def evol_refine(msa, **kwargs):
from prody import parseMSA, refineMSA, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_refined' + ext
writeMSA(outname, refineMSA(parseMSA(msa), **kwargs), **kwargs)
LOGGER.info('Refined MSA is written in file: ' + outname)
def evol_refine(msa, **kwargs):
import prody
from prody import parseMSA, refineMSA, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_refined' + ext
writeMSA(outname, refineMSA(parseMSA(msa), **kwargs), **kwargs)
LOGGER.info('Refined MSA is written in file: ' + outname)
def evol_refine(msa, **kwargs):
import prody
from prody import parseMSA, refineMSA, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get("outname")
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == ".gz":
outname, _ = splitext(msa)
outname += "_refined" + ext
writeMSA(outname, refineMSA(parseMSA(msa), **kwargs), **kwargs)
LOGGER.info("Refined MSA is written in file: " + outname)
def evol_merge(*msa, **kwargs):
import prody
from prody import parseMSA, mergeMSA, LOGGER, writeMSA, MSAFile
from prody.sequence.msafile import MSAEXTMAP
from os.path import splitext
if len(msa) < 2:
raise ValueError('multiple msa filenames must be specified')
msaobj = []
try:
msaobj = [parseMSA(fn) for fn in msa]
except:
raise IOError('failed to parse {0}'.format(fn))
msafile = MSAFile(msa[0])
format = kwargs.get('format') or msafile.format
outname = kwargs.get('outname') or (msafile.getTitle() + '_merged' +
MSAEXTMAP[msafile.format])
writeMSA(outname, mergeMSA(*msaobj), **kwargs)
LOGGER.info('Merged MSA is saved as: {0}'.format(outname))
def evol_filter(msa, *word, **kwargs):
import prody
from prody import MSAFile, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_filtered' + ext
single = len(word) == 1
if single:
word = word[0]
if kwargs.get('startswith', False):
if single:
filter = lambda label, seq, word=word: label.startswith(word)
elif kwargs.get('endswith', False):
if single:
filter = lambda label, seq, word=word: label.endswith(word)
elif kwargs.get('contains', False):
if single:
filter = lambda label, seq, word=word: word in label
elif kwargs.get('equals', False):
if single:
filter = lambda label, seq, word=word: word == label
else:
filter = lambda label, seq, word=set(word): label in word
else:
raise TypeError('one of startswith, endswith, contains, or equals '
'must be specified')
msa = MSAFile(msa,
filter=filter,
filter_full=kwargs.get('filter_full', False))
LOGGER.info('Filtered MSA is written in file: ' +
writeMSA(outname, msa, **kwargs))
def evol_filter(msa, *word, **kwargs):
import prody
from prody import MSAFile, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get('outname')
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == '.gz':
outname, _ = splitext(msa)
outname += '_filtered' + ext
single = len(word) == 1
if single:
word = word[0]
if kwargs.get('startswith', False):
if single:
filter = lambda label, seq, word=word: label.startswith(word)
elif kwargs.get('endswith', False):
if single:
filter = lambda label, seq, word=word: label.endswith(word)
elif kwargs.get('contains', False):
if single:
filter = lambda label, seq, word=word: word in label
elif kwargs.get('equals', False):
if single:
filter = lambda label, seq, word=word: word == label
else:
filter = lambda label, seq, word=set(word): label in word
else:
raise TypeError('one of startswith, endswith, contains, or equals '
'must be specified')
msa = MSAFile(msa, filter=filter,
filter_full=kwargs.get('filter_full', False))
LOGGER.info('Filtered MSA is written in file: ' +
writeMSA(outname, msa, **kwargs))
def evol_filter(msa, *word, **kwargs):
import prody
from prody import MSAFile, writeMSA, LOGGER
from os.path import splitext
outname = kwargs.get("outname")
if outname is None:
outname, ext = splitext(msa)
if ext.lower() == ".gz":
outname, _ = splitext(msa)
outname += "_filtered" + ext
single = len(word) == 1
if single:
word = word[0]
if kwargs.get("startswith", False):
if single:
filter = lambda label, seq, word=word: label.startswith(word)
elif kwargs.get("endswith", False):
if single:
filter = lambda label, seq, word=word: label.endswith(word)
elif kwargs.get("contains", False):
if single:
filter = lambda label, seq, word=word: word in label
elif kwargs.get("equals", False):
if single:
filter = lambda label, seq, word=word: word == label
else:
filter = lambda label, seq, word=set(word): label in word
else:
raise TypeError("one of startswith, endswith, contains, or equals " "must be specified")
msa = MSAFile(msa, filter=filter, filter_full=kwargs.get("filter_full", False))
LOGGER.info("Filtered MSA is written in file: " + writeMSA(outname, msa, **kwargs))
def testFasta(self):
filename = writeMSA(join(TEMPDIR, 'test.fasta.gz'), FASTA)
fasta = list(MSAFile(pathDatafile(filename)))
self.assertListEqual(list(FASTA), list(fasta))
if os.path.isfile(filename):
os.remove(filename)
def testSelex(self):
filename = writeMSA(join(TEMPDIR, 'test.slx'), SELEX)
selex = parseMSA(pathDatafile(filename))
self.assertListEqual(list(SELEX), list(selex))
if os.path.isfile(filename):
os.remove(filename)
def testFasta(self):
filename = writeMSA(join(TEMPDIR, 'test.fasta.gz'), FASTA)
fasta = list(MSAFile(pathDatafile(filename)))
self.assertListEqual(list(FASTA), list(fasta))
if os.path.isfile(filename):
os.remove(filename)
def testSelex(self):
filename = writeMSA(join(TEMPDIR, 'test.slx'), SELEX)
selex = parseMSA(pathDatafile(filename))
self.assertListEqual(list(SELEX), list(selex))
if os.path.isfile(filename):
os.remove(filename)
import prody.sequence as sequence
import prody
import matplotlib.pyplot as plt
alignment = prody.MSAFile("pkinase.fasta")
#get positions -> by hand for now
positions = [72, 83, 117, 119, 194, 251, 354, 355, 357, 429, 432]
#user alignSequenceToMSA instead to derive positions automatically
#set up webservice to get correspondance between MSA position and a particular PDB structure
alignment.setSlice(positions)
prody.writeMSA("test.fasta", alignment)
pa = prody.parseMSA("pocket_type1.fasta")
labs = pa.getLabels()
seqidmatrix = prody.buildSeqidMatrix(pa)
scamatrix = prody.buildSCAMatrix(pa)
tree = prody.calcTree(names=labs, distance_matrix=seqidmatrix)
plt.figure()
show = prody.showTree(tree, format='plt')