def muscle_handler(cds, chromosome, est_contig,begin,end):
handle2 = open("/home/mamun/Desktop/opuntia.fasta", "w")
global value
global value1
global chrome
chrome=str(chromosome)
print "+++++++++++++++++++++++++++++++++++++++\n"
print chrome
print "+++++++++++++++++++++++++++++++++++++++\n"
# Step 1:
# Open opuntia.fasta as temporary file
# Write CDS and Chromosome one after another to that file
handle2.write(">CDS")
handle2.write("\n")
handle2.write(cds)
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
handle2.write(chrome)
handle2.write("\n")
handle2.close()
# Close the temporary file
#calling muscle_aligner() from checker.py
checker.muscle_aligner()
# calling cds_handler 1st time
# it returns CDS values after alignment
message=cds_handler()
value1=""
value=""
#TESTING validity
# sample.func()
# if beginning or end of the CDS contains any gap
# then call checker.x_and_y - here, 0 argument means I am handling CDS
# - for more details see checker.x_and_y
# remove the beginning and end gaps from the CDS sequence
# Then write the new CDS sequence, and Chromosome again to the temporary file
# - here, temporary file is opuntia.fasta
if(message[0]=="-" or message[:-1]=="-"):
value1=checker.x_and_y(0)
handle2 = open("/home/mamun/Desktop/opuntia.fasta", "w")
#chromosome=str(value)
handle2.write(">CDS")
handle2.write("\n")
handle2.write(cds)
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
print "Inside CDS and Chromosome"
print value1
handle2.write(value1)
handle2.close()
# else there will be no change in the chromosome
else:
print "CDS and Chromosome part is done!\n"
value1=chrome
#calling check() function to insert est contig into fasta file
value=checker.check(est_contig)
#aligning with all three (CDS, Chromosome, and EST Contig)
## checker.muscle_aligner()
print "\nHandler Number: 2\n"
#time.sleep(4)
# message1=cds_handler()
# argument 1 means, we are handling EST Contig in checker.x_and_y
# test=checker.x_and_y(1)
print "*********************************\n"
print "TESTing.........................\n"
# print test
#TESTING validity
# sample.func()
# if(message1[0]=="-" or message1[:-1]=="-"):
#value=checker.x_and_y(1)
print value
os.remove("/home/mamun/Desktop/opuntia.fasta")
# else:
# print "Life goes on!"
#time.sleep(3)
handle2 = open("/home/mamun/Desktop/opuntia.fasta", "w")
handle2.write(">CDS")
handle2.write("\n")
handle2.write(cds)
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
if (value1==""):
handle2.write(str(chrome))
else:
handle2.write(str(value1))
handle2.write("\n")
handle2.write(">"+est_contig)
handle2.write("\n")
print "Inside EST part"
print "Chrome......................"
print value1
print "EST.........................."
print value
#Getting first occurane position of ATG
if value.find('ATG'):
position=value.find('ATG')
temp_value=value[position:]
handle2.write(str(temp_value))
value=str(temp_value)
else:
handle2.write(str(value))
handle2.close()
checker.muscle_aligner()
print "COMPLETE ALIGNMENT is DONE"
message1=cds_handler()
if(message1[0]=="-" or message1[:-1]=="-"):
value=checker.x_and_y(1)
print value
print "Getting perfect EST\n"
#time.sleep(5)
handle2 = open("/home/mamun/Desktop/opuntia.fasta", "w")
handle2.write(">CDS")
handle2.write("\n")
handle2.write(cds)
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
if (value1==""):
handle2.write(str(chrome))
else:
handle2.write(str(value1))
handle2.write("\n")
handle2.write(">"+est_contig)
handle2.write("\n")
handle2.write(str(value))
handle2.close()
checker.muscle_aligner()
else:
print "We are really done!\n"
#time.sleep(3)
## Working with Amino Acid Alignment
# End of iteration and alignment
# Copying temp files to seperate Directory
shutil.copy2('opuntia.fasta','/home/mamun/Desktop/Output/'+est_contig+'.fasta')
shutil.copy2('opuntia.aln','/home/mamun/Desktop/Output/'+est_contig+'.aln')
handle2 = open("/home/mamun/Desktop/opuntia.fasta", "w")
coding_dna1 = Seq(cds, IUPAC.ambiguous_dna)
handle2.write(">CDS")
handle2.write("\n")
handle2.write(str(coding_dna1.translate()))
handle2.write("\n")
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
if (value1==""):
coding_dna2 = Seq(chrome, IUPAC.ambiguous_dna)
handle2.write(str(coding_dna2.translate()))
handle2.write("\n")
handle2.write("\n")
else:
coding_dna2 = Seq(value1, IUPAC.ambiguous_dna)
handle2.write(str(coding_dna2.translate()))
handle2.write("\n")
handle2.write("\n")
handle2.write(">"+est_contig)
handle2.write("\n")
coding_dna3 = Seq(value, IUPAC.ambiguous_dna)
if (coding_dna3!=""):
handle2.write(str(coding_dna3.translate()))
else:
handle2.write("")
handle2.close()
checker.muscle_aligner()
# Copyting current file to system!
shutil.copy2('opuntia.fasta','/home/mamun/Desktop/Output/'+est_contig+'_acid.fasta')
shutil.copy2('opuntia.aln','/home/mamun/Desktop/Output/'+est_contig+'_acid.aln')
def main():
#print cds.translate(cds=True)
#chrome=work(cds, dna)
global cds
global dna
global chrome
global CDS
global CHROME
global tracker_cds
global tracker_dna
path = "/home/mamun/Desktop/Output_test/"
for infile in glob.glob( os.path.join(path, '*.fasta') ):
handle1 = open(infile, "r")
parsedfasta = SeqIO.parse(handle1, "fasta")
for i in parsedfasta:
if (i.id=="CDS"):
cds = Seq(str(i.seq),IUPAC.ambiguous_dna)
print "CDS is", cds
elif (i.id=="Chromosome"):
dna = Seq(str(i.seq), IUPAC.ambiguous_dna)
print "DNA is", dna
else:
campoletis = Seq(str(i.seq), IUPAC.ambiguous_dna)
print campoletis
## making empty list!!
## for the global variables!!
tracker_cds = 0
tracker_dna = 0
# chrome = ""
pos = 0
work(cds, dna)
#if(chrome[-7:]!=(cds[-7:]) and (len(chrome)<len(cds))):
# try:
# pos = chrome[-7:].find(cds)
# chrome += cds[pos:]
# except:
# pass
print "New DNA", dna
print "New Chromosome", chrome
print "********************"
print "current file is: " + infile
print "** Working with ALIGNMENT file **"
handle2 = open("opuntia1.fasta", "w")
handle2.write(">CDS")
handle2.write("\n")
handle2.write(str(cds))
handle2.write("\n")
handle2.write(">Chromosome")
handle2.write("\n")
handle2.write(str(chrome))
#handle2.write("\n")
#handle2.write(">EST")
#handle2.write("\n")
#handle2.write(str(campoletis))
handle2.close()
checker.muscle_aligner()
## Checking whether there is a stop codon or not
## at the very beginning of the EST Contig!
## My hypothesis is to check within the first 20 seq
temp = Seq(str(campoletis), IUPAC.ambiguous_dna)
i=0
while(i<3):
temp1 = temp[i:].translate()
value = temp1[0:20].find("*")
if (value==-1):
break
else:
i+=1
print CDS
print chrome
handle4 = open("manual.aln", "w")
handle4.write(">CDS")
handle4.write("\n")
handle4.write(str(CDS))
handle4.write("\n")
handle4.write(">Chromosome")
handle4.write("\n")
handle4.write(str(CHROME))
handle4.close()
handle3 = open("opuntia2.aln", "w")
handle3.write(">EST")
handle3.write("\n")
handle3.write(str(campoletis[i:]))
handle3.close()
print "About to end!!"
## Editing for profile-profile alignment
os.system("muscle -profile -in1 manual.aln -in2 opuntia2.aln -out combinedAlignment.fasta -maxmb 15000")
#muscle_cline=MuscleCommandline(input="opuntia1.fasta", out="opuntia1.afa")
#print muscle_cline
#align=os.system(str(muscle_cline))
#checker.muscle_aligner()
shutil.copy2('combinedAlignment.fasta', infile+'.aln')
#time.sleep(4)
chrome = ""
print "------------End of main---------------"
