def run_mafft(mafftdir, outputDir, fastaFileList, outputFileNameList,
startNum, endNum, algorithm):
# Set up
import platform
for i in range(startNum, endNum):
# Run MAFFT
if platform.system() == 'Windows':
mafft_cline = MafftCommandline(os.path.join(
mafftdir, 'mafft.bat'),
input=fastaFileList[i])
else:
mafft_cline = MafftCommandline(os.path.join(mafftdir, 'mafft'),
input=fastaFileList[i])
if algorithm != None:
if algorithm.lower() == 'genafpair':
mafft_cline.genafpair = True
elif algorithm.lower() == 'localpair':
mafft_cline.localpair = True
elif algorithm.lower() == 'globalpair':
mafft_cline.globalpair = True
stdout, stderr = mafft_cline()
if stdout == '':
raise Exception('MAFFT error text below' + str(stderr))
# Process MAFFT output
stdout = stdout.split('\n')
while stdout[-1] == '\n' or stdout[-1] == '' or stdout[
-1] == 'Terminate batch job (Y/N)?\n': # Remove junk, sometimes MAFFT will have the 'Terminate ...' line
del stdout[-1]
stdout = '\n'.join(stdout)
# Create output alignment files
with open(outputFileNameList[i], 'w') as fileOut:
fileOut.write(stdout)
os.mkdir("Alignments")
directory = './Extracted_Sequences'
i = 1
for filename in os.listdir(directory):
#Check that we are using only fasta files and setting mafft parameters
if filename.endswith(".fasta"):
print(filename, "(", i, "/", Blast_bed['query'].nunique(), ")")
in_file = os.path.join(directory, filename)
mafft_cline = MafftCommandline(input=in_file)
mafft_cline.thread = int(NTHREADS)
mafft_cline.adjustdirection = True
if MAFFT_OPT == 'einsi':
mafft_cline.genafpair = True
mafft_cline.maxiterate = 1000
stdout, stderr = mafft_cline()
i += 1
with open("./Alignments/%s.mafft" % filename, "w") as output:
output.write(stdout)
align = AlignIO.read("./Alignments/%s.mafft" % filename, "fasta")
print("########DONE")
############################################################################################################
#----------------------------------------------CLEAN-------------------------------------------------------#
############################################################################################################
print("Cleaning alignments...")