<commit_before>from Bio.Align.Applications import MuscleCommandline
from StringIO import StringIO
from Bio import AlignIO
import glob

##get list of all new fasta files

print "\n\nGetting a list of FASTA files..."
fasta_files = glob.glob("fasta/expanded-fasta/*.FASTA") # get a list of all fasta files in /fasta
file_count = len(fasta_files)
print "%s files successful found.\n" %file_count


### iterate through each file doing the following:

for f in fasta_files: 
	print "Aligning FASTA file %s" % f
	file_name = f[21:-6]
	alignment = MuscleCommandline(input=f, out="".join([file_name,"align.FASTA"]))
	stdout, stderr = alignment()
	print "Success."
<commit_msg>Added the clwstrict=True parameter to maximize compatibility. Also fixed a typo bug in the file store location.<commit_after>from Bio.Align.Applications import MuscleCommandline
from StringIO import StringIO
from Bio import AlignIO
import glob

##get list of all new fasta files

print "\n\nGetting a list of FASTA files..."
fasta_files = glob.glob("fasta/expanded-fasta/*.FASTA") # get a list of all fasta files in /fasta
file_count = len(fasta_files)
print "%s files successful found.\n" %file_count


### iterate through each file doing the following:

for f in fasta_files: 
	print "Aligning FASTA file %s" % f
	file_name = f[21:-6]
	alignment = MuscleCommandline(input=f, out="".join(["alignments/",file_name,".align"]), clwstrict=True)
	stdout, stderr = alignment()
	print "Success."

{'fraction_non_alphanumeric': 0.10775566231983527, 'fraction_numerical': 0.004118050789293068, 'mean_word_length': 4.951020408163266, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3470859', 'n_tokens_mistral': 484, 'n_tokens_neox': 461, 'n_words': 165}