<commit_before>import subprocess
from os.path import splitext

def clustalo( fasta_file, threads=1 ) :
    
    base = splitext(fasta_file)[0]
    alignment_file = base + '_clustalo.fasta'
    log_file = base + '_clustalo.log'

    args = ['clustalo', '-v',
            '-i', fasta_file,
            '--threads=' + str(threads),
            '-o', alignment_file,
            '-l', log_file ]

    return subprocess.check_output( args )<commit_msg>force fasta output for clustalo<commit_after>import subprocess
from os.path import splitext

def clustalo( fasta_file, threads=1 ) :
    
    base = splitext(fasta_file)[0]
    alignment_file = base + '_clustalo.fasta'
    log_file = base + '_clustalo.log'

    args = ['clustalo', '-v',
            '-i', fasta_file,
            '--outfmt=fasta',
            '--threads=' + str(threads),
            '-o', alignment_file,
            '-l', log_file ]

    return subprocess.check_output( args )
{'fraction_non_alphanumeric': 0.1337579617834395, 'fraction_numerical': 0.004246284501061571, 'mean_word_length': 2.4166666666666665, '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': '7099199', 'n_tokens_mistral': 318, 'n_tokens_neox': 310, 'n_words': 69}