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addSeqToPrimers.py
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import argparse,xlrd,os
import xlsxwriter as xls
thisDir=os.path.dirname(os.path.realpath(__file__))+'/'
parser=argparse.ArgumentParser(description='This script adds tags to primers for NGS')
parser.add_argument('--input','-in',
dest='input',type=str,
help='input XLS-file with designed primers')
parser.add_argument('--tags-file','-tags',
dest='tagsFile',type=str,
help='text file with tags that we want to add to each primer. Default: "'+thisDir+'kplex_for_primers.txt"',
default=thisDir+'kplex_for_primers.txt')
parser.add_argument('--add-cells','-cells',
dest='addCells',action='store_true',
help='use this argument, if you want to add cell ID for the synthesis in plate')
args=parser.parse_args()
try:
file=open(args.tagsFile)
except FileNotFoundError:
print('ERROR! File with tags was not found:',args.tagsFile)
exit(0)
addSeq=[]
for string in file:
if 'For ' in string:
continue
addSeq.append(string.replace('\n','').replace('\r',''))
file.close()
wb=xlrd.open_workbook(args.input)
ws=wb.sheet_by_index(0)
primerNames=[]
primers=[]
wbw=xls.Workbook(args.input[:-4]+'_with_seq.xls')
wswAll=wbw.add_worksheet('All_Primers')
wsws={'All_Primers':wswAll}
wswRowNum={'All_Primers':1}
wswLetters={'All_Primers':ord('A')}
wswNums={'All_Primers':1}
wswAll.write_row(0,0,['Primer',"5' to 3' sequence"])
wswAll.set_column(0,0,25)
wswAll.set_column(1,1,60)
for i in range(ws.nrows):
row=ws.row_values(i)
if i==0 or row[0]=='':
continue
if row[17]!='':
multNum=str(int(row[17]))
if multNum not in wsws.keys():
# Check if all previous multiplexes are absent, too
for i in range(1,int(multNum)):
if str(i) not in wsws.keys():
wsw=wbw.add_worksheet(str(i))
wsws[str(i)]=wsw
wswRowNum[str(i)]=1
wswLetters[str(i)]=ord('A')
wswNums[str(i)]=1
wsw.write_row(0,0,['Primer',"5' to 3' sequence"])
wsw.set_column(0,0,25)
wsw.set_column(1,1,60)
wsw=wbw.add_worksheet(multNum)
wsws[multNum]=wsw
wswRowNum[multNum]=1
wswLetters[multNum]=ord('A')
wswNums[multNum]=1
wsw.write_row(0,0,['Primer',"5' to 3' sequence"])
wsw.set_column(0,0,25)
wsw.set_column(1,1,60)
else:
wsw=wsws[multNum]
if row[1]!='':
wswAll.write_row(wswRowNum['All_Primers'],0,[row[3]+'_F',
addSeq[0]+row[1]])
if args.addCells:
wswAll.write(wswRowNum['All_Primers'],2,chr(wswLetters['All_Primers'])+str(wswNums['All_Primers']))
wswRowNum['All_Primers']+=1
if row[17]!='':
wsw.write_row(wswRowNum[multNum],0,[row[3]+'_F',
addSeq[0]+row[1]])
if args.addCells:
wsw.write(wswRowNum[multNum],2,chr(wswLetters[multNum])+str(wswNums[multNum]))
wswRowNum[multNum]+=1
if row[2]!='':
wswAll.write_row(wswRowNum['All_Primers'],0,[row[3]+'_R',
addSeq[1]+row[2]])
if args.addCells:
wswAll.write(wswRowNum['All_Primers'],2,chr(wswLetters['All_Primers'])+str(wswNums['All_Primers']+1))
wswRowNum['All_Primers']+=1
if row[17]!='':
wsw.write_row(wswRowNum[multNum],0,[row[3]+'_R',
addSeq[1]+row[2]])
if args.addCells:
wsw.write(wswRowNum[multNum],2,chr(wswLetters[multNum])+str(wswNums[multNum]+1))
wswRowNum[multNum]+=1
if args.addCells:
if wswLetters['All_Primers']==ord('H'):
wswLetters['All_Primers']=ord('A')
if wswNums['All_Primers']==11:
wswNums['All_Primers']=1
else:
wswNums['All_Primers']+=2
else:
wswLetters['All_Primers']+=1
if row[17]!='':
if wswLetters[multNum]==ord('H'):
wswLetters[multNum]=ord('A')
if wswNums[multNum]==11:
wswNums[multNum]=1
else:
wswNums[multNum]+=2
else:
wswLetters[multNum]+=1
# If there is also external primers
if len(wb.sheet_names())>1:
ws=wb.sheet_by_index(1)
for i in range(ws.nrows):
row=ws.row_values(i)
if i==0 or row[0]=='':
continue
if row[18]!='':
multNum=str(int(row[18]))
if row[1]!='':
wswAll.write_row(wswRowNum['All_Primers'],0,[row[3]+'_F',
addSeq[0]+row[1]])
if args.addCells:
wswAll.write(wswRowNum['All_Primers'],2,chr(wswLetters['All_Primers'])+str(wswNums['All_Primers']))
wswRowNum['All_Primers']+=1
if row[18]!='':
wsw.write_row(wswRowNum[multNum],0,[row[3]+'_F',
addSeq[0]+row[1]])
if args.addCells:
wsw.write(wswRowNum[multNum],2,chr(wswLetters[multNum])+str(wswNums[multNum]))
wswRowNum[multNum]+=1
if row[2]!='':
wswAll.write_row(wswRowNum['All_Primers'],0,[row[3]+'_R',
addSeq[1]+row[2]])
if args.addCells:
wswAll.write(wswRowNum['All_Primers'],2,chr(wswLetters['All_Primers'])+str(wswNums['All_Primers']+1))
wswRowNum['All_Primers']+=1
if row[18]!='':
wsw.write_row(wswRowNum[multNum],0,[row[3]+'_R',
addSeq[1]+row[2]])
if args.addCells:
wsw.write(wswRowNum[multNum],2,chr(wswLetters[multNum])+str(wswNums[multNum]+1))
wswRowNum[multNum]+=1
if args.addCells:
if wswLetters['All_Primers']==ord('H'):
wswLetters['All_Primers']=ord('A')
if wswNums['All_Primers']==11:
wswNums['All_Primers']=1
else:
wswNums['All_Primers']+=2
else:
wswLetters['All_Primers']+=1
if row[18]!='':
if wswLetters[multNum]==ord('H'):
wswLetters[multNum]=ord('A')
if wswNums[multNum]==11:
wswNums[multNum]=1
else:
wswNums[multNum]+=2
else:
wswLetters[multNum]+=1
wbw.close()
print('NGS-PrimerPlex finished!')