QCTableFormatter_V3.py

import re
# Separator for when multiple values are nested in one cell:
delim = "|"
# Separator for output of the table:
sep = ';'

def codonQCReformatter(inFile):
        formattedNames = ''
        formattedNotCodList = ''
        formattedProtCodList = ''
        nameList = []
        notCodList = []
        protCodList = []

        for line in inFile:
                name = re.search("\".*\"", line)
                coding = re.split("\".*\"", line.strip())
                notCod = int(coding[1].split(",")[1])
                protCod = int(coding[1].split(",")[2])
                totCod = notCod+protCod
                nameList.append(name.group(0)[1:-1])
                notCodList.append(round(notCod/totCod, 2))
                protCodList.append(round(protCod/totCod, 2))

        for i in nameList:
                formattedNames = formattedNames + str(i) + delim
        for j in notCodList:
                formattedNotCodList = formattedNotCodList + str(j) + delim
        for k in protCodList:
                formattedProtCodList = formattedProtCodList + str(k) + delim
        return formattedNames[:-1], formattedProtCodList[:-1], formattedNotCodList[:-1]

def NCountReformatter(Ns):
        percentage = []
        count = []
        NPercent = ''
        NCount = ''
        for line in Ns:
                percentage.append(line.split(',')[0])
                count.append(line.split(',')[1])
        for i in percentage:
                NPercent = NPercent + str(i) + delim
        for j in count:
                NCount = NCount + str(j).rstrip() + delim
        return NPercent[:-1], NCount[:-1]

def ComplexityReformatter(Cmplx):
        values = []
        for line in Cmplx:
                try:
#                       int(line.split(',')[1])
                        values.append(int(line.split(',')[1]))
                except:
                        pass
        prctCplx = round ((values[0]/(values[0]+values[1]))*100, 1)
        prctNtCplx = round ((values[1]/(values[0]+values[1]))*100, 1)
        return prctCplx, prctNtCplx

def letterQuality(inFile):
        for line in inFile:
                if line.split(',')[0] == 'A':
                        ct_a = line.split(',')[1]
                        qual_a = line.split(',')[2]
                elif line.split(',')[0] == 'C':
                        ct_c = line.split(',')[1]
                        qual_c = line.split(',')[2]
                if line.split(',')[0] == 'G':
                        ct_g = line.split(',')[1]
                        qual_g = line.split(',')[2]
                if line.split(',')[0] == 'T':
                        ct_t = line.split(',')[1]
                        qual_t = line.split(',')[2]
                else:
                        pass
        return ct_a, qual_a.rstrip(), ct_c, qual_c.rstrip(), ct_g, qual_g.rstrip(), ct_t, qual_t.rstrip()

def inputGrabber(inFile):
        HIVEIDs = ''
        for line in inFile:
                HIVEIDs = HIVEIDs + str(line.rstrip())
                return str(HIVEIDs)

with open ("TEMPIDFile.txt") as IDList, open ("TEMPcodonQCTable.csv") as CQC, open ("TEMPcountNsPercentageTable.csv") as NCT, open ("TEMPComplexityTable.csv") as Complexity, open ("TEMPLetterCountQuality.csv") as LCQ:
        IDs = inputGrabber(IDList)
        codonName, codonCoding, codonNotCoding = codonQCReformatter(CQC)
        NPercent, NCount = NCountReformatter(NCT)
        PercentComplex, PercentNotComplex = ComplexityReformatter(Complexity)
        count_a, avg_quality_a, count_c, avg_quality_c, count_g, avg_quality_g, count_t, avg_quality_t = letterQuality(LCQ)
        print (IDs + sep + codonName + sep + codonCoding + sep + codonNotCoding + sep + NCount + sep + NPercent + sep + str(PercentComplex) + sep + str(PercentNotComplex) + sep + avg_quality_a + sep + avg_quality_t + sep + avg_quality_g + sep + avg_quality_c + sep + count_a + sep + count_c + sep + count_g + sep + count_t)