main.py

import csv
import os
import re

def naturalSort(l): 
    convert = lambda text: int(text) if text.isdigit() else text.lower()
    alphanumericKey = lambda key: [convert(c) for c in re.split('([0-9]+)', key)]
    return sorted(l, key=alphanumericKey)


def getFilePaths(basePath):
    files = []

    with os.scandir(basePath) as entries:
        for entry in entries:
            if entry.is_file():
                files.append(entry.path)

    return files


def getSampleName(filePath: str):
    return filePath.split('/')[-1].split('_', 1)[0]


def getPeakAreasFromTsv(filePath):
    peakAreas = []

    with open(filePath, 'r') as tsvFile:
        tsvReader = csv.reader(tsvFile, delimiter='\t')

        areaRowIndex = -1
        i = 0

        for row in tsvReader:
            if len(row) > 0 and row[0] == '[area]':
                areaRowIndex = i

            if areaRowIndex != -1 and i >= areaRowIndex + 2:
                if len(row) == 0:
                    break

                peakAreas.append((row[0], row[-2]))

            i += 1
    
    return peakAreas


basePath = 'data/H3_04_15_27'
files = getFilePaths(basePath)

results = {}

for filePath in files:
    sampleName = getSampleName(filePath)
    results[sampleName] = getPeakAreasFromTsv(filePath)

keys = naturalSort(list(results.keys()))

with open(basePath + '/results.tsv', 'w') as outputFile:
    outputWriter = csv.writer(outputFile, delimiter='\t')
    outputWriter.writerow(['sample', 'peptide', 'peak_area'])
    for key in keys:
        for peak in results[key]:
            outputWriter.writerow([key, peak[0], peak[1]])