def __init__(self):
QtGui.QMainWindow.__init__(self)
self.ui = Ui_SNPConvert()
self.ui.setupUi(self)
###############################################
###### TAB1 - Illumina MATRIX Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab1.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab1='';self.inputSnpMapFile_tab1=''
self.ui.FinRep_tab1.clicked.connect(self.FinRep_open_tab1)
self.ui.SnpMap_tab1.clicked.connect(self.SnpMap_open_tab1)
#Setting linedit read (breed code)
self.BrdCode_tab1='UNKN_BRD'
self.ui.BrdCode_tab1.setPlaceholderText(self.BrdCode_tab1) #default (example) value
self.ui.BrdCode_tab1.cursorPositionChanged.connect(self.BrdCodeChange_tab1)
#Setting linedit read (output name)
self.OutName_tab1='Output_name'
self.ui.OutName_tab1.setPlaceholderText(self.OutName_tab1) #default (example) name
self.ui.OutName_tab1.cursorPositionChanged.connect(self.OutNameChange_tab1)
#Setting action of buttons RUN
self.ui.ConvertFile_tab1.clicked.connect(self.ConvertFile_run_tab1)
###############################################
###### TAB2 - Illumina ROW Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab2.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab2='';self.inputSnpMap_tab2=''
self.ui.FinRep_tab2.clicked.connect(self.FinRep_open_tab2)
self.ui.SnpMap_tab2.clicked.connect(self.SnpMap_open_tab2)
#Setting the combo box
self.Chosen_allele='Forward'
self.items = ('Forward','Top','AB')
self.ui.AlleleCod_box_tab2.addItems(self.items)
self.ui.AlleleCod_box_tab2.currentIndexChanged.connect(self.OutAlleleCoding_tab2)
#Setting linedit read (breed code)
self.BrdCode_tab2='UNKN_BRD'
self.ui.BrdCode_tab2.setPlaceholderText(self.BrdCode_tab2) #default (example) value
self.ui.BrdCode_tab2.cursorPositionChanged.connect(self.BrdCodeChange_tab2)
#Setting linedit read (output name)
self.OutName_tab2='Output_name'
self.ui.OutName_tab2.setPlaceholderText(self.OutName_tab2) #default (example) name
self.ui.OutName_tab2.cursorPositionChanged.connect(self.OutNameChange_tab2)
#Setting action of buttons RUN
self.ui.ConvertFile_tab2.clicked.connect(self.ConvertFile_run_tab2)
################################
###### TAB3 - iConvert #########
################################
#Setting log screen as readonly
self.ui.Log_wdg_tab3.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputPedFile_tab3='';self.inputMapFile_tab3='';self.inputSnpChimpFile_tab3=''
self.ui.PedFile_tab3.clicked.connect(self.PedFile_open_tab3)
self.ui.MapFile_tab3.clicked.connect(self.MapFile_open_tab3)
self.ui.SnpChimp_tab3.clicked.connect(self.SnpChimp_open_tab3)
#Setting the combo box
self.items1=['ILMN_Forward','ILMN_Top','ILMN_AB','AFFY_Forward','AFFY_AB','NO_allele_conv']
self.INChosen_allele='ILMN_Forward'
self.ui.AlleleCodIn_box_tab3.addItems(self.items1)
self.ui.AlleleCodIn_box_tab3.currentIndexChanged.connect(self.InAlleleCoding_tab3)
self.items2=['ILMN_Top','ILMN_Forward','ILMN_AB','AFFY_Forward','AFFY_AB','NO_allele_conv']
self.OUTChosen_allele='ILMN_Top'
self.ui.AlleleCodOut_box_tab3.addItems(self.items2)
self.ui.AlleleCodOut_box_tab3.currentIndexChanged.connect(self.OutAlleleCoding_tab3)
#Setting radio buttons
self.UpdateMap = True
self.ui.YesRadioButton_tab3.clicked.connect(self.YesRadio_clicked)
self.ui.NoRadioButton_tab3.clicked.connect(self.NoRadio_clicked)
#Setting linedit read (output name)
self.OutName_tab3='Output_name'
self.ui.OutName_tab3.setPlaceholderText(self.OutName_tab3) #default (example) name
self.ui.OutName_tab3.cursorPositionChanged.connect(self.OutNameChange_tab3)
#Setting action of buttons RUN
self.ui.ConvertFile_tab3.clicked.connect(self.ConvertFile_run_tab3)
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.ui = Ui_SNPConvert()
self.ui.setupUi(self)
###############################################
###### TAB1 - Illumina MATRIX Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab1.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab1 = ''
self.inputSnpMapFile_tab1 = ''
self.ui.FinRep_tab1.clicked.connect(self.FinRep_open_tab1)
self.ui.SnpMap_tab1.clicked.connect(self.SnpMap_open_tab1)
#Setting linedit read (breed code)
self.BrdCode_tab1 = 'UNKN_BRD'
self.ui.BrdCode_tab1.setPlaceholderText(
self.BrdCode_tab1) #default (example) value
self.ui.BrdCode_tab1.cursorPositionChanged.connect(
self.BrdCodeChange_tab1)
#Setting linedit read (output name)
self.OutName_tab1 = 'Output_name'
self.ui.OutName_tab1.setPlaceholderText(
self.OutName_tab1) #default (example) name
self.ui.OutName_tab1.cursorPositionChanged.connect(
self.OutNameChange_tab1)
#Setting action of buttons RUN
self.ui.ConvertFile_tab1.clicked.connect(self.ConvertFile_run_tab1)
###############################################
###### TAB2 - Illumina ROW Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab2.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab2 = ''
self.inputSnpMap_tab2 = ''
self.ui.FinRep_tab2.clicked.connect(self.FinRep_open_tab2)
self.ui.SnpMap_tab2.clicked.connect(self.SnpMap_open_tab2)
#Setting the combo box
self.Chosen_allele = 'Forward'
self.items = ('Forward', 'Top', 'AB')
self.ui.AlleleCod_box_tab2.addItems(self.items)
self.ui.AlleleCod_box_tab2.currentIndexChanged.connect(
self.OutAlleleCoding_tab2)
#Setting linedit read (breed code)
self.BrdCode_tab2 = 'UNKN_BRD'
self.ui.BrdCode_tab2.setPlaceholderText(
self.BrdCode_tab2) #default (example) value
self.ui.BrdCode_tab2.cursorPositionChanged.connect(
self.BrdCodeChange_tab2)
#Setting linedit read (output name)
self.OutName_tab2 = 'Output_name'
self.ui.OutName_tab2.setPlaceholderText(
self.OutName_tab2) #default (example) name
self.ui.OutName_tab2.cursorPositionChanged.connect(
self.OutNameChange_tab2)
#Setting action of buttons RUN
self.ui.ConvertFile_tab2.clicked.connect(self.ConvertFile_run_tab2)
################################
###### TAB3 - iConvert #########
################################
#Setting log screen as readonly
self.ui.Log_wdg_tab3.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputPedFile_tab3 = ''
self.inputMapFile_tab3 = ''
self.inputSnpChimpFile_tab3 = ''
self.ui.PedFile_tab3.clicked.connect(self.PedFile_open_tab3)
self.ui.MapFile_tab3.clicked.connect(self.MapFile_open_tab3)
self.ui.SnpChimp_tab3.clicked.connect(self.SnpChimp_open_tab3)
#Setting the combo box
self.items1 = [
'ILMN_Forward', 'ILMN_Top', 'ILMN_AB', 'AFFY_Forward', 'AFFY_AB',
'NO_allele_conv'
]
self.INChosen_allele = 'ILMN_Forward'
self.ui.AlleleCodIn_box_tab3.addItems(self.items1)
self.ui.AlleleCodIn_box_tab3.currentIndexChanged.connect(
self.InAlleleCoding_tab3)
self.items2 = [
'ILMN_Top', 'ILMN_Forward', 'ILMN_AB', 'AFFY_Forward', 'AFFY_AB',
'NO_allele_conv'
]
self.OUTChosen_allele = 'ILMN_Top'
self.ui.AlleleCodOut_box_tab3.addItems(self.items2)
self.ui.AlleleCodOut_box_tab3.currentIndexChanged.connect(
self.OutAlleleCoding_tab3)
#Setting radio buttons
self.UpdateMap = True
self.ui.YesRadioButton_tab3.clicked.connect(self.YesRadio_clicked)
self.ui.NoRadioButton_tab3.clicked.connect(self.NoRadio_clicked)
#Setting linedit read (output name)
self.OutName_tab3 = 'Output_name'
self.ui.OutName_tab3.setPlaceholderText(
self.OutName_tab3) #default (example) name
self.ui.OutName_tab3.cursorPositionChanged.connect(
self.OutNameChange_tab3)
#Setting action of buttons RUN
self.ui.ConvertFile_tab3.clicked.connect(self.ConvertFile_run_tab3)
class Main(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.ui = Ui_SNPConvert()
self.ui.setupUi(self)
###############################################
###### TAB1 - Illumina MATRIX Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab1.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab1='';self.inputSnpMapFile_tab1=''
self.ui.FinRep_tab1.clicked.connect(self.FinRep_open_tab1)
self.ui.SnpMap_tab1.clicked.connect(self.SnpMap_open_tab1)
#Setting linedit read (breed code)
self.BrdCode_tab1='UNKN_BRD'
self.ui.BrdCode_tab1.setPlaceholderText(self.BrdCode_tab1) #default (example) value
self.ui.BrdCode_tab1.cursorPositionChanged.connect(self.BrdCodeChange_tab1)
#Setting linedit read (output name)
self.OutName_tab1='Output_name'
self.ui.OutName_tab1.setPlaceholderText(self.OutName_tab1) #default (example) name
self.ui.OutName_tab1.cursorPositionChanged.connect(self.OutNameChange_tab1)
#Setting action of buttons RUN
self.ui.ConvertFile_tab1.clicked.connect(self.ConvertFile_run_tab1)
###############################################
###### TAB2 - Illumina ROW Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab2.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab2='';self.inputSnpMap_tab2=''
self.ui.FinRep_tab2.clicked.connect(self.FinRep_open_tab2)
self.ui.SnpMap_tab2.clicked.connect(self.SnpMap_open_tab2)
#Setting the combo box
self.Chosen_allele='Forward'
self.items = ('Forward','Top','AB')
self.ui.AlleleCod_box_tab2.addItems(self.items)
self.ui.AlleleCod_box_tab2.currentIndexChanged.connect(self.OutAlleleCoding_tab2)
#Setting linedit read (breed code)
self.BrdCode_tab2='UNKN_BRD'
self.ui.BrdCode_tab2.setPlaceholderText(self.BrdCode_tab2) #default (example) value
self.ui.BrdCode_tab2.cursorPositionChanged.connect(self.BrdCodeChange_tab2)
#Setting linedit read (output name)
self.OutName_tab2='Output_name'
self.ui.OutName_tab2.setPlaceholderText(self.OutName_tab2) #default (example) name
self.ui.OutName_tab2.cursorPositionChanged.connect(self.OutNameChange_tab2)
#Setting action of buttons RUN
self.ui.ConvertFile_tab2.clicked.connect(self.ConvertFile_run_tab2)
################################
###### TAB3 - iConvert #########
################################
#Setting log screen as readonly
self.ui.Log_wdg_tab3.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputPedFile_tab3='';self.inputMapFile_tab3='';self.inputSnpChimpFile_tab3=''
self.ui.PedFile_tab3.clicked.connect(self.PedFile_open_tab3)
self.ui.MapFile_tab3.clicked.connect(self.MapFile_open_tab3)
self.ui.SnpChimp_tab3.clicked.connect(self.SnpChimp_open_tab3)
#Setting the combo box
self.items1=['ILMN_Forward','ILMN_Top','ILMN_AB','AFFY_Forward','AFFY_AB','NO_allele_conv']
self.INChosen_allele='ILMN_Forward'
self.ui.AlleleCodIn_box_tab3.addItems(self.items1)
self.ui.AlleleCodIn_box_tab3.currentIndexChanged.connect(self.InAlleleCoding_tab3)
self.items2=['ILMN_Top','ILMN_Forward','ILMN_AB','AFFY_Forward','AFFY_AB','NO_allele_conv']
self.OUTChosen_allele='ILMN_Top'
self.ui.AlleleCodOut_box_tab3.addItems(self.items2)
self.ui.AlleleCodOut_box_tab3.currentIndexChanged.connect(self.OutAlleleCoding_tab3)
#Setting radio buttons
self.UpdateMap = True
self.ui.YesRadioButton_tab3.clicked.connect(self.YesRadio_clicked)
self.ui.NoRadioButton_tab3.clicked.connect(self.NoRadio_clicked)
#Setting linedit read (output name)
self.OutName_tab3='Output_name'
self.ui.OutName_tab3.setPlaceholderText(self.OutName_tab3) #default (example) name
self.ui.OutName_tab3.cursorPositionChanged.connect(self.OutNameChange_tab3)
#Setting action of buttons RUN
self.ui.ConvertFile_tab3.clicked.connect(self.ConvertFile_run_tab3)
#####################################################################################################################
###### DEFS FOR TAB1 - Illumina MATRIX Format
#####################################################################################################################
def FinRep_open_tab1(self):
self.inputFinRepFile_tab1 = QtGui.QFileDialog.getOpenFileName(self,"Open FinalReport file", "Open FinalReport file", self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputFinRepFile_tab1.isEmpty():self.ui.Log_wdg_tab1.append("<font color=red><b>WARNING:</b>FinalReport file not selected!</font>")
else:self.ui.Log_wdg_tab1.append("FinalReport file selected <font color=green><b>OK</b></font>")
def SnpMap_open_tab1(self):
self.inputSnpMapFile_tab1 = QtGui.QFileDialog.getOpenFileName(self,"Open SNP map file", "Open SNP map file", self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputSnpMapFile_tab1.isEmpty():self.ui.Log_wdg_tab1.append("<font color=red><b>WARNING:</b>SNP map file not selected!</font>")
else:self.ui.Log_wdg_tab1.append("SNP map file selected <font color=green><b>OK</b></font>")
def BrdCodeChange_tab1(self):
self.BrdCode_tab1 = self.ui.BrdCode_tab1.text()
def OutNameChange_tab1(self):
self.OutName_tab1 = self.ui.OutName_tab1.text()
def ConvertFile_run_tab1(self):
### Check that parameters are not void and replace values when possible (if not return an error message!)
self.ui.Log_wdg_tab1.clear()
if not self.inputFinRepFile_tab1 or self.inputFinRepFile_tab1.isEmpty():return self.ui.Log_wdg_tab1.append("<font color=red><b>ERROR: Please select a FinalReport file!</b></font>")
if not self.inputSnpMapFile_tab1 or self.inputSnpMapFile_tab1.isEmpty():return self.ui.Log_wdg_tab1.append("<font color=red><b>ERROR: Please select a SNP map file!</b></font>")
if not self.BrdCode_tab1:self.BrdCode_tab1 = 'UNKN_BRD'
if not self.OutName_tab1:self.OutName_tab1 = 'Output_name'
### Print the options used
self.ui.Log_wdg_tab1.append("<b><i>PEDDA MATRIX software - ILMN Matrix --> PLINK</i></b>")
self.ui.Log_wdg_tab1.append("<i>Conversion and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab1.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab1.append(time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S", time.localtime()))
self.ui.Log_wdg_tab1.append(" - FinalReport: <b>%s</b>" % self.inputFinRepFile_tab1)
self.ui.Log_wdg_tab1.append(" - SNP map: <b>%s</b>" % self.inputSnpMapFile_tab1)
self.ui.Log_wdg_tab1.append(" - Pop code: <b>%s</b>" % self.BrdCode_tab1)
self.ui.Log_wdg_tab1.append(" - Output name: <b>%s</b><br>" % self.OutName_tab1)
### Start processing the Map file first
self.ui.Log_wdg_tab1.append("<b>A) Processing SnpMap file</b>")
conv={};chroms={}
for a in open(self.inputSnpMapFile_tab1):
if 'chromosome' in a.lower():continue #.lower is used to avoid problems with capital letters
# Automatic identifier of the separator (at least 4 fields should be enough)
try:
if len(a.strip().split(','))>5:
line=a.strip().split(',')[:5]
nn,snpid,cro,pos,rest=line
elif len(a.strip().split('\t'))>5:
line=a.strip().split('\t')[:5]
nn,snpid,cro,pos,rest=line
else:
line=a.strip().split()[:5]
nn,snpid,cro,pos,rest=line
except:return self.ui.Log_wdg_tab1.append("<font color=red><b>ERROR: Bad/Corrupt SNP map file! Please check the file and make sure it is an (original) Illumina SnpMap file!</b></font>")
conv[snpid]=(cro,pos) #This dictionary keeps map info related to the SNP name
chroms[cro]=0 #This dictionary is useful only to inform the user
self.ui.Log_wdg_tab1.append("====> Total number of SNPs processed: <b>%s</b>" % len(conv))
self.ui.Log_wdg_tab1.append("====> Total number of chromosomes found: <b>%s</b>" % len(chroms))
self.ui.Log_wdg_tab1.append("====> List of chromosomes found: <b>%s</b><br>" % ','.join(sorted(chroms.keys())))
#Adapt slashes to unix/mac or Windows
direct_name=os.path.abspath(os.path.dirname(str(self.inputFinRepFile_tab1)))
if '/' in direct_name:slsh='/'
else:slsh='\\'
#Rebuild the (full) path of the original inputFinRepFile_tab1 - for compatibility with Windows
#Open the output files
outnam = direct_name+slsh+self.OutName_tab1
outgen = open(outnam+'.ped','w')
outmap = open(outnam+'.map','w')
### Start processing the genotypes
self.ui.Log_wdg_tab1.append("<b>B) Processing FinalReport file</b>")
readfrom=False
genos=[];anims=[];n=0
for en,a in enumerate(open(self.inputFinRepFile_tab1)):
if '[data]' in a.lower(): #.lower is used to avoid problems with capital letters
readfrom=True
continue
if not readfrom:continue # Skip the header of the illumina file
n+=1 # Start counting SNPs
# Automatic identifier of the file separator
if len(a.strip().split(','))>=2:
line=a.strip().split(',');sep=','
elif len(a.strip().split('\t'))>=2:
line=a.strip().split('\t');sep='\t'
else:
line=a.strip().split();sep=' '
# This is the first line containing the IDs of individuals
if n==1:
for x in range(len(line)):
if x==0:continue
anims.append(line[x]) # keep trace of individual IDs
genos.append([])
genos.append([]) # create a list n.individuals long x2
continue # Jump to the genotypes
#If it is a , or \t separator, do it easy, otherise
snp,geno=a.strip().split(sep,1)
geno.strip()
#Write the Map file as soon as it is read (to maintain the order)
try:outmap.write('%s %s 0 %s\n' % (conv[snp][0],snp,conv[snp][1]))
except:return self.ui.Log_wdg_tab1.append("<font color=red><b>ERROR: Map file writing failed at row"+str(en+1)+". Missing snp in Map?? </b></font>")
#read the genotype line as long string separated by...
if sep==',' or sep=='\t':geno=geno.replace('-','0').strip().split(sep)
else:geno=geno.replace('-','0').strip().split()
# Keep genos in memory (in order)
for x in range(len(geno)):genos[x].append(geno[x])
#check if reading of the file went ok.
if not n:return self.ui.Log_wdg_tab1.append("<font color=red><b>ERROR: Bad/Corrupt FinalReport file! Please check the file!</b></font>")
self.ui.Log_wdg_tab1.append("====> Total number of INDIVIDUALS processed: <b>%s</b><br>" % len(geno))
self.ui.Log_wdg_tab1.append("<b>C) Writing output files</b>")
for x in range(len(anims)):
gty=[genos[x][i][0]+' '+genos[x][i][1] for i in range(len(genos[x]))]
outgen.write('%s %s 0 0 0 0 %s\n' % (self.BrdCode_tab1,anims[x],' '.join(gty)))
self.ui.Log_wdg_tab1.append("<br><br>====> Bazinga! <font color=green><b><i>Conversion run OK!</i></b></font>")
self.ui.Log_wdg_tab1.append("<font color=blue>PED file available: <b>"+outnam+'.ped</b></font>')
self.ui.Log_wdg_tab1.append("<font color=blue>MAP file available: <b>"+outnam+'.map</b></font>')
#####################################################################################################################
###### DEFS FOR TAB2 - Illumina ROW Format
#####################################################################################################################
def FinRep_open_tab2(self):
self.inputFinRepFile_tab2 = QtGui.QFileDialog.getOpenFileName(self,"Open FinalReport file", "Open FinalReport file", self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputFinRepFile_tab2.isEmpty():self.ui.Log_wdg_tab2.append("<font color=red><b>WARNING:</b>FinalReport file not selected!</font>")
else:self.ui.Log_wdg_tab2.append("FinalReport file selected <font color=green><b>OK</b></font>")
def SnpMap_open_tab2(self):
self.inputSnpMapFile_tab2 = QtGui.QFileDialog.getOpenFileName(self,"Open SNP map file", "Open SNP map file", self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputSnpMapFile_tab2.isEmpty():self.ui.Log_wdg_tab2.append("<font color=red><b>WARNING:</b>SNP map file not selected!</font>")
else:self.ui.Log_wdg_tab2.append("SNP map file selected <font color=green><b>OK</b></font>")
def OutAlleleCoding_tab2(self,indice):
self.Chosen_allele = self.items[indice]
def BrdCodeChange_tab2(self):
self.BrdCode_tab2 = self.ui.BrdCode_tab2.text()
def OutNameChange_tab2(self):
self.OutName_tab2 = self.ui.OutName_tab2.text()
def ConvertFile_run_tab2(self):
### Check that parameters are not void and replace values when possible (if not return an error message!)
self.ui.Log_wdg_tab2.clear()
if not self.inputFinRepFile_tab2 or self.inputFinRepFile_tab2.isEmpty():return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR: Please select a FinalReport file!</b></font>")
if not self.inputSnpMapFile_tab2 or self.inputSnpMapFile_tab2.isEmpty():return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR: Please select a SNP map file!</b></font>")
if not self.BrdCode_tab2:self.BrdCode_tab2 = 'UNKN_BRD'
if not self.OutName_tab2:self.OutName_tab2 = 'Output_name'
### Print the options used
self.ui.Log_wdg_tab2.append("<b><i>Pedda ROW software - ILMN ROW --> PLINK</i></b>")
self.ui.Log_wdg_tab2.append("<i>Conversion and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab2.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab2.append(time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S", time.localtime()))
self.ui.Log_wdg_tab2.append(" - FinalReport: <b>%s</b>" % self.inputFinRepFile_tab2)
self.ui.Log_wdg_tab2.append(" - SNP map: <b>%s</b>" % self.inputSnpMapFile_tab2)
self.ui.Log_wdg_tab2.append(" - Output allele coding: <b>%s</b>" % self.Chosen_allele)
self.ui.Log_wdg_tab2.append(" - Pop code: <b>%s</b>" % self.BrdCode_tab2)
self.ui.Log_wdg_tab2.append(" - Output name: <b>%s</b><br>" % self.OutName_tab2)
self.ui.Log_wdg_tab2.append("<b>A) Processing SNP map file file</b>")
conv={};chroms={}
for a in open(self.inputSnpMapFile_tab2):
if 'chromosome' in a.lower():continue #.lower is used to avoid problems with capital letters
# Automatic identifier of the separator (at least 4 fields should be enough)
try:
if len(a.strip().split(','))>5:
line=a.strip().split(',')[:5]
nn,snpid,cro,pos,rest=line
elif len(a.strip().split('\t'))>5:
line=a.strip().split('\t')[:5]
nn,snpid,cro,pos,rest=line
else:
line=a.strip().split()[:5]
nn,snpid,cro,pos,rest=line
except:return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR: Bad/Corrupt SNP map file! Please check the file and make sure it is an (original) Illumina SnpMap file!</b></font>")
conv[snpid]=(cro,pos) #This dictionary keeps map info related to the SNP name
chroms[cro]=0 #This dictionary is useful only to inform the user
self.ui.Log_wdg_tab2.append("====> Total number of SNPs processed: <b>%s</b>" % len(conv))
self.ui.Log_wdg_tab2.append("====> Total number of chromosomes found: <b>%s</b>" % len(chroms))
self.ui.Log_wdg_tab2.append("====> List of chromosomes found: <b>%s</b><br>" % ','.join(sorted(chroms.keys())))
### Start processing the Map file first
self.ui.Log_wdg_tab2.append("<b>B) Processing FinRep file</b>")
direct_name=os.path.abspath(os.path.dirname(str(self.inputFinRepFile_tab2)))
if '/' in direct_name:slsh='/'
else:slsh='\\'
#Rebuild the (full) path of the original inputFinRepFile_tab1 - for compatibility with Windows
#Open the output files
outnam = direct_name+slsh+self.OutName_tab2
outgen = open(outnam+'.ped','w')
outmap = open(outnam+'.map','w')
readfrom=False
SNPname=[]
c=0;anim=-1;snp=0
for en,a in enumerate(open(self.inputFinRepFile_tab2)):
if 'allele1' in a.lower():
readfrom=True
if len(a.strip().split(','))>=3:
sep=',';
line=a.lower().strip().split(sep)
elif len(a.strip().split('\t'))>=3:
sep='\t'
line=a.lower().strip().split(sep)
else:
sep=''
line=a.lower().strip().split()
### Seraching for 'SNP name' header
if not 'snp name' in line and not 'snpname' in line:
return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> The header does not contain the required information: 'SNP name' or 'SNPname' (not case sensitive)<\font><br>")
else:
try:
SNPid_pos = line.index('snp name')
except:
SNPid_pos = line.index('snpname')
### Searching for 'Sample ID' header
if not 'sample id' in line and not 'sampleid' in line:
return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> The header does not contain the required information: 'Sample ID' or 'SampleId' (not case sensitive)<\font><br>")
else:
try:
INDid_pos = line.index('sample id')
except:
INDid_pos = line.index('sampleid')
### Searching for the required allele coding format.
if not 'allele1 - '+self.Chosen_allele.lower() in line:
self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> The header does not contain the chosen allele coding: Allele1 - "+self.Chosen_allele+'<\font><br>')
self.ui.Log_wdg_tab2.append("<font color=red> Header read:'<b><i>"+a+"'</i></b></font><br>")
self.ui.Log_wdg_tab2.append("<font color=red> Possible causes: </font>")
self.ui.Log_wdg_tab2.append("<font color=red> - The requested allele format is not present in your header <i>[SOLUTION: choose an allele format that is available]</i></font>")
self.ui.Log_wdg_tab2.append("<font color=red> - The header in the Illumina header has changed (no 'Allele1 - "+self.Chosen_allele+"' field is present - not case sensitive) <i>[SOLUTION: Contact [email protected], or if you know how to code in python, change the if string related to this]</i></font>")
self.ui.Log_wdg_tab2.append("<font color=red> - The FinalReport file separator is not right <i>[SOLUTION: Contact [email protected], or if you know how to code in python, change the if string related to this]</i></font>")
self.ui.Log_wdg_tab2.append("<font color=red> - The FinalReport file is in Matrix format <i>[SOLUTION: Use the 'Illumina MATRIX format' tag instead]</i></font>")
self.ui.Log_wdg_tab2.append("<font color=red> - Other <i>[SOLUTION: Contact [email protected] ... send me the header (e.g. first 10 rows) of the FinalReport file you're using]</i></font>")
return
else:
alle_pos1=line.index('allele1 - '+self.Chosen_allele.lower())
alle_pos2=alle_pos1+1
continue
if not readfrom:continue
if sep:line=a.strip().split(sep)
else: line=a.strip().split()
if alle_pos2 > len(line):
return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> Probable error in the separator.. Position of Allele2 found in "+str(alle_pos2)+", but length of line in row "+str(en)+" is "+str(len(line))+" !!</font><br>"+\
"<font color=red>Please check your choice of separator is correct and that you don't have strange fields in you FinalReport file!</font>")
snp_name=line[SNPid_pos]
if not conv.has_key(snp_name):
return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> SNP name: "+snp_name+" in FinalReport file not found in SNP map file!</font><br>")
id_sample=line[INDid_pos]
alle1=line[alle_pos1]
alle2=line[alle_pos2]
if alle1=='-':alle1='0'
if alle2=='-':alle2='0'
c+=1
if c==1:
snp=-1
geno=[]
name=[]
name.append(id_sample)
if id_sample in name:
geno.append(alle1+' '+alle2)
snp+=1
if len(name)==1:
outmap.write('%s %s 0 %s\n' % (conv[snp_name][0],snp_name,conv[snp_name][1]))
SNPname.append(snp_name)
else:
if snp_name!=SNPname[snp]:
return self.ui.Log_wdg_tab2.append("The order of the SNPs in the different individuals is consistent. Check "+snp_name+" and "+SNPname[snp])
else:
snp=0
anim+=1
outgen.write('%s %s 0 0 0 -9 %s\n' % (self.BrdCode_tab2,name[anim],' '.join(geno)))
self.ui.Log_wdg_tab2.append('Finshed processing individual: '+name[anim]+' - Total SNPs: '+str(len(geno)))
geno=[]
geno.append(alle1+' '+alle2)
name.append(id_sample)
outgen.write('%s %s 0 0 0 -9 %s\n' % (self.BrdCode_tab2,id_sample,' '.join(geno)))
anim+=2
self.ui.Log_wdg_tab2.append('Finshed processing individual: '+id_sample+' - Total SNPs: '+str(len(geno)))
self.ui.Log_wdg_tab2.append('<br><b>====> Total number of INDIVIDUALS processed: '+str(anim)+'</b><br><br>')
self.ui.Log_wdg_tab2.append("====> Bazinga! <font color=green><b><i>Conversion run OK!</i></b></font>")
self.ui.Log_wdg_tab2.append("<font color=blue>PED file available: <b>"+outnam+'.ped</b></font>')
self.ui.Log_wdg_tab2.append("<font color=blue>MAP file available: <b>"+outnam+'.map</b></font>')
def PedFile_open_tab3(self):
self.inputPedFile_tab3 = QtGui.QFileDialog.getOpenFileName(self,"Open PED file", "Open PED file", self.tr("PED files (*.ped);;All files (*)"))
if self.inputPedFile_tab3.isEmpty():self.ui.Log_wdg_tab3.append("<font color=red><b>WARNING:</b>PED file not selected!</font>")
else:self.ui.Log_wdg_tab3.append("PED file selected <font color=green><b>OK</b></font>")
def MapFile_open_tab3(self):
self.inputMapFile_tab3 = QtGui.QFileDialog.getOpenFileName(self,"Open MAP file", "Open MAP file", self.tr("MAP files (*.map);;All files (*)"))
if self.inputMapFile_tab3.isEmpty():self.ui.Log_wdg_tab3.append("<font color=red><b>WARNING:</b>MAP file not selected!</font>")
else:self.ui.Log_wdg_tab3.append("MAP file selected <font color=green><b>OK</b></font>")
def SnpChimp_open_tab3(self):
self.inputSnpChimpFile_tab3 = QtGui.QFileDialog.getOpenFileName(self,"Open SNPchimp_v3 file", "Open SNPchimp_v3 file", self.tr("CSV files (*.csv);; TSV files (*.tsv);; All Files (*)"))
if self.inputSnpChimpFile_tab3.isEmpty():self.ui.Log_wdg_tab3.append("<font color=red><b>WARNING:</b>SNPchimp_v3 file not selected!</font>")
else:self.ui.Log_wdg_tab3.append("SNPchimp_v3 file selected <font color=green><b>OK</b></font>")
def InAlleleCoding_tab3(self,indice):
self.INChosen_allele = self.items1[indice]
def YesRadio_clicked(self):
self.UpdateMap = True
def NoRadio_clicked(self):
self.UpdateMap = False
def OutAlleleCoding_tab3(self,indice):
self.OUTChosen_allele = self.items2[indice]
def OutNameChange_tab3(self):
self.OutName_tab3 = self.ui.OutName_tab3.text()
def ConvertFile_run_tab3(self):
#Clear screen
self.ui.Log_wdg_tab3.clear()
#Only update map info (do not ask for ped file
if self.INChosen_allele == 'NO_allele_conv' and self.OUTChosen_allele == 'NO_allele_conv': onlymap=True
else:onlymap=False
if not onlymap:
if not self.inputPedFile_tab3 or self.inputPedFile_tab3.isEmpty():return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Please select a PED file!</b></font>")
if not self.inputMapFile_tab3 or self.inputMapFile_tab3.isEmpty():return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Please select a MAP file!</b></font>")
if not self.inputSnpChimpFile_tab3 or self.inputSnpChimpFile_tab3.isEmpty():return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Please select a SNPchimp_v3 file! (visit http://bioinformatics.tecnoparco.org/SNPchimp/)</b></font>")
if not str(self.inputSnpChimpFile_tab3[-3:]).lower() in ['csv','tsv']:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Original SNPchimp v.3 files are csv (comma separated) or tsv (tab separated).</b></font>")
if not self.OutName_tab3:self.OutName_tab3 = 'Output_name'
if not onlymap:
if self.INChosen_allele==self.OUTChosen_allele:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Input and Output allele coding MUST be different!</b></font>")
if self.INChosen_allele[:4]=='ILMN' and self.OUTChosen_allele[:4]!='ILMN':return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>")
if self.INChosen_allele[:4]=='AFFY' and self.OUTChosen_allele[:4]!='AFFY':return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>")
if self.INChosen_allele[:2]=='NO' and self.OUTChosen_allele[:2]!='NO':return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>")
if os.path.basename(str(self.inputPedFile_tab3)) == self.OutName_tab3+'.ped':
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Bad output name - Must be different from PED filename!</b></font>")
if os.path.basename(str(self.inputMapFile_tab3)) == self.OutName_tab3+'.map':
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Bad output name - Must be different from MAP filename!</b></font>")
### Print the options used
answer={True:'Yes',False:'No'}
self.ui.Log_wdg_tab3.append("<b><i>iConvert software - Allele conversion and map update <i></b>")
self.ui.Log_wdg_tab3.append("<i>Software and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab3.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab3.append(time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S", time.localtime()))
self.ui.Log_wdg_tab3.append(" - PLINK fmt - Ped file: <b>%s</b>" % self.inputPedFile_tab3)
self.ui.Log_wdg_tab3.append(" - PLINK fmt - Map file: <b>%s</b>" % self.inputMapFile_tab3)
self.ui.Log_wdg_tab3.append(" - SNPchimp v.3 file : <b>%s</b>" % self.inputSnpChimpFile_tab3)
self.ui.Log_wdg_tab3.append(" - Input allele coding : <b>%s</b><br>" % self.INChosen_allele)
self.ui.Log_wdg_tab3.append(" - Map update requested: <b>%s</b><br>" % answer[self.UpdateMap])
self.ui.Log_wdg_tab3.append(" - Output allele coding: <b>%s</b>" % self.OUTChosen_allele)
self.ui.Log_wdg_tab3.append(" - Output name : <b>%s</b><br>" % self.OutName_tab3)
self.ui.Log_wdg_tab3.append("<br><b>A) Processing SNPchimp v.3 file file</b><br>")
othinfo = []
chips = {};SNPdata = {}
formats = [0,0]
SEP = ','
if self.UpdateMap: mapupd = {}
readfrom=False
for en,line in enumerate(open(self.inputSnpChimpFile_tab3)):
if str(self.inputSnpChimpFile_tab3[-3:]).lower()=='csv':SEP=','
elif str(self.inputSnpChimpFile_tab3[-3:]).lower()=='tsv':SEP='\t'
if 'chip_name' in line.lower():
readfrom=True
hlin=line.lower().strip().split(SEP)
####### FILE header and stuff checks
#Check SEPARATOR is right
if len(hlin)<3:
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNPchimp v.3 separator is not comma or tab, as assumed by the extension name - Download original SNPchimp v.3 files and try again</b></font>")
# Check if user choices are coherent with the infor in SNPchimp v.3
if self.INChosen_allele=='ILMN_Top' or self.OUTChosen_allele=='ILMN_Top':
try:
head_finder=hlin.index('alleles_a_b_top')
if self.INChosen_allele=='ILMN_Top':formats[0]=head_finder
else:formats[1]=head_finder
except ValueError:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Illumina TOP allele coding</b></font>")
if self.INChosen_allele=='ILMN_Forward' or self.OUTChosen_allele=='ILMN_Forward':
try:
head_finder=hlin.index('alleles_a_b_forward')
if self.INChosen_allele=='ILMN_Forward':formats[0]=head_finder
else:formats[1]=head_finder
except ValueError:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Illumina FORWARD allele coding</b></font>")
if self.INChosen_allele=='AFFY_Forward' or self.OUTChosen_allele=='AFFY_Forward':
try:
head_finder=hlin.index('alleles_a_b_affymetrix')
if self.INChosen_allele=='AFFY_Forward':formats[0]=head_finder
else:formats[1]=head_finder
except ValueError:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Affymetrix FORWARD allele coding</b></font>")
# Check accessory information is there, otherwise stop
try:
othinfo.append(hlin.index('chip_name'))
othinfo.append(hlin.index('chromosome'))
othinfo.append(hlin.index('position'))
othinfo.append(hlin.index('snp_name'))
continue
except ValueError:
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR:'chip name', 'chromosome', 'position' and 'SNP_name' header variables not found. These are always present in SNPchiMp downloaded files!</b></font>")
if not readfrom:continue
lista = line.strip().split(SEP)
# Keep only useful info (skip other not wanted chips)
if not chips.has_key(lista[othinfo[0]]): chips[lista[othinfo[0]]] = 0
if 'AFFY' in self.INChosen_allele:
if not 'Bov_AffyHD' in lista[0]:continue
if 'ILMN' in self.INChosen_allele:
if 'Bov_AffyHD' in lista[0]:continue
# Keep SNPchimp map information only if required by the user.
if self.UpdateMap: mapupd[lista[othinfo[3]]] = [lista[othinfo[1]],lista[othinfo[2]]]
# If INPUT allele format is AB, use AB as IN and custom allele format as OUT
if self.INChosen_allele == 'ILMN_AB' or self.INChosen_allele == 'AFFY_AB':
SNPdata[lista[othinfo[3]]] = {'A':lista[formats[1]][0], 'B':lista[formats[1]][2]}
# If OUTPUT allele format is AB, use AB as OUT and custom allele in format as IN
elif self.OUTChosen_allele == 'ILMN_AB' or self.OUTChosen_allele == 'AFFY_AB':
SNPdata[lista[othinfo[3]]] = {lista[formats[0]][0]:'A', lista[formats[0]][2]:'B'}
else:
SNPdata[lista[othinfo[3]]] = {lista[formats[0]][0]:lista[formats[1]][0],
lista[formats[0]][2]:lista[formats[1]][2]}
if en == 0:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNPchimp file is empty!</b></font>")
if len(SNPdata) == 0:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Problem reading SNPchimp file! Probable causes: file is empty, conversion info is not available or header is incorrect</b></font>")
if len(chips)>1:self.ui.Log_wdg_tab3.append("<font color=orange><b>WARNING: More than 1 chip in SNPchimp file. This might result in incorrect allele conversion!</b></font>")
self.ui.Log_wdg_tab3.append("- Rows read in SNP chimp file :<b>%s</b>" % str(en+1))
self.ui.Log_wdg_tab3.append("- SNPs with allele conversion information available :<b>%s</b>" % str(len(SNPdata)))
###### Process Map file
self.ui.Log_wdg_tab3.append("<br><b>B) Processing PLINK MAP file and converting map information (if required)</b><br>")
maporder = [];convert = []
tab = False
# Create new file if new remapping is needed
if self.UpdateMap:
#Adapt slashes to unix/mac or Windows
direct_name=os.path.abspath(os.path.dirname(str(self.inputMapFile_tab3)))
if '/' in direct_name:slsh='/'
else:slsh='\\'
#Rebuild the (full) path of the original inputMapFile_tab3 - for compatibility with Windows
outnammap = direct_name+slsh+self.OutName_tab3+'.map'
remap=open(outnammap,'w')
enmap=0
for enm,line in enumerate(open(self.inputMapFile_tab3)):
#Check for tab or blank space spearator (only these 2 are accepted here)
if enm == 0: test = line.strip().split('\t')
if len(test) == 4: # Warning: this only accepts "normal" MAP files (no --map3 or other options are allowed)
linea = line.strip().split('\t')
tab = True
else:
linea = line.strip().split()
if len(linea) == 0: continue # Skips void lines
enmap+=1
snp = linea[1]
maporder.append(snp)
if not SNPdata.has_key(linea[1]):return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: SNP: "+ snp +" not found in SNPchimp file. Probable causes: you downloaded the wrong SNPchip or modified SNP names </b></font>")
else:convert.append(SNPdata[linea[1]])
if self.UpdateMap:remap.write('%s %s %s %s\n' % (mapupd[snp][0],snp,linea[2],mapupd[snp][1]))
if enmap==0:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: MAP file is empty!</b></font>")
self.ui.Log_wdg_tab3.append("- Rows read in PLINK MAP file (number of SNPs) : <b>%s</b>" % str(enmap))
if self.UpdateMap: self.ui.Log_wdg_tab3.append("<font color=blue>- MAP file updated: <b>%s</b></font>" % outnammap)
# Process PED file (if required)
if not onlymap:
self.ui.Log_wdg_tab3.append("<br><b>C) Processing PLINK PED file and converting allele format</b><br>")
tab = False
#Get full path of PED file
#Adapt slashes to unix/mac or Windows
direct_name=os.path.abspath(os.path.dirname(str(self.inputMapFile_tab3)))
if '/' in direct_name:slsh='/'
else:slsh='\\'
#Rebuild the (full) path of the original inputMapFile_tab3 - for compatibility with Windows
outnamped = direct_name+slsh+self.OutName_tab3+'.ped'
reped=open(outnamped,'w')
#Read ped file
enped=0
for enped,line in enumerate(open(self.inputPedFile_tab3)):
if enped == 0:
test = line.strip().split('\t')
if len(test) == (6 + enmap * 2): tab = True
if tab: pedline = line.strip().split('\t')
else: pedline = line.strip().split()
if (enmap*2+6) != len(pedline):
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Number of SNPs in PLINK MAP (" +str(enmap)+") should result in "+str(enmap*2+6)+" columns PLINK PED but found "+str(len(pedline))+"<br>Check your .ped and .map files. Usually the problem is in the first line(s)...</font><br>")
genotypes = [pedline[6 + x] + pedline[7 + x] for x in range(0, (enmap*2)-1, 2)]
seq = -1
genout = []
nfailed = 0
name_snps=[]
for alle in genotypes:
seq += 1
alle1 = alle[0];alle2 = alle[1]
if alle1 == '0' or alle1 =='?':
genout.append('0');genout.append('0')
continue
try:
genout.append(convert[seq][alle1])
genout.append(convert[seq][alle2])
except KeyError:
nfailed += 1
name_snps.append(maporder[seq])
if nfailed:
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Individual " + pedline[1] + " failed conversion for " + str(nfailed) + \
" SNPs [ "+', '.join(name_snps)+"]. Probably their INPUT allele coding format is not as specified</font>")
reped.write('%s %s\n' % (' '.join(pedline[:6]),' '.join(genout)))
if enped==0:return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: PED file is empty!</b></font>")
self.ui.Log_wdg_tab3.append("- Rows read in PLINK PED file (number of animals) : <b>%s</b>" % str(enped + 1))
self.ui.Log_wdg_tab3.append("<font color=blue>- PED file updated: <b>%s</b></font><br><br>" % outnamped)
self.ui.Log_wdg_tab3.append('<br><font color=green><b> PROGRAM ENDS OK! </b></font>')
class Main(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.ui = Ui_SNPConvert()
self.ui.setupUi(self)
###############################################
###### TAB1 - Illumina MATRIX Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab1.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab1 = ''
self.inputSnpMapFile_tab1 = ''
self.ui.FinRep_tab1.clicked.connect(self.FinRep_open_tab1)
self.ui.SnpMap_tab1.clicked.connect(self.SnpMap_open_tab1)
#Setting linedit read (breed code)
self.BrdCode_tab1 = 'UNKN_BRD'
self.ui.BrdCode_tab1.setPlaceholderText(
self.BrdCode_tab1) #default (example) value
self.ui.BrdCode_tab1.cursorPositionChanged.connect(
self.BrdCodeChange_tab1)
#Setting linedit read (output name)
self.OutName_tab1 = 'Output_name'
self.ui.OutName_tab1.setPlaceholderText(
self.OutName_tab1) #default (example) name
self.ui.OutName_tab1.cursorPositionChanged.connect(
self.OutNameChange_tab1)
#Setting action of buttons RUN
self.ui.ConvertFile_tab1.clicked.connect(self.ConvertFile_run_tab1)
###############################################
###### TAB2 - Illumina ROW Format ##########
###############################################
#Setting log screen as readonly
self.ui.Log_wdg_tab2.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputFinRepFile_tab2 = ''
self.inputSnpMap_tab2 = ''
self.ui.FinRep_tab2.clicked.connect(self.FinRep_open_tab2)
self.ui.SnpMap_tab2.clicked.connect(self.SnpMap_open_tab2)
#Setting the combo box
self.Chosen_allele = 'Forward'
self.items = ('Forward', 'Top', 'AB')
self.ui.AlleleCod_box_tab2.addItems(self.items)
self.ui.AlleleCod_box_tab2.currentIndexChanged.connect(
self.OutAlleleCoding_tab2)
#Setting linedit read (breed code)
self.BrdCode_tab2 = 'UNKN_BRD'
self.ui.BrdCode_tab2.setPlaceholderText(
self.BrdCode_tab2) #default (example) value
self.ui.BrdCode_tab2.cursorPositionChanged.connect(
self.BrdCodeChange_tab2)
#Setting linedit read (output name)
self.OutName_tab2 = 'Output_name'
self.ui.OutName_tab2.setPlaceholderText(
self.OutName_tab2) #default (example) name
self.ui.OutName_tab2.cursorPositionChanged.connect(
self.OutNameChange_tab2)
#Setting action of buttons RUN
self.ui.ConvertFile_tab2.clicked.connect(self.ConvertFile_run_tab2)
################################
###### TAB3 - iConvert #########
################################
#Setting log screen as readonly
self.ui.Log_wdg_tab3.setReadOnly(True)
#Setting action of buttons opening to Open file
self.inputPedFile_tab3 = ''
self.inputMapFile_tab3 = ''
self.inputSnpChimpFile_tab3 = ''
self.ui.PedFile_tab3.clicked.connect(self.PedFile_open_tab3)
self.ui.MapFile_tab3.clicked.connect(self.MapFile_open_tab3)
self.ui.SnpChimp_tab3.clicked.connect(self.SnpChimp_open_tab3)
#Setting the combo box
self.items1 = [
'ILMN_Forward', 'ILMN_Top', 'ILMN_AB', 'AFFY_Forward', 'AFFY_AB',
'NO_allele_conv'
]
self.INChosen_allele = 'ILMN_Forward'
self.ui.AlleleCodIn_box_tab3.addItems(self.items1)
self.ui.AlleleCodIn_box_tab3.currentIndexChanged.connect(
self.InAlleleCoding_tab3)
self.items2 = [
'ILMN_Top', 'ILMN_Forward', 'ILMN_AB', 'AFFY_Forward', 'AFFY_AB',
'NO_allele_conv'
]
self.OUTChosen_allele = 'ILMN_Top'
self.ui.AlleleCodOut_box_tab3.addItems(self.items2)
self.ui.AlleleCodOut_box_tab3.currentIndexChanged.connect(
self.OutAlleleCoding_tab3)
#Setting radio buttons
self.UpdateMap = True
self.ui.YesRadioButton_tab3.clicked.connect(self.YesRadio_clicked)
self.ui.NoRadioButton_tab3.clicked.connect(self.NoRadio_clicked)
#Setting linedit read (output name)
self.OutName_tab3 = 'Output_name'
self.ui.OutName_tab3.setPlaceholderText(
self.OutName_tab3) #default (example) name
self.ui.OutName_tab3.cursorPositionChanged.connect(
self.OutNameChange_tab3)
#Setting action of buttons RUN
self.ui.ConvertFile_tab3.clicked.connect(self.ConvertFile_run_tab3)
#####################################################################################################################
###### DEFS FOR TAB1 - Illumina MATRIX Format
#####################################################################################################################
def FinRep_open_tab1(self):
self.inputFinRepFile_tab1 = QtGui.QFileDialog.getOpenFileName(
self, "Open FinalReport file", "Open FinalReport file",
self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputFinRepFile_tab1.isEmpty():
self.ui.Log_wdg_tab1.append(
"<font color=red><b>WARNING:</b>FinalReport file not selected!</font>"
)
else:
self.ui.Log_wdg_tab1.append(
"FinalReport file selected <font color=green><b>OK</b></font>")
def SnpMap_open_tab1(self):
self.inputSnpMapFile_tab1 = QtGui.QFileDialog.getOpenFileName(
self, "Open SNP map file", "Open SNP map file",
self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputSnpMapFile_tab1.isEmpty():
self.ui.Log_wdg_tab1.append(
"<font color=red><b>WARNING:</b>SNP map file not selected!</font>"
)
else:
self.ui.Log_wdg_tab1.append(
"SNP map file selected <font color=green><b>OK</b></font>")
def BrdCodeChange_tab1(self):
self.BrdCode_tab1 = self.ui.BrdCode_tab1.text()
def OutNameChange_tab1(self):
self.OutName_tab1 = self.ui.OutName_tab1.text()
def ConvertFile_run_tab1(self):
### Check that parameters are not void and replace values when possible (if not return an error message!)
self.ui.Log_wdg_tab1.clear()
if not self.inputFinRepFile_tab1 or self.inputFinRepFile_tab1.isEmpty(
):
return self.ui.Log_wdg_tab1.append(
"<font color=red><b>ERROR: Please select a FinalReport file!</b></font>"
)
if not self.inputSnpMapFile_tab1 or self.inputSnpMapFile_tab1.isEmpty(
):
return self.ui.Log_wdg_tab1.append(
"<font color=red><b>ERROR: Please select a SNP map file!</b></font>"
)
if not self.BrdCode_tab1: self.BrdCode_tab1 = 'UNKN_BRD'
if not self.OutName_tab1: self.OutName_tab1 = 'Output_name'
### Print the options used
self.ui.Log_wdg_tab1.append(
"<b><i>PEDDA MATRIX software - ILMN Matrix --> PLINK</i></b>")
self.ui.Log_wdg_tab1.append(
"<i>Conversion and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab1.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab1.append(
time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S",
time.localtime()))
self.ui.Log_wdg_tab1.append(" - FinalReport: <b>%s</b>" %
self.inputFinRepFile_tab1)
self.ui.Log_wdg_tab1.append(" - SNP map: <b>%s</b>" %
self.inputSnpMapFile_tab1)
self.ui.Log_wdg_tab1.append(" - Pop code: <b>%s</b>" %
self.BrdCode_tab1)
self.ui.Log_wdg_tab1.append(" - Output name: <b>%s</b><br>" %
self.OutName_tab1)
### Start processing the Map file first
self.ui.Log_wdg_tab1.append("<b>A) Processing SnpMap file</b>")
conv = {}
chroms = {}
for a in open(self.inputSnpMapFile_tab1):
if 'chromosome' in a.lower():
continue #.lower is used to avoid problems with capital letters
# Automatic identifier of the separator (at least 4 fields should be enough)
try:
if len(a.strip().split(',')) > 5:
line = a.strip().split(',')[:5]
nn, snpid, cro, pos, rest = line
elif len(a.strip().split('\t')) > 5:
line = a.strip().split('\t')[:5]
nn, snpid, cro, pos, rest = line
else:
line = a.strip().split()[:5]
nn, snpid, cro, pos, rest = line
except:
return self.ui.Log_wdg_tab1.append(
"<font color=red><b>ERROR: Bad/Corrupt SNP map file! Please check the file and make sure it is an (original) Illumina SnpMap file!</b></font>"
)
conv[snpid] = (
cro, pos
) #This dictionary keeps map info related to the SNP name
chroms[cro] = 0 #This dictionary is useful only to inform the user
self.ui.Log_wdg_tab1.append(
"====> Total number of SNPs processed: <b>%s</b>" % len(conv))
self.ui.Log_wdg_tab1.append(
"====> Total number of chromosomes found: <b>%s</b>" % len(chroms))
self.ui.Log_wdg_tab1.append(
"====> List of chromosomes found: <b>%s</b><br>" %
','.join(sorted(chroms.keys())))
#Adapt slashes to unix/mac or Windows
direct_name = os.path.abspath(
os.path.dirname(str(self.inputFinRepFile_tab1)))
if '/' in direct_name: slsh = '/'
else: slsh = '\\'
#Rebuild the (full) path of the original inputFinRepFile_tab1 - for compatibility with Windows
#Open the output files
outnam = direct_name + slsh + self.OutName_tab1
outgen = open(outnam + '.ped', 'w')
outmap = open(outnam + '.map', 'w')
### Start processing the genotypes
self.ui.Log_wdg_tab1.append("<b>B) Processing FinalReport file</b>")
readfrom = False
genos = []
anims = []
n = 0
for en, a in enumerate(open(self.inputFinRepFile_tab1)):
if '[data]' in a.lower(
): #.lower is used to avoid problems with capital letters
readfrom = True
continue
if not readfrom: continue # Skip the header of the illumina file
n += 1 # Start counting SNPs
# Automatic identifier of the file separator
if len(a.strip().split(',')) >= 2:
line = a.strip().split(',')
sep = ','
elif len(a.strip().split('\t')) >= 2:
line = a.strip().split('\t')
sep = '\t'
else:
line = a.strip().split()
sep = ' '
# This is the first line containing the IDs of individuals
if n == 1:
for x in range(len(line)):
if x == 0: continue
anims.append(line[x]) # keep trace of individual IDs
genos.append([])
genos.append([]) # create a list n.individuals long x2
continue # Jump to the genotypes
#If it is a , or \t separator, do it easy, otherise
snp, geno = a.strip().split(sep, 1)
geno.strip()
#Write the Map file as soon as it is read (to maintain the order)
try:
outmap.write('%s %s 0 %s\n' %
(conv[snp][0], snp, conv[snp][1]))
except:
return self.ui.Log_wdg_tab1.append(
"<font color=red><b>ERROR: Map file writing failed at row"
+ str(en + 1) + ". Missing snp in Map?? </b></font>")
#read the genotype line as long string separated by...
if sep == ',' or sep == '\t':
geno = geno.replace('-', '0').strip().split(sep)
else:
geno = geno.replace('-', '0').strip().split()
# Keep genos in memory (in order)
for x in range(len(geno)):
genos[x].append(geno[x])
#check if reading of the file went ok.
if not n:
return self.ui.Log_wdg_tab1.append(
"<font color=red><b>ERROR: Bad/Corrupt FinalReport file! Please check the file!</b></font>"
)
self.ui.Log_wdg_tab1.append(
"====> Total number of INDIVIDUALS processed: <b>%s</b><br>" %
len(geno))
self.ui.Log_wdg_tab1.append("<b>C) Writing output files</b>")
for x in range(len(anims)):
gty = [
genos[x][i][0] + ' ' + genos[x][i][1]
for i in range(len(genos[x]))
]
outgen.write('%s %s 0 0 0 0 %s\n' %
(self.BrdCode_tab1, anims[x], ' '.join(gty)))
self.ui.Log_wdg_tab1.append(
"<br><br>====> Bazinga! <font color=green><b><i>Conversion run OK!</i></b></font>"
)
self.ui.Log_wdg_tab1.append(
"<font color=blue>PED file available: <b>" + outnam +
'.ped</b></font>')
self.ui.Log_wdg_tab1.append(
"<font color=blue>MAP file available: <b>" + outnam +
'.map</b></font>')
#####################################################################################################################
###### DEFS FOR TAB2 - Illumina ROW Format
#####################################################################################################################
def FinRep_open_tab2(self):
self.inputFinRepFile_tab2 = QtGui.QFileDialog.getOpenFileName(
self, "Open FinalReport file", "Open FinalReport file",
self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputFinRepFile_tab2.isEmpty():
self.ui.Log_wdg_tab2.append(
"<font color=red><b>WARNING:</b>FinalReport file not selected!</font>"
)
else:
self.ui.Log_wdg_tab2.append(
"FinalReport file selected <font color=green><b>OK</b></font>")
def SnpMap_open_tab2(self):
self.inputSnpMapFile_tab2 = QtGui.QFileDialog.getOpenFileName(
self, "Open SNP map file", "Open SNP map file",
self.tr("TXT Files (*.txt);;CSV Files (*.csv);;All Files (*)"))
if self.inputSnpMapFile_tab2.isEmpty():
self.ui.Log_wdg_tab2.append(
"<font color=red><b>WARNING:</b>SNP map file not selected!</font>"
)
else:
self.ui.Log_wdg_tab2.append(
"SNP map file selected <font color=green><b>OK</b></font>")
def OutAlleleCoding_tab2(self, indice):
self.Chosen_allele = self.items[indice]
def BrdCodeChange_tab2(self):
self.BrdCode_tab2 = self.ui.BrdCode_tab2.text()
def OutNameChange_tab2(self):
self.OutName_tab2 = self.ui.OutName_tab2.text()
def ConvertFile_run_tab2(self):
### Check that parameters are not void and replace values when possible (if not return an error message!)
self.ui.Log_wdg_tab2.clear()
if not self.inputFinRepFile_tab2 or self.inputFinRepFile_tab2.isEmpty(
):
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR: Please select a FinalReport file!</b></font>"
)
if not self.inputSnpMapFile_tab2 or self.inputSnpMapFile_tab2.isEmpty(
):
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR: Please select a SNP map file!</b></font>"
)
if not self.BrdCode_tab2: self.BrdCode_tab2 = 'UNKN_BRD'
if not self.OutName_tab2: self.OutName_tab2 = 'Output_name'
### Print the options used
self.ui.Log_wdg_tab2.append(
"<b><i>Pedda ROW software - ILMN ROW --> PLINK</i></b>")
self.ui.Log_wdg_tab2.append(
"<i>Conversion and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab2.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab2.append(
time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S",
time.localtime()))
self.ui.Log_wdg_tab2.append(" - FinalReport: <b>%s</b>" %
self.inputFinRepFile_tab2)
self.ui.Log_wdg_tab2.append(" - SNP map: <b>%s</b>" %
self.inputSnpMapFile_tab2)
self.ui.Log_wdg_tab2.append(" - Output allele coding: <b>%s</b>" %
self.Chosen_allele)
self.ui.Log_wdg_tab2.append(" - Pop code: <b>%s</b>" %
self.BrdCode_tab2)
self.ui.Log_wdg_tab2.append(" - Output name: <b>%s</b><br>" %
self.OutName_tab2)
self.ui.Log_wdg_tab2.append("<b>A) Processing SNP map file file</b>")
conv = {}
chroms = {}
for a in open(self.inputSnpMapFile_tab2):
if 'chromosome' in a.lower():
continue #.lower is used to avoid problems with capital letters
# Automatic identifier of the separator (at least 4 fields should be enough)
try:
if len(a.strip().split(',')) > 5:
line = a.strip().split(',')[:5]
nn, snpid, cro, pos, rest = line
elif len(a.strip().split('\t')) > 5:
line = a.strip().split('\t')[:5]
nn, snpid, cro, pos, rest = line
else:
line = a.strip().split()[:5]
nn, snpid, cro, pos, rest = line
except:
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR: Bad/Corrupt SNP map file! Please check the file and make sure it is an (original) Illumina SnpMap file!</b></font>"
)
conv[snpid] = (
cro, pos
) #This dictionary keeps map info related to the SNP name
chroms[cro] = 0 #This dictionary is useful only to inform the user
self.ui.Log_wdg_tab2.append(
"====> Total number of SNPs processed: <b>%s</b>" % len(conv))
self.ui.Log_wdg_tab2.append(
"====> Total number of chromosomes found: <b>%s</b>" % len(chroms))
self.ui.Log_wdg_tab2.append(
"====> List of chromosomes found: <b>%s</b><br>" %
','.join(sorted(chroms.keys())))
### Start processing the Map file first
self.ui.Log_wdg_tab2.append("<b>B) Processing FinRep file</b>")
direct_name = os.path.abspath(
os.path.dirname(str(self.inputFinRepFile_tab2)))
if '/' in direct_name: slsh = '/'
else: slsh = '\\'
#Rebuild the (full) path of the original inputFinRepFile_tab1 - for compatibility with Windows
#Open the output files
outnam = direct_name + slsh + self.OutName_tab2
outgen = open(outnam + '.ped', 'w')
outmap = open(outnam + '.map', 'w')
readfrom = False
SNPname = []
c = 0
anim = -1
snp = 0
for en, a in enumerate(open(self.inputFinRepFile_tab2)):
if 'allele1' in a.lower():
readfrom = True
if len(a.strip().split(',')) >= 3:
sep = ','
line = a.lower().strip().split(sep)
elif len(a.strip().split('\t')) >= 3:
sep = '\t'
line = a.lower().strip().split(sep)
else:
sep = ''
line = a.lower().strip().split()
### Seraching for 'SNP name' header
if not 'snp name' in line and not 'snpname' in line:
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR:</b> The header does not contain the required information: 'SNP name' or 'SNPname' (not case sensitive)<\font><br>"
)
else:
try:
SNPid_pos = line.index('snp name')
except:
SNPid_pos = line.index('snpname')
### Searching for 'Sample ID' header
if not 'sample id' in line and not 'sampleid' in line:
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR:</b> The header does not contain the required information: 'Sample ID' or 'SampleId' (not case sensitive)<\font><br>"
)
else:
try:
INDid_pos = line.index('sample id')
except:
INDid_pos = line.index('sampleid')
### Searching for the required allele coding format.
if not 'allele1 - ' + self.Chosen_allele.lower() in line:
self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR:</b> The header does not contain the chosen allele coding: Allele1 - "
+ self.Chosen_allele + '<\font><br>')
self.ui.Log_wdg_tab2.append(
"<font color=red> Header read:'<b><i>" + a +
"'</i></b></font><br>")
self.ui.Log_wdg_tab2.append(
"<font color=red> Possible causes: </font>")
self.ui.Log_wdg_tab2.append(
"<font color=red> - The requested allele format is not present in your header <i>[SOLUTION: choose an allele format that is available]</i></font>"
)
self.ui.Log_wdg_tab2.append(
"<font color=red> - The header in the Illumina header has changed (no 'Allele1 - "
+ self.Chosen_allele +
"' field is present - not case sensitive) <i>[SOLUTION: Contact [email protected], or if you know how to code in python, change the if string related to this]</i></font>"
)
self.ui.Log_wdg_tab2.append(
"<font color=red> - The FinalReport file separator is not right <i>[SOLUTION: Contact [email protected], or if you know how to code in python, change the if string related to this]</i></font>"
)
self.ui.Log_wdg_tab2.append(
"<font color=red> - The FinalReport file is in Matrix format <i>[SOLUTION: Use the 'Illumina MATRIX format' tag instead]</i></font>"
)
self.ui.Log_wdg_tab2.append(
"<font color=red> - Other <i>[SOLUTION: Contact [email protected] ... send me the header (e.g. first 10 rows) of the FinalReport file you're using]</i></font>"
)
return
else:
alle_pos1 = line.index('allele1 - ' +
self.Chosen_allele.lower())
alle_pos2 = alle_pos1 + 1
continue
if not readfrom: continue
if sep: line = a.strip().split(sep)
else: line = a.strip().split()
if alle_pos2 > len(line):
return self.ui.Log_wdg_tab2.append("<font color=red><b>ERROR:</b> Probable error in the separator.. Position of Allele2 found in "+str(alle_pos2)+", but length of line in row "+str(en)+" is "+str(len(line))+" !!</font><br>"+\
"<font color=red>Please check your choice of separator is correct and that you don't have strange fields in you FinalReport file!</font>")
snp_name = line[SNPid_pos]
if not conv.has_key(snp_name):
return self.ui.Log_wdg_tab2.append(
"<font color=red><b>ERROR:</b> SNP name: " + snp_name +
" in FinalReport file not found in SNP map file!</font><br>"
)
id_sample = line[INDid_pos]
alle1 = line[alle_pos1]
alle2 = line[alle_pos2]
if alle1 == '-': alle1 = '0'
if alle2 == '-': alle2 = '0'
c += 1
if c == 1:
snp = -1
geno = []
name = []
name.append(id_sample)
if id_sample in name:
geno.append(alle1 + ' ' + alle2)
snp += 1
if len(name) == 1:
outmap.write(
'%s %s 0 %s\n' %
(conv[snp_name][0], snp_name, conv[snp_name][1]))
SNPname.append(snp_name)
else:
if snp_name != SNPname[snp]:
return self.ui.Log_wdg_tab2.append(
"The order of the SNPs in the different individuals is consistent. Check "
+ snp_name + " and " + SNPname[snp])
else:
snp = 0
anim += 1
outgen.write('%s %s 0 0 0 -9 %s\n' %
(self.BrdCode_tab2, name[anim], ' '.join(geno)))
self.ui.Log_wdg_tab2.append('Finshed processing individual: ' +
name[anim] + ' - Total SNPs: ' +
str(len(geno)))
geno = []
geno.append(alle1 + ' ' + alle2)
name.append(id_sample)
outgen.write('%s %s 0 0 0 -9 %s\n' %
(self.BrdCode_tab2, id_sample, ' '.join(geno)))
anim += 2
self.ui.Log_wdg_tab2.append('Finshed processing individual: ' +
id_sample + ' - Total SNPs: ' +
str(len(geno)))
self.ui.Log_wdg_tab2.append(
'<br><b>====> Total number of INDIVIDUALS processed: ' +
str(anim) + '</b><br><br>')
self.ui.Log_wdg_tab2.append(
"====> Bazinga! <font color=green><b><i>Conversion run OK!</i></b></font>"
)
self.ui.Log_wdg_tab2.append(
"<font color=blue>PED file available: <b>" + outnam +
'.ped</b></font>')
self.ui.Log_wdg_tab2.append(
"<font color=blue>MAP file available: <b>" + outnam +
'.map</b></font>')
def PedFile_open_tab3(self):
self.inputPedFile_tab3 = QtGui.QFileDialog.getOpenFileName(
self, "Open PED file", "Open PED file",
self.tr("PED files (*.ped);;All files (*)"))
if self.inputPedFile_tab3.isEmpty():
self.ui.Log_wdg_tab3.append(
"<font color=red><b>WARNING:</b>PED file not selected!</font>")
else:
self.ui.Log_wdg_tab3.append(
"PED file selected <font color=green><b>OK</b></font>")
def MapFile_open_tab3(self):
self.inputMapFile_tab3 = QtGui.QFileDialog.getOpenFileName(
self, "Open MAP file", "Open MAP file",
self.tr("MAP files (*.map);;All files (*)"))
if self.inputMapFile_tab3.isEmpty():
self.ui.Log_wdg_tab3.append(
"<font color=red><b>WARNING:</b>MAP file not selected!</font>")
else:
self.ui.Log_wdg_tab3.append(
"MAP file selected <font color=green><b>OK</b></font>")
def SnpChimp_open_tab3(self):
self.inputSnpChimpFile_tab3 = QtGui.QFileDialog.getOpenFileName(
self, "Open SNPchimp_v3 file", "Open SNPchimp_v3 file",
self.tr("CSV files (*.csv);; TSV files (*.tsv);; All Files (*)"))
if self.inputSnpChimpFile_tab3.isEmpty():
self.ui.Log_wdg_tab3.append(
"<font color=red><b>WARNING:</b>SNPchimp_v3 file not selected!</font>"
)
else:
self.ui.Log_wdg_tab3.append(
"SNPchimp_v3 file selected <font color=green><b>OK</b></font>")
def InAlleleCoding_tab3(self, indice):
self.INChosen_allele = self.items1[indice]
def YesRadio_clicked(self):
self.UpdateMap = True
def NoRadio_clicked(self):
self.UpdateMap = False
def OutAlleleCoding_tab3(self, indice):
self.OUTChosen_allele = self.items2[indice]
def OutNameChange_tab3(self):
self.OutName_tab3 = self.ui.OutName_tab3.text()
def ConvertFile_run_tab3(self):
#Clear screen
self.ui.Log_wdg_tab3.clear()
#Only update map info (do not ask for ped file
if self.INChosen_allele == 'NO_allele_conv' and self.OUTChosen_allele == 'NO_allele_conv':
onlymap = True
else:
onlymap = False
if not onlymap:
if not self.inputPedFile_tab3 or self.inputPedFile_tab3.isEmpty():
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Please select a PED file!</b></font>"
)
if not self.inputMapFile_tab3 or self.inputMapFile_tab3.isEmpty():
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Please select a MAP file!</b></font>"
)
if not self.inputSnpChimpFile_tab3 or self.inputSnpChimpFile_tab3.isEmpty(
):
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Please select a SNPchimp_v3 file! (visit http://bioinformatics.tecnoparco.org/SNPchimp/)</b></font>"
)
if not str(self.inputSnpChimpFile_tab3[-3:]).lower() in ['csv', 'tsv']:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Original SNPchimp v.3 files are csv (comma separated) or tsv (tab separated).</b></font>"
)
if not self.OutName_tab3: self.OutName_tab3 = 'Output_name'
if not onlymap:
if self.INChosen_allele == self.OUTChosen_allele:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Input and Output allele coding MUST be different!</b></font>"
)
if self.INChosen_allele[:
4] == 'ILMN' and self.OUTChosen_allele[:
4] != 'ILMN':
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>"
)
if self.INChosen_allele[:
4] == 'AFFY' and self.OUTChosen_allele[:
4] != 'AFFY':
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>"
)
if self.INChosen_allele[:
2] == 'NO' and self.OUTChosen_allele[:
2] != 'NO':
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Input and Output allele coding MUST be compatible (ILMN-ILMN, AFFY-AFFY or NO-NO)!</b></font>"
)
if os.path.basename(str(
self.inputPedFile_tab3)) == self.OutName_tab3 + '.ped':
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Bad output name - Must be different from PED filename!</b></font>"
)
if os.path.basename(str(
self.inputMapFile_tab3)) == self.OutName_tab3 + '.map':
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Bad output name - Must be different from MAP filename!</b></font>"
)
### Print the options used
answer = {True: 'Yes', False: 'No'}
self.ui.Log_wdg_tab3.append(
"<b><i>iConvert software - Allele conversion and map update <i></b>"
)
self.ui.Log_wdg_tab3.append(
"<i>Software and GUI coded by E.L.Nicolazzi (PTP)</i><br>")
self.ui.Log_wdg_tab3.append("<b>PARAMETERS USED</i></b>")
self.ui.Log_wdg_tab3.append(
time.strftime("- Analysis run on %d/%m/%y at %H:%M:%S",
time.localtime()))
self.ui.Log_wdg_tab3.append(" - PLINK fmt - Ped file: <b>%s</b>" %
self.inputPedFile_tab3)
self.ui.Log_wdg_tab3.append(" - PLINK fmt - Map file: <b>%s</b>" %
self.inputMapFile_tab3)
self.ui.Log_wdg_tab3.append(" - SNPchimp v.3 file : <b>%s</b>" %
self.inputSnpChimpFile_tab3)
self.ui.Log_wdg_tab3.append(" - Input allele coding : <b>%s</b><br>" %
self.INChosen_allele)
self.ui.Log_wdg_tab3.append(" - Map update requested: <b>%s</b><br>" %
answer[self.UpdateMap])
self.ui.Log_wdg_tab3.append(" - Output allele coding: <b>%s</b>" %
self.OUTChosen_allele)
self.ui.Log_wdg_tab3.append(" - Output name : <b>%s</b><br>" %
self.OutName_tab3)
self.ui.Log_wdg_tab3.append(
"<br><b>A) Processing SNPchimp v.3 file file</b><br>")
othinfo = []
chips = {}
SNPdata = {}
formats = [0, 0]
SEP = ','
if self.UpdateMap: mapupd = {}
readfrom = False
for en, line in enumerate(open(self.inputSnpChimpFile_tab3)):
if str(self.inputSnpChimpFile_tab3[-3:]).lower() == 'csv':
SEP = ','
elif str(self.inputSnpChimpFile_tab3[-3:]).lower() == 'tsv':
SEP = '\t'
if 'chip_name' in line.lower():
readfrom = True
hlin = line.lower().strip().split(SEP)
####### FILE header and stuff checks
#Check SEPARATOR is right
if len(hlin) < 3:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNPchimp v.3 separator is not comma or tab, as assumed by the extension name - Download original SNPchimp v.3 files and try again</b></font>"
)
# Check if user choices are coherent with the infor in SNPchimp v.3
if self.INChosen_allele == 'ILMN_Top' or self.OUTChosen_allele == 'ILMN_Top':
try:
head_finder = hlin.index('alleles_a_b_top')
if self.INChosen_allele == 'ILMN_Top':
formats[0] = head_finder
else:
formats[1] = head_finder
except ValueError:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Illumina TOP allele coding</b></font>"
)
if self.INChosen_allele == 'ILMN_Forward' or self.OUTChosen_allele == 'ILMN_Forward':
try:
head_finder = hlin.index('alleles_a_b_forward')
if self.INChosen_allele == 'ILMN_Forward':
formats[0] = head_finder
else:
formats[1] = head_finder
except ValueError:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Illumina FORWARD allele coding</b></font>"
)
if self.INChosen_allele == 'AFFY_Forward' or self.OUTChosen_allele == 'AFFY_Forward':
try:
head_finder = hlin.index('alleles_a_b_affymetrix')
if self.INChosen_allele == 'AFFY_Forward':
formats[0] = head_finder
else:
formats[1] = head_finder
except ValueError:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNPchimp v.3 file does not contain the required Affymetrix FORWARD allele coding</b></font>"
)
# Check accessory information is there, otherwise stop
try:
othinfo.append(hlin.index('chip_name'))
othinfo.append(hlin.index('chromosome'))
othinfo.append(hlin.index('position'))
othinfo.append(hlin.index('snp_name'))
continue
except ValueError:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR:'chip name', 'chromosome', 'position' and 'SNP_name' header variables not found. These are always present in SNPchiMp downloaded files!</b></font>"
)
if not readfrom: continue
lista = line.strip().split(SEP)
# Keep only useful info (skip other not wanted chips)
if not chips.has_key(lista[othinfo[0]]):
chips[lista[othinfo[0]]] = 0
if 'AFFY' in self.INChosen_allele:
if not 'Bov_AffyHD' in lista[0]: continue
if 'ILMN' in self.INChosen_allele:
if 'Bov_AffyHD' in lista[0]: continue
# Keep SNPchimp map information only if required by the user.
if self.UpdateMap:
mapupd[lista[othinfo[3]]] = [
lista[othinfo[1]], lista[othinfo[2]]
]
# If INPUT allele format is AB, use AB as IN and custom allele format as OUT
if self.INChosen_allele == 'ILMN_AB' or self.INChosen_allele == 'AFFY_AB':
SNPdata[lista[othinfo[3]]] = {
'A': lista[formats[1]][0],
'B': lista[formats[1]][2]
}
# If OUTPUT allele format is AB, use AB as OUT and custom allele in format as IN
elif self.OUTChosen_allele == 'ILMN_AB' or self.OUTChosen_allele == 'AFFY_AB':
SNPdata[lista[othinfo[3]]] = {
lista[formats[0]][0]: 'A',
lista[formats[0]][2]: 'B'
}
else:
SNPdata[lista[othinfo[3]]] = {
lista[formats[0]][0]: lista[formats[1]][0],
lista[formats[0]][2]: lista[formats[1]][2]
}
if en == 0:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNPchimp file is empty!</b></font>")
if len(SNPdata) == 0:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Problem reading SNPchimp file! Probable causes: file is empty, conversion info is not available or header is incorrect</b></font>"
)
if len(chips) > 1:
self.ui.Log_wdg_tab3.append(
"<font color=orange><b>WARNING: More than 1 chip in SNPchimp file. This might result in incorrect allele conversion!</b></font>"
)
self.ui.Log_wdg_tab3.append(
"- Rows read in SNP chimp file :<b>%s</b>" % str(en + 1))
self.ui.Log_wdg_tab3.append(
"- SNPs with allele conversion information available :<b>%s</b>" %
str(len(SNPdata)))
###### Process Map file
self.ui.Log_wdg_tab3.append(
"<br><b>B) Processing PLINK MAP file and converting map information (if required)</b><br>"
)
maporder = []
convert = []
tab = False
# Create new file if new remapping is needed
if self.UpdateMap:
#Adapt slashes to unix/mac or Windows
direct_name = os.path.abspath(
os.path.dirname(str(self.inputMapFile_tab3)))
if '/' in direct_name: slsh = '/'
else: slsh = '\\'
#Rebuild the (full) path of the original inputMapFile_tab3 - for compatibility with Windows
outnammap = direct_name + slsh + self.OutName_tab3 + '.map'
remap = open(outnammap, 'w')
enmap = 0
for enm, line in enumerate(open(self.inputMapFile_tab3)):
#Check for tab or blank space spearator (only these 2 are accepted here)
if enm == 0: test = line.strip().split('\t')
if len(
test
) == 4: # Warning: this only accepts "normal" MAP files (no --map3 or other options are allowed)
linea = line.strip().split('\t')
tab = True
else:
linea = line.strip().split()
if len(linea) == 0: continue # Skips void lines
enmap += 1
snp = linea[1]
maporder.append(snp)
if not SNPdata.has_key(linea[1]):
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: SNP: " + snp +
" not found in SNPchimp file. Probable causes: you downloaded the wrong SNPchip or modified SNP names </b></font>"
)
else:
convert.append(SNPdata[linea[1]])
if self.UpdateMap:
remap.write('%s %s %s %s\n' %
(mapupd[snp][0], snp, linea[2], mapupd[snp][1]))
if enmap == 0:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: MAP file is empty!</b></font>")
self.ui.Log_wdg_tab3.append(
"- Rows read in PLINK MAP file (number of SNPs) : <b>%s</b>" %
str(enmap))
if self.UpdateMap:
self.ui.Log_wdg_tab3.append(
"<font color=blue>- MAP file updated: <b>%s</b></font>" %
outnammap)
# Process PED file (if required)
if not onlymap:
self.ui.Log_wdg_tab3.append(
"<br><b>C) Processing PLINK PED file and converting allele format</b><br>"
)
tab = False
#Get full path of PED file
#Adapt slashes to unix/mac or Windows
direct_name = os.path.abspath(
os.path.dirname(str(self.inputMapFile_tab3)))
if '/' in direct_name: slsh = '/'
else: slsh = '\\'
#Rebuild the (full) path of the original inputMapFile_tab3 - for compatibility with Windows
outnamped = direct_name + slsh + self.OutName_tab3 + '.ped'
reped = open(outnamped, 'w')
#Read ped file
enped = 0
for enped, line in enumerate(open(self.inputPedFile_tab3)):
if enped == 0:
test = line.strip().split('\t')
if len(test) == (6 + enmap * 2): tab = True
if tab: pedline = line.strip().split('\t')
else: pedline = line.strip().split()
if (enmap * 2 + 6) != len(pedline):
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: Number of SNPs in PLINK MAP ("
+ str(enmap) + ") should result in " +
str(enmap * 2 + 6) + " columns PLINK PED but found " +
str(len(pedline)) +
"<br>Check your .ped and .map files. Usually the problem is in the first line(s)...</font><br>"
)
genotypes = [
pedline[6 + x] + pedline[7 + x]
for x in range(0, (enmap * 2) - 1, 2)
]
seq = -1
genout = []
nfailed = 0
name_snps = []
for alle in genotypes:
seq += 1
alle1 = alle[0]
alle2 = alle[1]
if alle1 == '0' or alle1 == '?':
genout.append('0')
genout.append('0')
continue
try:
genout.append(convert[seq][alle1])
genout.append(convert[seq][alle2])
except KeyError:
nfailed += 1
name_snps.append(maporder[seq])
if nfailed:
return self.ui.Log_wdg_tab3.append("<font color=red><b>ERROR: Individual " + pedline[1] + " failed conversion for " + str(nfailed) + \
" SNPs [ "+', '.join(name_snps)+"]. Probably their INPUT allele coding format is not as specified</font>")
reped.write('%s %s\n' %
(' '.join(pedline[:6]), ' '.join(genout)))
if enped == 0:
return self.ui.Log_wdg_tab3.append(
"<font color=red><b>ERROR: PED file is empty!</b></font>")
self.ui.Log_wdg_tab3.append(
"- Rows read in PLINK PED file (number of animals) : <b>%s</b>"
% str(enped + 1))
self.ui.Log_wdg_tab3.append(
"<font color=blue>- PED file updated: <b>%s</b></font><br><br>"
% outnamped)
self.ui.Log_wdg_tab3.append(
'<br><font color=green><b> PROGRAM ENDS OK! </b></font>')
