RVC Quality Control Methods

RVC QAQC

class newOne:
    def__init__(self, new_one)

class dataEntryFile:
    def __init__(self, entryFile):
        self.entryFile = entryFile

    def readFileToList(self):
        return [line.strip().split('~') for line in open(self.entryFile).readlines()]


class QualityControl:
    def __init__(self, sampleList, speciesList, substrateList, ):
        self.sampleList = sampleList
        self.speciesList = speciesList
        self.substrateList = substrateList
        self.msnSamples =[msn[0] for msn in sampleList]
        self.msnSpecies = [msn[0] for msn in speciesList]
        self.msnSubstrate = [msn[0] for msn in substrateList]
    def chkSamSubCnt(self):
        missingSubstrateFiles = 0
        missingSampleFiles = 0
        if len(self.sampleList) == len(self.substrateList):
            print " # of samples equals # of substrates"
        else:
            print "samples and substrates mismatch"
            print str(missingSubstrateFiles) + "missing from substrate files"
            print str(missingSampleFiles) + "missing from sample files"
            for msn in self.msnSamples:
                if msn in self.msnSubstrate:
                    pass
                else:
                    missingSubstrateFiles += 1
                    print msn + " not found in Substrate list"
            for msn in self.msnSubstrate:
                if msn in self.msnSamples:
                    pass
                else:
                    missingSampleFiles += 1
                    print msn + " not found in Samples list"
        print "Check Complete"

    def chkSamSubCnt2(self):
        missingSubstrateFiles = []
        missingSampleFiles = []
        for msn in self.msnSamples:
            if not msn in self.msnSubstrate:
                missingSubstrateFiles.append(msn)
        print "(" + str(len(missingSubstrateFiles)) + ")" + " missing from substrate files"
        for item in missingSubstrateFiles:
            print item + " not found in substrate list"
        for msn in self.msnSubstrate:
            if not msn in self.msnSamples:
                missingSampleFiles.append(msn)
        print "(" + str(len(missingSampleFiles)) + ")" + " missing from sample files"
        for item in missingSampleFiles:
            print item + " not found in sample list"
        print "Check Complete"

    def chkSamSpe(self):
        missingSpeciesFiles = []
        missingSampleFiles = []
        for msn in self.msnSamples:
            if not msn in self.msnSpecies:
                missingSpeciesFiles.append(msn)
        print "(" + str(len(missingSpeciesFiles)) + ")" + " missing from species files"
        for item in missingSpeciesFiles:
            print item + " not found in species list"
        for msn in self.msnSpecies:
            if not msn in self.msnSamples:
                missingSampleFiles.append(msn)
        print "(" + str(len(set(missingSampleFiles))) + ")" + " missing from sample files"
        for item in set(missingSampleFiles):
            print item + " not found in sample list"
        print "Check Complete"

    def duplicates(self):
        sampleDict = {}
        substrateDict = {}
        for msn in self.msnSamples:
            if msn in sampleDict:
                sampleDict[msn] += 1
            else:
                sampleDict[msn] = 1
        
        print "List of Duplicate MSN in Samples file"
        print [ key for key, value in sampleDict.items() if value > 1]

    do you see this now in edit, I changed it

def self.missing_sample_files(self):
    missingSampleFiles = []
    for msn in self.msnSamples:
        if not msn in self.msnSpecies:
            missingSpeciesFiles.append(msn)
    return missingSampleFiles

def chkSamSpe(self):
missingSpeciesFiles = []

    missingSampleFiles = self.missing_sample_files()

    print "(" + str(len(missingSpeciesFiles)) + ")" + " missing from species files"
    for item in missingSpeciesFiles:
        print item + " not found in species list"
    for msn in self.msnSpecies:
        if not msn in self.msnSamples:
            missingSampleFiles.append(msn)
    print "(" + str(len(set(missingSampleFiles))) + ")" + " missing from sample files"
    for item in set(missingSampleFiles):
        print item + " not found in sample list"
    print "Check Complete"

def self.missing_samples(self):
    missingSamples = []
    for msn in self.msnSamples:
        if not msn in self.msnSpecies:
            missingSpecies.append(msn)
    return missingSamples

def self.report_missing(self, missing_sample_list):

   print "(" + str(len(missing_sample_list)) + ")" + " missing from species files"

   for item in set(missing_sample_list):
        print item + " not found in sample list"

def check_sample_species(self):

    missing_species_files = self.missing_samples()

    report_missing(self, missing_species_files ):

    missing_sample_files = self.missing_samples()

    report_missing(self, missing_sample_files ):

    print "Check Complete"