INNER CODE UNIT · Python
MUSCLE
TobyBaril/EarlGrey · scripts/extract_align.py:88
def MUSCLE(TOALIGN):
TOALIGNPREFIX = os.path.splitext(TOALIGN)[0]
SOFTWARE = '/usr/bin'
subprocess.check_call(SOFTWARE + '/muscle -in {} -out {}'.format('catTEfiles/' + TOALIGN, 'muscle/' + TOALIGNPREFIX + '.fa'), shell=True)
##Consensus generation function
def CONSENSUSGEN(ALIGNED):
FILEPREFIX = os.path.splitext(ALIGNED)[0]
SOFTWARE = '/home/toby/Programs/'
if TRIMAL == 'y':
subprocess.run(SOFTWARE + 'trimal/source/trimal -in {} -gt 0.6 -cons 60 -fasta -out {}'.format('muscle/' + ALIGNED, 'muscle/' + FILEPREFIX + '_trimal.fa'), shell=True)
subprocess.run(SOFTWARE + 'EMBOSS-6.6.0/emboss/cons -sequence muscle/' + FILEPREFIX + '_trimal.fa -outseq muscle/' + FILEPREFIX + '_cons.fa -name ' + FILEPREFIX + '_cons -plurality 3 -identity 3', shell=True)
subprocess.run('cat {} {} >{}'.format('muscle/' + FILEPREFIX + '_trimal.fa', 'muscle/' + FILEPREFIX + '_cons.fa', 'consensusfiles/' + FILEPREFIX + '_cons.fa'), shell=True)
if TRIMAL == 'n':
# subprocess.run(SOFTWARE + 'trimal/source/trimal -in {} -gt 0.6 -cons 60 -fasta -out {}'.format('muscle/' + ALIGNED, 'muscle/' + FILEPREFIX + '_trimal.fa'), shell=True)
subprocess.run(SOFTWARE + 'EMBOSS-6.6.0/emboss/cons -sequence muscle/' + ALIGNED + ' -outseq muscle/' + FILEPREFIX + '_cons.fa -name ' + FILEPREFIX + '_cons -plurality 3 -identity 3', shell=True)
subprocess.run('cat {} {} >{}'.format('muscle/' + ALIGNED, 'muscle/' + FILEPREFIX + '_cons.fa', 'consensusfiles/' + FILEPREFIX + '_cons.fa'), shell=True)