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)
#!/usr/bin/env python
# coding: utf-8
# In[2]:
from Bio.Align.Applications import MafftCommandline
mafft_exe = "/usr/bin/mafft"
in_file = "/home/corinn/Documents/sequences/ITS/pops/fasta/full_renamed_minus_aw_d_og_renamed.fasta"
mafft_cline = MafftCommandline(mafft_exe, input=in_file)
mafft_cline.adjustdirection = True
mafft_cline.globalpair = True
print(mafft_cline)
stdout, stderr = mafft_cline()
output_loc = "/home/corinn/Documents/sequences/ITS/pops/fasta/"
output_prefix = in_file.split("/")[-1].split(".")[0]
output = output_loc + output_prefix + "mafft.fasta"
with open(output, 'w') as handle:
handle.write(stdout)
print("DONE")
# In[ ]:
