def main():
print('##############################################################')
print(
'This script must be in a directory with the folder called "Alignment" and the fastas you want to concatenate.'
)
print('The fastas must have the extension ".fasta" or it wont work.')
print(
'The output files are the concatenated seqs as a fasta and as a phylip for raxml-ing and a logfile.'
)
print(
'The log file tells the length of the added sequence and the order in which they are added, so you can figure out your breakpoints. '
)
print('##############################################################')
path2alignments = (input("path to the purged alignments: ")).strip() + "/"
outfile = open('concat_alignment.fasta', 'w')
newAlignment = Alignment('')
# newAlignment = ''
for f in os.listdir(path2alignments):
# if re.search('.fas',f):
if f.endswith('.fas'):
tempAlignment = concat(newAlignment, path2alignments + f, 'LG')
newAlignment = tempAlignment
newAlignment.write('concat')
time.sleep(20)
makephy('concat_alignment.fasta')
