for i,line in enumerate(fp):
# read pdbCode and chain
pdbFile = line.strip()
path, pdbFile = os.path.split(pdbFile)
if pdbFile[0:3]=='pdb': pdbCode=pdbFile[3:]
else: pdbCodeC=pdbFile
pdbCodeC = pdbCodeC.replace('.pdb','')
pdbCodeC = pdbCodeC.replace('.ent','')
if len(pdbCodeC) == 4:
pdbCode = pdbCodeC[0:4]
chain = pdbCode[4]
else:
pdbCode = pdbCodeC
chain = ''
if verbose: print('Reading '+pdbCode+chain)
# read pdb
pdb = Pdb()
pdb.ReadFile(filename=pdbFile, keepChainLabel=True)
pdb.PrintFasta(filename='tmp.fasta', fileOpt='a', chain=chain)
del pdb
# sequence alignment
muscle_cline = MuscleCommandline('/Users/guido/prog/muscle-3.8.31', input='tmp.fasta', out='align.fasta')
print(muscle_cline)
muscle_cline()
