def findMotifsFromSeqs(seqs,Alphabet=None):
"""Runs MEME using alignment created from list of sequences.
- Returns MotifResults object.
- seqs can be Sequence objects or strings.
"""
#Make Fasta Alignment
fasta_aln = fasta_from_sequences(seqs)
#Make an Alignment object
aln = Alignment(list(FastaParser(fasta_aln)))
app = MEME(InputHandler='_input_as_multiline_string')
if Alphabet == 'dna':
app.Parameters['-dna'].on()
else:
app.Parameters['-protein'].on()
app.Parameters['-maxw'].Value = 40
app.Parameters['-nmotifs'].Value = 20
app.Parameters['-evt'].Value = 0.01
app.Parameters['-mod'].Value = "anr"
app.Parameters['-maxsize'].Value = len(fasta_aln) + 1
print app.BaseCommand
output = app(fasta_aln)
meme_results = MemeParser(output['StdOut'].readlines())
meme_results.Alignment = aln
return add_p_values(meme_results)
def findMotifsFromAlignment(aln,WorkingDir=None):
"""Runs MEME using an Alignment object.
- Returns MotifResults object
- seqs can be an Alignment object or dict
"""
#Make Fasta Alignment
fasta_aln = fasta_from_alignment(aln)
#Make sure aln is Alignment object
aln = Alignment(aln)
app = MEME(InputHandler='_input_as_lines')
output = app(fasta_aln)
meme_results = MemeParser(output['StdOut'])
meme_results.Alignment = aln
return add_p_values(meme_results)
def findMotifsFromFile(filename,Alphabet=None):
"""Runs MEME using a Fasta file.
- Returns MotifResults object.
"""
#Make an Alignment object
aln = Alignment(list(MinimalFastaParser(open(filename))))
app = MEME(InputHandler='_input_as_string')
if Alphabet == 'dna':
app.Parameters['-dna'].on()
print app.BaseCommand
output = app(filename)
print app.BaseCommand
print 'standard out'
print output['StdOut']
print 'standard error'
print output['StdErr']
meme_results = MemeParser(output['StdOut'])
meme_results.Alignment = aln
return add_p_values(meme_results)