": [],
        "index_column": [],
        "loader_function": GenericLoader,
    },
     "mzTab": {
        "import_file": "Please upload your .mzTab file with quantitative proteomics data.",
        "intensity_column": ["protein_abundance_[sample]"],
        "index_column": ["accession"],
        "loader_function": mzTabLoader,
    },
}

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software_options = {'MaxQuant': {'import_file':
    'Please upload proteinGroups.txt', 'intensity_column': [
    'LFQ intensity [sample]', 'Intensity [sample]'], 'index_column': [
    'Protein IDs', 'Gene names', 'Majority protein IDs', 'Protein names'],
    'loader_function': MaxQuantLoader}, 'AlphaPept': {'import_file':
    'Please upload results_proteins.csv or results.hdf', 'intensity_column':
    ['[sample]_LFQ'], 'index_column': ['Unnamed: 0'], 'loader_function':
    AlphaPeptLoader}, 'DIANN': {'import_file':
    'Please upload report.pg_matrix.tsv', 'intensity_column': ['[sample]'],
    'index_column': ['Protein.Group'], 'loader_function': DIANNLoader},
    'FragPipe': {'import_file':
    'Please upload combined_protein.tsv file from FragPipe.',
    'intensity_column': ['[sample] MaxLFQ Intensity', '[sample] Intensity'],
    'index_column': ['Protein', 'Protein ID'], 'loader_function':
    FragPipeLoader}, 'Spectronaut': {'import_file':
    'Please upload spectronaut.tsv', 'intensity_column': ['PG.Quantity',
    'F.PeakArea', 'PG.Log2Quantity'], 'index_column': ['PG.ProteinGroups',
    'PEP.StrippedSequence'], 'loader_function': SpectronautLoader}, 'Other':
    {'import_file': 'Please upload your proteomics file.',
    'intensity_column': [], 'index_column': [], 'loader_function':
    GenericLoader}, 'mzTab': {'import_file':
    'Please upload your .mzTab file with quantitative proteomics data.',
    'intensity_column': ['protein_abundance_[sample]'], 'index_column': [
    'accession'], 'loader_function': mzTabLoader}}

from alphastats.loader.MaxQuantLoader import MaxQuantLoader
from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
from alphastats.loader.FragPipeLoader import FragPipeLoader
from alphastats.loader.DIANNLoader import DIANNLoader
from alphastats.loader.SpectronautLoader import SpectronautLoader
from alphastats.loader.GenericLoader import GenericLoader
from alphastats.loader.mzTabLoader import mzTabLoader
software_options = {'MaxQuant': {'import_file':
    'Please upload proteinGroups.txt', 'intensity_column': [
    'LFQ intensity [sample]', 'Intensity [sample]'], 'index_column': [
    'Protein IDs', 'Gene names', 'Majority protein IDs', 'Protein names'],
    'loader_function': MaxQuantLoader}, 'AlphaPept': {'import_file':
    'Please upload results_proteins.csv or results.hdf', 'intensity_column':
    ['[sample]_LFQ'], 'index_column': ['Unnamed: 0'], 'loader_function':
    AlphaPeptLoader}, 'DIANN': {'import_file':
    'Please upload report.pg_matrix.tsv', 'intensity_column': ['[sample]'],
    'index_column': ['Protein.Group'], 'loader_function': DIANNLoader},
    'FragPipe': {'import_file':
    'Please upload combined_protein.tsv file from FragPipe.',
    'intensity_column': ['[sample] MaxLFQ Intensity', '[sample] Intensity'],
    'index_column': ['Protein', 'Protein ID'], 'loader_function':
    FragPipeLoader}, 'Spectronaut': {'import_file':
    'Please upload spectronaut.tsv', 'intensity_column': ['PG.Quantity',
    'F.PeakArea', 'PG.Log2Quantity'], 'index_column': ['PG.ProteinGroups',
    'PEP.StrippedSequence'], 'loader_function': SpectronautLoader}, 'Other':
    {'import_file': 'Please upload your proteomics file.',
    'intensity_column': [], 'index_column': [], 'loader_function':
    GenericLoader}, 'mzTab': {'import_file':
    'Please upload your .mzTab file with quantitative proteomics data.',
    'intensity_column': ['protein_abundance_[sample]'], 'index_column': [
    'accession'], 'loader_function': mzTabLoader}}

from alphastats.loader.MaxQuantLoader import MaxQuantLoader
from alphastats.loader.AlphaPeptLoader import AlphaPeptLoader
from alphastats.loader.FragPipeLoader import FragPipeLoader
from alphastats.loader.DIANNLoader import DIANNLoader
from alphastats.loader.SpectronautLoader import SpectronautLoader
from alphastats.loader.GenericLoader import GenericLoader
from alphastats.loader.mzTabLoader import mzTabLoader

software_options = {
    "MaxQuant": {
        "import_file": "Please upload proteinGroups.txt",
        "intensity_column": ["LFQ intensity [sample]", "Intensity [sample]"],
        "index_column": ["Protein IDs", "Gene names", "Majority protein IDs", "Protein names"],
        "loader_function": MaxQuantLoader,
    },
    "AlphaPept": {
        "import_file": "Please upload results_proteins.csv or results.hdf",
        "intensity_column": ["[sample]_LFQ"],
        "index_column": ["Unnamed: 0"],
        "loader_function": AlphaPeptLoader,
    },
    "DIANN": {
        "import_file": "Please upload report.pg_matrix.tsv",
        "intensity_column": ["[sample]"],
        "index_column": ["Protein.Group"],
        "loader_function": DIANNLoader,
    },
    "FragPipe": {
        "import_file": "Please upload combined_protein.tsv file from FragPipe.",
        "intensity_column": ["[sample] MaxLFQ Intensity", "[sample] Intensity"],
        "index_column": ["Protein", "Protein ID"],
        "loader_function": FragPipeLoader,
    },
    "Spectronaut": {
        "import_file": "Please upload spectronaut.tsv",
        "intensity_column": ["PG.Quantity", "F.PeakArea", "PG.Log2Quantity"],
        "index_column": ["PG.ProteinGroups", "PEP.StrippedSequence"],
        "loader_function": SpectronautLoader,
    },
     "Other": {
        "import_file": "Please upload your proteomics file.",
        "intensity_column": [],
        "index_column": [],
        "loader_function": GenericLoader,
    },
     "mzTab": {
        "import_file": "Please upload your .mzTab file with quantitative proteomics data.",
        "intensity_column": ["protein_abundance_[sample]"],
        "index_column": ["accession"],
        "loader_function": mzTabLoader,
    },
}
