def _ID(a):
r"""The function saves ids in a list.
Arguments:
-a- alignment file
Example:
>>> with open("alignment.fasta", "w") as alignment_file:
... alignment_file.write(">ENSG0997"+"\n"+"TGA"+"\n"+">ENSG1233"+"\n"+"AAA")
>>> import os
>>> from Bio import AlignIO
>>> ID = _ID("alignment.fasta")
>>> ID
['ENSG0997','ENSG1233']"""
fileName, fileExtension = os.path.splitext(a)
if fileExtension == ".phylip":
try:
l = list(AlignIO.read(a,"phylip"))
except (ValueError):
l = list(AlignIO.read(a,"phylip-relaxed"))
except:
pass
elif fileExtension == ".fasta":
l = list(AlignIO.read(a,"fasta"))
else:
raise Exception("Wrong format. Choose accepted format.")
ID = [str(l[j].id) for j in range(0,len(l))]
return(ID)
def fas_to_nex(infile,outfile,protein=True): '''Convert fasta infile to nexus and write to outfile. Uses BioPython''' if protein: aln = AlignIO.read(infile,'fasta',alphabet=Gapped(IUPAC.extended_protein)) else: aln = AlignIO.read(infile,'fasta',alphabet=Gapped(IUPAC.unambiguous_dna)) AlignIO.write(aln,outfile,'nexus')
def main_origin(args, stdout, stderr) :
if not os.path.isdir(args.geneTable) :
stderr.write("Loading gene table\n")
geneTable = pygenes.GeneTable()
geneTable.loadTable(args.geneTable)
for inputFile in args.alnFiles :
aln = AlignIO.read(inputFile, "fasta")
origins = collections.defaultdict(lambda : [])
for seq in aln :
origins[geneTable.geneId(seq.description).recordId].append(seq.description)
multipleOrigins = [(x,y) for (x,y) in origins.items() if len(y) > 1]
for (x,y) in multipleOrigins :
stdout.write(inputFile + "\t" + str(x) + "\t" + str(len(y)) + "\t" +
";".join(y) + "\n")
else :
n = str(len(args.alnFiles))
for (i, inputFile) in enumerate(args.alnFiles) :
stderr.write("Processing file " + str(i+1) + "/" + n + "\n")
geneTableFile = os.path.join(args.geneTable, os.path.basename(inputFile) + ".geneTable")
geneTable = pygenes.GeneTable()
geneTable.loadTable(geneTableFile)
aln = AlignIO.read(inputFile, "fasta")
origins = collections.defaultdict(lambda : [])
for seq in aln :
origins[geneTable.geneId(seq.description).recordId].append(seq.description)
multipleOrigins = [(x,y) for (x,y) in origins.items() if len(y) > 1]
for (x,y) in multipleOrigins :
stdout.write(inputFile + "\t" + str(x) + "\t" + str(len(y)) + "\t" +
";".join(y) + "\n")
def get_second_seq(self):
start_buf, end_buf = self.second_seq_text_buffer.get_bounds()
seq_direct = self.second_seq_text_buffer.get_text(start_buf, end_buf, False).upper()
seq_file = self.second_seq_file_entry.get_text()
seq_online = self.second_seq_online_entry.get_text()
if (seq_direct):
self.second_seq = seq_direct
if (seq_file):
align = AlignIO.read(seq_file, self.file_type)
self.second_seq = str(align[0].seq)
if (seq_online):
if self.file_type == 'fasta':
f_type = 'fasta'
elif self.file_type == 'genbank':
f_type = 'gb'
url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id='+seq_online+'&rettype='+f_type+''
f = urllib.request.urlopen(url)
result = f.read().decode('utf-8')
if len(result) < 10:
self.show_message("Error", "Failed to retrieve the second sequence (please check your ID Number)")
return
else:
file_name = "cache/"+seq_online+"."+self.file_type+""
file = open(file_name, "w")
file.write(result)
file.close()
align = AlignIO.read(file_name, self.file_type)
self.second_seq = str(align[0].seq)
def concat_sequences(file1, file2, file3, file4, file5, file6, file7, file8, file9, file10):
sequences1 = AlignIO.read(file1, 'fasta')
sequences2 = AlignIO.read(file2, 'fasta')
sequences3 = AlignIO.read(file3, 'fasta')
sequences4 = AlignIO.read(file4, 'fasta')
sequences5 = AlignIO.read(file5, 'fasta')
sequences6 = AlignIO.read(file6, 'fasta')
sequences7 = AlignIO.read(file7, 'fasta')
sequences8 = AlignIO.read(file8, 'fasta')
sequences9 = AlignIO.read(file9, 'fasta')
sequences10 = AlignIO.read(file10, 'fasta')
complete_sequences = []
for sequence1 in sequences1:
strain_name = util.get_strain_name(sequence1)
sequence2 = util.get_matching_sequence(sequences2, strain_name=strain_name)
sequence3 = util.get_matching_sequence(sequences3, strain_name=strain_name)
sequence4 = util.get_matching_sequence(sequences4, strain_name=strain_name)
sequence5 = util.get_matching_sequence(sequences5, strain_name=strain_name)
sequence6 = util.get_matching_sequence(sequences6, strain_name=strain_name)
sequence7 = util.get_matching_sequence(sequences7, strain_name=strain_name)
sequence8 = util.get_matching_sequence(sequences8, strain_name=strain_name)
sequence9 = util.get_matching_sequence(sequences9, strain_name=strain_name)
sequence10 = util.get_matching_sequence(sequences10, strain_name=strain_name)
if (sequence2 and sequence3 and sequence4 and sequence5 and sequence6 and sequence7 and sequence8 and sequence9 and sequence10):
complete_sequence=[]
complete_sequence.append(util.get_strain_name(sequence1))
complete_sequence.append(sequence1.seq+sequence2.seq+sequence3.seq+sequence4.seq+sequence5.seq+sequence6.seq+sequence7.seq+sequence8.seq+sequence9.seq+sequence10.seq)
complete_sequences.append(complete_sequence)
return complete_sequences
def main():
"""
The main function
"""
parser = cmdline_parser()
args = parser.parse_args()
#read in the alignment
aln_viral = AlignIO.read(open(args.viral, 'r'), "fasta")
aln_gta = AlignIO.read(open(args.gta, 'r'), "fasta")
aln_viral_stereo = stereo_score(aln_viral)
aln_gta_stereo = stereo_score(aln_gta)
#convert to tuples
viral_stereo_posi = [(i, j) for i, j in enumerate(aln_viral_stereo)]
gta_stereo_posi = [(i, j) for i, j in enumerate(aln_viral_stereo)]
#convert to pandas dataframe
viral_stereo_posi_df = pd.DataFrame.from_records(viral_stereo_posi)
gta_stereo_posi_df = pd.DataFrame.from_records(gta_stereo_posi)
#add column headers
viral_stereo_posi_df.columns = ['position', 'score']
gta_stereo_posi_df.columns = ['position', 'score']
#plot the figures
fig = plt.figure(figsize=(30, 10))
plt.bar(viral_stereo_posi_df['position'], viral_stereo_posi_df['score'])
plt.bar(ta_stereo_posi_df['position'], -gta_stereo_posi_df['score'], color='r')
plt.axis([0, 700, -1.2, 1.2])
savefig('args.output')
def load_tree(seqfname):
"""Load an alignment, build & prep a tree, return the tree object."""
if seqfname.endswith('.aln'):
aln = AlignIO.read(seqfname, 'clustal')
elif seqfname.endswith('.fasta'):
# Run MAFFT quickly
alndata = subprocess.check_output(['mafft', '--quiet', '--auto',
seqfname])
aln = AlignIO.read(StringIO(alndata), 'fasta')
else:
raise ValueError("Input sequences must be a Clustal alignment (.aln) "
"or unaligned FASTA (.fasta)")
# Use conserved (less-gappy) blocks to build the tree
aln = alnutils.blocks(aln, 0.4)
with tempfile.NamedTemporaryFile(mode='w') as tmp:
AlignIO.write(aln, tmp, 'fasta')
tmp.flush()
treedata = subprocess.check_output(['fasttree',
'-pseudo', '-gamma', '-wag',
tmp.name])
tree = Phylo.read(StringIO(treedata), 'newick')
# Collapse weakly supported splits
confs = [c.confidence
for c in tree.find_clades()
if c.confidence is not None]
# ENH: accept min_confidence as an option
min_confidence = math.fsum(confs) / len(confs)
tree.collapse_all(lambda c: c.confidence < min_confidence)
tree.ladderize(reverse=True)
tree.root.branch_length = 0.0
return tree
def design_primers(source_dir, target_dir, settings, logfile):
print("\nDesigning primers using PriFi...\n", file=logfile)
# get rid of previous files
utils.purge_dir(target_dir)
aln_files = glob(os.path.join(source_dir, '*.fasta'))
print("\tChecking for empty alignments...", file=logfile)
for f in aln_files:
try:
align = AlignIO.read(f, 'fasta')
filename = os.path.basename(f)
shutil.copyfile(f, os.path.join(target_dir, filename))
except Exception:
print("[WARNING] Empty alignment file?! (%s)" % f, file=logfile)
continue
# call PriFi for actual primer design
for f in glob(os.path.join(target_dir, '*.fasta')):
aln = AlignIO.read(f, 'fasta')
summary = AlignInfo.SummaryInfo(aln)
l = aln.get_alignment_length()
primerpairs = prifipy.findprimers(0, list(aln), summary, l, settings, logfile)
if not primerpairs:
print("%s: No valid primer pair found" % f, file=logfile)
else:
print('%s: Found %d primer pair suggestions. Writing primer files:' % (f, len(primerpairs)), file=logfile)
prifipy.writePrimersToFiles(f, primerpairs, 1, logfile)
def conversion(self, prank_number, prank_ext, format):
"""Get PRANK to do a conversion, and check it with SeqIO."""
filename = "%s.%s" % (self.output, prank_ext)
if os.path.isfile(filename):
os.remove(filename)
cmdline = PrankCommandline(prank_exe, d=self.input, convert=True, f=prank_number, o='"%s"' % self.output)
self.assertEqual(
str(cmdline),
prank_exe + " -d=%s" % self.input + ' -o="%s"' % self.output + " -f=%i" % prank_number + " -convert",
)
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
child = subprocess.Popen(
str(cmdline), stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=(sys.platform != "win32")
)
return_code = child.wait()
self.assertEqual(return_code, 0)
message = child.stdout.read().strip()
self.assert_(("PRANK: converting '%s' to '%s'" % (self.input, filename)) in message, message)
self.assertEqual(child.stderr.read(), "")
self.assert_(os.path.isfile(filename))
old = AlignIO.read(open(self.input), "fasta")
# Hack...
if format == "phylip":
for record in old:
record.id = record.id[:10]
new = AlignIO.read(open(filename), format)
assert len(old) == len(new)
for old_r, new_r in zip(old, new):
self.assertEqual(old_r.id, new_r.id)
self.assertEqual(str(old_r.seq), str(new_r.seq))
os.remove(filename)
del child
def conversion(self, prank_number, prank_ext, format) :
"""Get PRANK to do a conversion, and check it with SeqIO."""
filename = "%s.%s" % (self.output, prank_ext)
if os.path.isfile(filename) :
os.remove(filename)
cmdline = PrankCommandline(prank_exe, d=self.input,
convert=True, f=prank_number,
o='"%s"' % self.output)
self.assertEqual(str(cmdline), prank_exe \
+ ' -d=%s' % self.input \
+ ' -o="%s"' % self.output \
+ ' -f=%i' % prank_number \
+ ' -convert')
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, stdout, stderr = Application.generic_run(cmdline)
self.assertEqual(result.return_code, 0)
message = stdout.read().strip()
self.assert_(("PRANK: converting '%s' to '%s'" % (self.input, filename)) \
in message, message)
self.assertEqual(stderr.read(), "")
self.assertEqual(str(result._cl), str(cmdline))
self.assert_(os.path.isfile(filename))
old = AlignIO.read(open(self.input), "fasta")
#Hack...
if format=="phylip" :
for record in old :
record.id = record.id[:10]
new = AlignIO.read(open(filename), format)
assert len(old) == len(new)
for old_r, new_r in zip(old, new) :
self.assertEqual(old_r.id, new_r.id)
self.assertEqual(str(old_r.seq), str(new_r.seq))
os.remove(filename)
def multiple_alignment(fasta_dict, alignment_type=SeqTypeData().TYPE_DEFAULT):
in_handle = StringIO()
fasta_tools.write_fasta_handle(in_handle, fasta_dict)
muscle_cmd = SeqTypeData().type2cmd[alignment_type]
child = subprocess.Popen(str(muscle_cmd), stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
shell=(sys.platform != "win32"))
if not child:
print("Process was not created!")
return
if sys.version_info[0] == 3:
child.stdin.write(bytes(in_handle.getvalue(), 'utf-8'))
child.stdin.close()
align = AlignIO.read(StringIO("".join(line.decode() for line in child.stdout)), "clustal")
else:
child.stdin.write(in_handle.getvalue())
child.stdin.close()
align = AlignIO.read(child.stdout, "clustal")
fd = copy.deepcopy(fasta_dict)
for a in align:
fd.set(a.id, str(a.seq))
return fd
def conversion(self, prank_number, prank_ext, format):
"""Get PRANK to do a conversion, and check it with SeqIO."""
filename = "%s.%s" % (self.output, prank_ext)
if os.path.isfile(filename):
os.remove(filename)
cmdline = PrankCommandline(prank_exe, d=self.input,
convert=True, f=prank_number,
o='"%s"' % self.output)
self.assertEqual(str(cmdline), _escape_filename(prank_exe)
+ ' -d=%s' % self.input
+ ' -o="%s"' % self.output
+ ' -f=%i' % prank_number
+ ' -convert')
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
message, error = cmdline()
self.assertTrue("PRANK" in message, message)
self.assertTrue(("converting '%s' to '%s'" % (self.input, filename))
in message, message)
self.assertEqual(error, "")
self.assertTrue(os.path.isfile(filename))
old = AlignIO.read(self.input, "fasta")
# Hack...
if format == "phylip":
for record in old:
record.id = record.id[:10]
new = AlignIO.read(filename, format)
self.assertEqual(len(old), len(new))
for old_r, new_r in zip(old, new):
self.assertEqual(old_r.id, new_r.id)
self.assertEqual(str(old_r.seq), str(new_r.seq))
os.remove(filename)
def setUp(self):
self.aln_file = [TEST_ALIGN_FILE1,
TEST_ALIGN_FILE2,
TEST_ALIGN_FILE3,
TEST_ALIGN_FILE4,
TEST_ALIGN_FILE5,
TEST_ALIGN_FILE6]
alns = []
for i in self.aln_file:
if i[1] == 'parse':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet)
elif i[1] == 'index':
nucl = SeqIO.index(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, alphabet=codonalign.default_codon_alphabet, max_score=20)
elif i[1] == 'id':
nucl = SeqIO.parse(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=IUPAC.protein)
with open(i[0][2]) as handle:
id = dict((i.split()[0], i.split()[1]) for i in handle)
with warnings.catch_warnings():
warnings.simplefilter('ignore')
caln = codonalign.build(prot, nucl, corr_dict=id, alphabet=codonalign.default_codon_alphabet)
alns.append(caln)
nucl.close() # Close the indexed FASTA file
self.alns = alns
def muscle_align_protein(recs, work_dir, outfmt="fasta", inputorder=True):
"""
Align given proteins with muscle.
recs are iterable of Biopython SeqIO objects
"""
fasta_file = op.join(work_dir, "prot-start.fasta")
align_file = op.join(work_dir, "prot.aln")
SeqIO.write(recs, file(fasta_file, "w"), "fasta")
muscle_cl = MuscleCommandline(cmd=MUSCLE_BIN("muscle"),
input=fasta_file, out=align_file, seqtype="protein",
clwstrict=True)
stdout, stderr = muscle_cl()
alignment = AlignIO.read(muscle_cl.out, "clustal")
if inputorder:
try:
muscle_inputorder(muscle_cl.input, muscle_cl.out)
except ValueError:
return ""
alignment = AlignIO.read(muscle_cl.out, "fasta")
print >>sys.stderr, "\tDoing muscle alignment: %s" % muscle_cl
if outfmt == "fasta":
return alignment.format("fasta")
if outfmt == "clustal":
return alignment.format("clustal")
def _input(a):
"""The function converts alignments to matrix for further use.
Arguments:
-a- alignment file
Example:
>>>import os
>>>import numpy as np
>>>from Bio import AlignIO
>>>_input("example.fasta")"""
fileName, fileExtension = os.path.splitext(a)
if fileExtension == ".phylip":
try:
l = list(AlignIO.read(a,"phylip"))
except (ValueError):
l = list(AlignIO.read(a,"phylip-relaxed"))
except:
pass
elif fileExtension == ".fasta":
l = list(AlignIO.read(a,"fasta"))
else:
raise Exception("Wrong format. Choose accepted format.")
p = [[i for i in str(l[j].seq)] for j in range(0,len(l))]
y = np.array(p)
return(y)
def main(argv):
usage = 'ConvertAln -i <infile> -x <informat> -o <outfile> -f <outformat>'
infile = ''
informat = ''
outfile = ''
outformat = ''
try:
opts, args = getopt.getopt(argv,"hi:x:o:f:",["infile=", "informat=", "outfile=", "outformat="])
except getopt.GetoptError:
sys.exit(usage)
for opt, arg in opts:
if opt == '-h':
print usage
sys.exit()
elif opt in ("-i", "--infile"):
infile = arg
elif opt in ("-x", "--informat"):
informat = arg
elif opt in ("-o", "--outfile"):
outfile = arg
elif opt in ("-f", "--outformat"):
outformat = arg
if not infile:
sys.exit("must specify infile! %s" % usage)
if not outformat:
sys.exit("must specify format to convert to! %s" % usage)
if not informat:
informat = guess_format(infile)
if not outfile:
if '.' in infile:
outfile = '.'.join((infile.split('.')[:-1] + [get_extension(outformat)]))
else:
outfile = '.'.join((infile, get_extension(outformat)))
if infile == 'pipe' or infile == 'stdin' or infile == 'STDIN' or infile == '|':
infile = sys.stdin
if outformat == 'phylip':
alignment=AlignIO.read(infile, informat, alphabet=IUPAC.ambiguous_dna)
alignment = remove_blank(alignment)
if len(alignment) == 0 or len(alignment[0]) == 0:
sys.exit()
if outfile == 'pipe' or outfile == 'stdout' or outfile == 'STDOUT' or outfile == '|' or outfile == '>':
write_phylip(alignment, sys.stdout)
else:
out_fh = open(outfile, 'w')
write_phylip(alignment, out_fh)
out_fh.close()
else:
if outfile == 'pipe' or outfile == 'stdout' or outfile == 'STDOUT' or outfile == '|' or outfile == '>':
outfile = sys.stdout
if outformat == 'nexus':
alignment=AlignIO.read(infile, informat, alphabet=IUPAC.ambiguous_dna)
write_nexus(alignment, outfile)
else:
AlignIO.convert(infile, informat, outfile, outformat, alphabet=IUPAC.ambiguous_dna)
def codon_align(self, alignment_tool="mafft", prune=True, verbose=0):
''' takes a nucleotide alignment, translates it, aligns the amino acids, pads the gaps
note that this suppresses any compensated frameshift mutations
Parameters:
- alignment_tool: ['mafft', 'muscle'] the commandline tool to use
'''
from Bio import AlignIO,SeqIO
from Bio.SeqRecord import SeqRecord
make_dir(self.run_dir)
os.chdir(self.run_dir)
# translage
aa_seqs = {}
bad_seq = 0
for seq in self.seqs.values():
tempseq = seq.seq.translate()
# use only sequences that translate with out trouble
if '*' not in str(tempseq)[:-1] or prune==False:
aa_seqs[seq.id]=SeqRecord(tempseq,id=seq.id)
aa_seqs[seq.id].attributes = seq.attributes
else:
if verbose: print(seq.id,"has premature stops, discarding")
bad_seq+='*' in str(tempseq)[:-1]
print('Number of sequences with stops:',bad_seq,'out of total',len(self.seqs))
tmpfname = 'temp_in.fasta'
SeqIO.write(aa_seqs.values(), tmpfname,'fasta')
if alignment_tool=='muscle':
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input=tmpfname, out=tmpfname[:-5]+'aligned.fasta')
cline()
aln_aa = AlignIO.read(tmpfname[:-5]+'aligned.fasta', "fasta")
elif alignment_tool=='mafft':
from Bio.Align.Applications import MafftCommandline
from StringIO import StringIO
mafft_cline = MafftCommandline(input=tmpfname)
stdout, stderr = mafft_cline()
aln_aa = AlignIO.read(StringIO(stdout), "fasta")
else:
print('Alignment tool not supported:',alignment_tool)
return
#generate nucleotide alignment
self.aln = pad_nucleotide_sequences(aln_aa, self.seqs)
self.sequence_lookup = {seq.id:seq for seq in self.aln}
self.reference_aligned = self.sequence_lookup[self.reference.id]
# add attributes to alignment
for seq in self.seqs.values():
if seq.id in self.sequence_lookup:
self.sequence_lookup[seq.id].attributes = seq.attributes
os.chdir('..')
remove_dir(self.run_dir)
def read_alignment(self, *args, **kwargs):
filename = args[0]
args = args[1:]
with fileIO.freader(filename) as fl:
if ISPY3:
handle = io.TextIOWrapper(fl)
msa = AlignIO.read(handle, *args, **kwargs)
else:
msa = AlignIO.read(fl, *args, **kwargs)
self.infile = filename
# guess alphabet
self._msa = self._guess_alphabet(msa)
def main():
args = get_parser()
outfile1 = open(args.outputfile1, "w")
file1 = glob.glob(os.path.join(args.indirectory, "*.nexus"))
with open(file1[0], "r") as infile1:
aln = AlignIO.read(infile1, 'nexus')
AlignIO.write(aln, outfile1, 'phylip-relaxed')
outputfile2 = open(args.outputfile2, "w")
with open(file1[1], "r") as infile2:
aln = AlignIO.read(infile2, 'nexus')
AlignIO.write(aln, outputfile2, 'phylip-relaxed')
outputfile3 = open(args.outputfile3, "w")
with open(file1[2], "r") as infile3:
aln = AlignIO.read(infile3, 'nexus')
AlignIO.write(aln, outputfile3, 'phylip-relaxed')
def main():
options, args = interface()
# iterate through all the files to determine the longest alignment
files = get_files(options.input)
align_lengths = [AlignIO.read(f, 'nexus').get_alignment_length() \
for f in files]
max_align_length = max(align_lengths)
# find the middle
middle = int(round(max_align_length/2, 0))
# create a dict to hold the results by position in longest array
differences = dict((d,np.array([])) for d in range(-middle, middle + 1))
# iterate through all the files again
for f in files:
align = AlignIO.read(f, 'nexus')
align_length = align.get_alignment_length()
align_diff = int((round((max_align_length - align_length)/2.,0) - middle))
# determine relative start of this alignment to longest
for col in xrange(align_length):
bases = align.get_column(col)
b_counts = len(set(bases))
#pdb.set_trace()
differences[align_diff + col] = np.append(differences[align_diff + col],b_counts)
#pdb.set_trace()
position = differences.keys()
# create bins in groups of 100
#bins = np.array(range(0,500,100))
#print bins
#pdb.set_trace()
if options.output:
outp = open(options.output, 'w')
else:
outp = sys.stdout
outp.write('bp, mean, ci, onediff, greaterthanonediff, fourdiff, count\n')
ignore = []
for p in sorted(position):
#pdb.set_trace()
# how many only have 0-1 difference
try:
one_diff = sum(differences[p] <= 1)/float(len(differences[p]))
four_diff = sum(differences[p] >= 4)/float(len(differences[p]))
greater_than_one_diff = sum(differences[p] > 1)/float(len(differences[p]))
total = len(differences[p])
except ZeroDivisionError:
ignore.append(p)
if p not in ignore:
outp.write('{0},{1},{2},{3},{4},{5},{6}\n'.format(p, np.mean(differences[p]), 1.96 * np.std(differences[p]), one_diff, four_diff, greater_than_one_diff, total))
if options.output:
outp.close()
def standard_test_procedure(self, cline):
"""Standard testing procedure used by all tests."""
# Overwrite existing files.
cline.force = True
# Mark output files for later cleanup.
self.add_file_to_clean(cline.outfile)
if cline.guidetree_out:
self.add_file_to_clean(cline.guidetree_out)
input_records = SeqIO.to_dict(SeqIO.parse(cline.infile, "fasta"))
self.assertEqual(str(eval(repr(cline))), str(cline))
output, error = cline()
self.assertTrue(not output or output.strip().startswith("CLUSTAL"))
# Test if ClustalOmega executed successfully.
self.assertTrue(error.strip() == "" or
error.startswith("WARNING: Sequence type is DNA.") or
error.startswith("WARNING: DNA alignment is still experimental."))
# Check the output...
align = AlignIO.read(cline.outfile, "clustal")
output_records = SeqIO.to_dict(SeqIO.parse(cline.outfile, "clustal"))
self.assertEqual(len(set(input_records.keys())), len(set(output_records.keys())))
for record in align:
self.assertEqual(str(record.seq), str(output_records[record.id].seq))
# TODO - Try and parse this with Bio.Nexus?
if cline.guidetree_out:
self.assertTrue(os.path.isfile(cline.guidetree_out))
def __init__(self, file_name=None, data = None, format='fasta'):
if file_name:
super(Alignment, self).__init__(AlignIO.read(file_name, format))
elif data:
super(Alignment, self).__init__(AlignIO.parse(StringIO(data), format))
else:
super(Alignment, self).__init__([])
def test_needle_file(self):
"""needle with the asis trick, output to a file."""
# Setup,
cline = NeedleCommandline(cmd=exes["needle"])
cline.set_parameter("-asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
# EMBOSS would guess this, but let's be explicit:
cline.set_parameter("-snucleotide", "True")
cline.set_parameter("-outfile", "Emboss/temp with space.needle")
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
stdout, stderr = cline()
# Check it worked,
self.assertTrue(stderr.strip().startswith("Needleman-Wunsch global alignment"), stderr)
self.assertEqual(stdout.strip(), "")
filename = cline.outfile
self.assertTrue(os.path.isfile(filename),
"Missing output file %r from:\n%s" % (filename, cline))
# Check we can parse the output...
align = AlignIO.read(filename, "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Clean up,
os.remove(filename)
def setUp(self):
nucl = SeqIO.parse(TEST_ALIGN_FILE6[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(TEST_ALIGN_FILE6[0][1], 'clustal', alphabet=IUPAC.protein)
with open(TEST_ALIGN_FILE6[0][2]) as handle:
id_corr = dict((i.split()[0], i.split()[1]) for i in handle)
aln = codonalign.build(prot, nucl, corr_dict=id_corr, alphabet=codonalign.default_codon_alphabet)
self.aln = aln
def standard_test_procedure(self, cline):
"""Standard testing procedure used by all tests."""
self.assertTrue(str(eval(repr(cline))) == str(cline))
input_records = SeqIO.to_dict(SeqIO.parse(cline.infile, "fasta"),
lambda rec : rec.id.replace(":", "_"))
#Determine name of tree file
if cline.newtree:
tree_file = cline.newtree
else:
#Clustalw will name it based on the input file
tree_file = os.path.splitext(cline.infile)[0] + ".dnd"
# Mark generated files for later removal
self.add_file_to_clean(cline.outfile)
self.add_file_to_clean(tree_file)
output, error = cline()
self.assertTrue(output.strip().startswith("CLUSTAL"))
self.assertTrue(error.strip() == "")
#Check the output...
align = AlignIO.read(cline.outfile, "clustal")
#The length of the alignment will depend on the version of clustalw
#(clustalw 2.1 and clustalw 1.83 are certainly different).
output_records = SeqIO.to_dict(SeqIO.parse(cline.outfile,"clustal"))
self.assertTrue(set(input_records.keys()) == set(output_records.keys()))
for record in align:
self.assertTrue(str(record.seq) == str(output_records[record.id].seq))
self.assertTrue(str(record.seq).replace("-", "") ==
str(input_records[record.id].seq))
#Check the DND file was created.
#TODO - Try and parse this with Bio.Nexus?
self.assertTrue(os.path.isfile(tree_file))
def align(cls, seq_records, outfile=None):
'''Align given sequences
@param seq_records: a list of SeqRecords objects
@param outfile: a filename for the output alignment or None
@return: if the outfile is none, return an AlignmentExt object;
otherwise return True on success. In both cases return None on error.'''
if not outfile:
outfile = mktmp_name('.aln.fasta')
remove_out = True
else: remove_out = False
msafile = mktmp_fasta(seq_records)
args = dict(thread=cpu_count, input=msafile)
if len(seq_records) < 10000:
args['auto'] = True
else:
args['parttree'] = True
args['partsize'] = 1000
ali = None
if run_cline(MafftCommandline(**args), stdout=outfile):
if remove_out:
ali = AlignmentExt.from_msa(AlignIO.read(outfile, 'fasta'))
else: ali = True
if remove_out: safe_unlink(outfile)
safe_unlink(msafile)
return ali
def __init__(self, fileName = None, msaBean = None, alphabet = "ACDEFGHIKLMNPQRSTVWY-", backtrack = None, jsBeanFile = None, id=None):
self.alphabet = alphabet
self.backtrack = backtrack
self.id = id if id else "id_default_msa"
if fileName:
fType = None
if fileName.endswith(".aln"): fType = "clustal"
else : fType = "fasta"
self.alignment = AlignIO.read(open(fileName), fType) # fasta
self.asMatrix = [[ aaCoherce(aa) for aa in list(record.seq) ] for record in self.alignment]
self.headers = [record.id for record in self.alignment]
# print dir(self.alignment)
# print dir (self.asMatrix)
# print self.alignment.annotations
elif msaBean:
self.asMatrix = msaBean.matrix
self.headers = msaBean.header
self.backtrack = msaBean.backtrack
#self.alignment = [seq for seq in msaBean.matrix]
# same for headers
elif jsBeanFile:
with open(jsBeanFile) as json_file:
json_data = json.load(json_file)
self.asMatrix = json_data['matrix']
self.headers = json_data['headers']
self.backtrack = json_data['backtrack']
else:
raise initError("You must specify a bean or a mfasta file")
self.nSeq = len(self.asMatrix)
self.length = len(self.asMatrix[0])
self._frequency = None
def test_long(self):
"""Simple muscle call using long file."""
#Create a large input file by converting some of another example file
temp_large_fasta_file = "temp_cw_prot.fasta"
handle = open(temp_large_fasta_file, "w")
records = list(SeqIO.parse(open("NBRF/Cw_prot.pir", "rU"), "pir"))[:40]
SeqIO.write(records, handle, "fasta")
handle.close()
#Prepare the command...
cmdline = MuscleCommandline(muscle_exe)
cmdline.set_parameter("in", temp_large_fasta_file)
#Preserve input record order
cmdline.set_parameter("stable", True) #Default None treated as False!
#Use fast options
cmdline.set_parameter("maxiters", 1)
cmdline.set_parameter("diags", True) #Default None treated as False!
#Use clustal output
cmdline.set_parameter("clwstrict", True) #Default None treated as False!
#Shoudn't need this, but just to make sure it is accepted
cmdline.set_parameter("maxhours", 0.1)
#No progress reports to stderr
cmdline.set_parameter("quiet", True) #Default None treated as False!
self.assertEqual(str(cmdline).rstrip(), muscle_exe + \
" -in temp_cw_prot.fasta -diags -maxhours 0.1" + \
" -maxiters 1 -clwstrict -stable -quiet")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
result, out_handle, err_handle = generic_run(cmdline)
align = AlignIO.read(out_handle, "clustal")
self.assertEqual(len(records), len(align))
for old, new in zip(records, align):
self.assertEqual(old.id, new.id)
self.assertEqual(str(new.seq).replace("-",""), str(old.seq))
os.remove(temp_large_fasta_file)
#See if quiet worked:
self.assertEqual("", err_handle.read().strip())
def generate_mask(refpkg, stockholm_alignment):
"""
Generate an AlignmentMask from a reference package and stockholm alignment
"""
with refpkg.open_resource('mask') as fp:
unmasked_positions = set(int(i.strip())
for i in fp.read().split(','))
# Get length of alignment
with open(stockholm_alignment) as fp:
align_length = len(AlignIO.read(stockholm_alignment, 'stockholm')[0])
# Load consensus columns
with open(stockholm_alignment) as fp:
consensus_columns = _parse_stockholm_consensus(fp)
if not align_length == len(consensus_columns.mask):
raise ValueError("Consensus Columns and Alignment have "
"differing lengths")
counter = itertools.count().next
consensus_column_indexes = (counter() if i else None
for i in consensus_columns.mask)
consensus_mask = AlignmentMask([i in unmasked_positions for i
in consensus_column_indexes])
return consensus_mask
def test_needle_piped(self):
"""needle with asis trick, output piped to stdout."""
cline = NeedleCommandline(cmd=exes["needle"],
asequence="asis:ACCCGGGCGCGGT",
bsequence="asis:ACCCGAGCGCGGT",
gapopen=10,
gapextend=0.5,
auto=True, filter=True)
self.assertEqual(str(cline),
exes["needle"] + " -auto -filter"
+ " -asequence=asis:ACCCGGGCGCGGT"
+ " -bsequence=asis:ACCCGAGCGCGGT"
+ " -gapopen=10 -gapextend=0.5")
# Run the tool,
child = subprocess.Popen(str(cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
child.stdin.close()
# Check we could read it's output
align = AlignIO.read(child.stdout, "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Check no error output:
self.assertEqual(child.stderr.read(), "")
self.assertEqual(0, child.wait())
child.stdout.close()
child.stderr.close()
def test_aln_to_leaves(self):
anc_t = treeanc.TreeAnc.from_file(resources_dir+'PR.B.100.nwk', 'newick')
aln = AlignIO.read(resources_dir+'PR.B.100.fasta', 'fasta')
err = anc_t.load_aln(aln)
assert (err==0) # all sequencs were set up successfully
with open("%s.fa" % fa_head, "w") as handle:
handle.write(">%s\n%s\n>%s\n%s\n" %
(germline, germs[germline], entry.id, entry.seq))
clustal_cline = ClustalwCommandline(cmd=clustalw,
infile="%s.fa" % fa_head)
try:
stdout, stderr = clustal_cline()
except:
print("Error in alignment of %s (will skip): %s" %
(entry.id, stderr))
for f in glob.glob("%s.*" % fa_head):
os.remove(f)
continue
alignment = AlignIO.read("%s.aln" % fa_head, "clustal")
shift = False
for record in alignment:
codons = re.sub(
"---", "", str(record.seq.strip("-"))
) #don't care about leading/trailing and full-codon indels are fine
if "-" in codons:
shift = True #likely frameshift --discard!
if not shift: #made it; save the sequence
good += 1
sequences.append(entry)
for f in glob.glob("%s.*" % fa_head):
os.remove(f)
aln = drbaln
alnindex = dict([(a.id, a) for a in aln])
compare_tepitope_alleles(alnindex)
#d1 = compare(ref1, ref2, alnindex)
#x = d1.merge(d2,right_index=1,left_index=1)
#print len(x)
#compare_ref(hla,bola,ref,alnindex)
plt.show()
return
pocket_residues = get_pocket_positions()
librarypssms = get_pssms()
#drb MHC alignment using IPD sequences, includes BoLA-DRB3 sequences
drbaln = AlignIO.read(drb_aln_file, "fasta")
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-t",
"--test",
dest="test",
action='store_true',
help="test")
opts, remainder = parser.parse_args()
if opts.test == True:
test()
usage = "%prog [options] < fasta_file > phylip file"
description = "Convert a fasta file to a phylip file"
parser = optparse.OptionParser(description=description, usage=usage)
parser.add_option(
"-c",
"--convfile",
help="File to convert new IDs back to original IDs (D = don't save file)",
action="store",
type="str",
dest="convfile",
default=None)
(options, args) = parser.parse_args()
# Read the FASTA file from stdin and convert it into a phylip file
# Use list so we actually edit in-place rather than
# just editing a copy that gets destroyed later!
aln = list(AlignIO.read(sys.stdin, "fasta"))
if not options.convfile == None:
fid = open(options.convfile, "w")
# We will use this to convert back to the IDs in the fasta file
for i in range(len(aln)):
newid = "S%09d" % (i)
if not options.convfile == None:
fid.write("%s\t%s\n" % (newid, aln[i].id))
aln[i].id = newid
SeqIO.write(aln, sys.stdout, "phylip")
from Bio import AlignIO
import sys
al = AlignIO.read( open(sys.argv[1]), "stockholm" )
print al.format("fasta")
def Calculate_BaseEdit_freq(self, lQuery_seq=[]):
dRef = {}
dResult = {}
dRef[sBarcode] = (
sRef) # total matched reads, insertion, deletion, complex
dResult[sBarcode] = [0, 0, 0, 0, [], [], [], [], [], [], []]
# lRef : [(ref_seq, ref_seq_after_barcode, barcode, barcode end pos, indel end pos, indel from barcode),(...)]
# dResult = [# of total, # of ins, # of del, # of com, [total FASTQ], [ins FASTQ], [del FASTQ], [com FASTQ], info]
iCount = 0
for sQuery_seq_raw in lQuery_seq:
iBarcode_matched = 0
iNeedle_matched = 0
iInsert_count = 0
iDelete_count = 0
iComplex_count = 0
try:
# Check the barcode pos and remove it.
sQuery_seq_raw = sQuery_seq_raw.replace('\r', '')
iBarcode_start_pos = sQuery_seq_raw.index(sBarcode)
iBarcode_matched += 1
sQuery_seq_with_barcode = sQuery_seq_raw[iBarcode_start_pos:]
# _check = 0
# if sQuery_seq_raw == 'TCTTGAAAAAGTGGCACCGAGTCGGTGCTTTTTTGTATCTCTATCAGCACACAAGCATGCAATCACCTTGGGTCCCAGCTTGGCGTAACTAGATCTCTACTCTACCACTTGTACTTCAGCGGTCAGCTTACTCGACTTAA':
# _check = 1
sRef_seq = r'<(echo -e ">{name}\n{seq}")'.format(
name=sBarcode + '_ref', seq=sRef)
sQuery_seq = r'<(echo -e ">{name}\n{seq}")'.format(
name=sBarcode + '_query', seq=sQuery_seq_with_barcode)
sNeedle_cmd = r"/bin/bash -c 'needle -filter {0} {1} -outfile stdout -gapopen {2} -gapextend {3} -endweight Y -endopen {4} -endextend {5}'".format(
sRef_seq, sQuery_seq, sOG, sOE, sEG, sEE)
Needle_result = sp.Popen(sNeedle_cmd,
stdout=sp.PIPE,
stderr=sp.PIPE,
universal_newlines=True,
shell=True)
lResult = [
Instance.seq._data for Instance in AlignIO.read(
Needle_result.stdout, "emboss")
]
sRef_needle_ori = lResult[0]
sQuery_needle_ori = lResult[1]
# if _check == 1:
# print(sRef_needle_ori)
# print(sQuery_needle_ori)
# set_trace()
Needle_result.stdout.close()
# detach forward ---, backward ---
# e.g. ref ------AAAGGCTACGATCTGCG------
# query AAAAAAAAATCGCTCTCGCTCTCCGATCT
# trimmed ref AAAGGCTACGATCTGCG
# trimmed qeury AAATCGCTCTCGCTCTC
iReal_ref_needle_start = 0
iReal_ref_needle_end = len(sRef_needle_ori)
iRef_needle_len = len(sRef_needle_ori)
for i, sRef_nucle in enumerate(sRef_needle_ori):
if sRef_nucle in ['A', 'C', 'G', 'T']:
iReal_ref_needle_start = i
break
for i, sRef_nucle in enumerate(sRef_needle_ori[::-1]):
if sRef_nucle in ['A', 'C', 'G', 'T']:
iReal_ref_needle_end = iRef_needle_len - (i + 1)
# forward 0 1 2 len : 3
# reverse 2 1 0, len - (2 + 1) = 0
break
sRef_needle = sRef_needle_ori[
iReal_ref_needle_start:iReal_ref_needle_end + 1]
if iReal_ref_needle_start:
sQuery_needle = sQuery_needle_ori[:iReal_ref_needle_end]
sQuery_needle = sQuery_needle_ori[:len(sRef_needle)]
# detaching completion
# indel info making.
iNeedle_match_pos_ref = 0
iNeedle_match_pos_query = 0
iNeedle_insertion = 0
iNeedle_deletion = 0
lInsertion_in_read = [
] # insertion result [[100, 1], [119, 13]]
lDeletion_in_read = [] # deletion result [[97, 1], [102, 3]]
# print 'sRef_needle', sRef_needle
# print 'sQuery_needle', sQuery_needle
for i, (sRef_nucle, sQuery_nucle) in enumerate(
zip(sRef_needle, sQuery_needle)):
if sRef_nucle == '-':
iNeedle_insertion += 1
if sQuery_nucle == '-':
iNeedle_deletion += 1
if sRef_nucle in ['A', 'C', 'G', 'T']:
if iNeedle_insertion:
lInsertion_in_read.append(
[iNeedle_match_pos_ref, iNeedle_insertion])
iNeedle_insertion = 0
iNeedle_match_pos_ref += 1
if sQuery_nucle in ['A', 'C', 'G', 'T']:
if iNeedle_deletion:
lDeletion_in_read.append(
[iNeedle_match_pos_query, iNeedle_deletion])
iNeedle_match_pos_query += iNeedle_deletion
iNeedle_deletion = 0
iNeedle_match_pos_query += 1
# print 'sRef_needle', sRef_needle
# print 'sQuery_needle', sQuery_needle
# print 'lInsertion_in_read: onebase', lInsertion_in_read
# print 'lDeletion_in_read: onebase', lDeletion_in_read
# print 'i5bp_front_Indel_end', i5bp_front_Indel_end
# print 'iIndel_end_from_barcode_pos', iIndel_end_from_barcode_pos
lTarget_indel_result = [] # ['20M2I', '23M3D' ...]
"""
ins case
...............................NNNNNNNNNNNNNN....NNNNNNNNNNNNNNNNNNN*NNNNNAGCTT
"""
iCleavage_window_start = int(lIndel_check_pos[0])
iCleavage_window_end = int(lIndel_check_pos[1]) - 1
for iMatch_pos, iInsertion_pos in lInsertion_in_read:
if iCleavage_window_start <= iMatch_pos <= iCleavage_window_end: # iMatch_pos is one base
iInsert_count = 1
lTarget_indel_result.append(
str(iMatch_pos) + 'M' + str(iInsertion_pos) + 'I')
"""
del case 1
...............................NNNNNNNNNNNNNN....NNNNNNNNNNNNNNNNNNNNN**NNNAGCTT
del case 2
...............................NNNNNNNNNNNNNN....NNNNNNNNNNNNNNNNNNNNN**NNNNNCTT
"""
for iMatch_pos, iDeletion_pos in lDeletion_in_read:
"""
Insertion: 30M3I
^
ACGT---ACGT
ACGTTTTACGT -> check this seq
Insertion just check two position
Deletion: 30M3D
^
ACGTTTTACGT
ACGT---ACGT -> check this seq
But deletion has to includes overlap deletion.
"""
if iMatch_pos <= iCleavage_window_end and iCleavage_window_start <= (
iMatch_pos + iDeletion_pos):
iDelete_count = 1
lTarget_indel_result.append(
str(iMatch_pos) + 'M' + str(iDeletion_pos) + 'D')
if iInsert_count == 1 and iDelete_count == 1:
iComplex_count = 1
iInsert_count = 0
iDelete_count = 0
# """ test set
# print 'sBarcode', sBarcode
# print 'sTarget_region', sTarget_region
# print 'sRef_seq_after_barcode', sRef_seq_after_barcode
# print 'sSeq_after_barcode', sQuery_seq
# print 'iIndel_start_from_barcode_pos', iIndel_start_from_barcode_pos
# print 'iIndel_end_from_barcode_pos', iIndel_end_from_barcode_pos
# """
"""
23M3I
23M is included junk_seq after barcode,
barcorde junk targetseq others
*********ACCCT-------------ACACACACC
so should select target region.
If junk seq is removed by target region seq index pos.
"""
## 8: indel info
dResult[sBarcode][8].append([
sRef, sQuery_seq_raw, lTarget_indel_result, "",
sRef_needle_ori, sQuery_needle_ori
]) ## "" -> target seq, but this is not used this project.
# end: try
except ValueError as e:
# print(e)
continue
# total matched reads, insertion, deletion, complex
dResult[sBarcode][0] += iBarcode_matched
dResult[sBarcode][1] += iInsert_count
dResult[sBarcode][2] += iDelete_count
dResult[sBarcode][3] += iComplex_count
## base editing frequency
"""
BaseEditPos : 0 1 2
[OrderedDict([('A',0),('C',0),('G',0),('T',0)]), OrderedDict([('A',0),('C',0),('G',0),('T',0)]), ...
and sum the counts each position
"""
if iInsert_count == 0 and iDelete_count == 0 and iComplex_count == 0:
lBaseEdit = []
iTarget_len = int(lTarget_window[1]) - int(
lTarget_window[0]) + 1
for i in range(iTarget_len):
lBaseEdit.append(
OrderedDict([('A', 0), ('C', 0), ('G', 0), ('T', 0)]))
iTarget_start = int(lTarget_window[0]) - 1
iTarget_end = int(lTarget_window[1])
"""
cleavage window start
^
[barcode]ACGACGTACGACGT[cleavage]
[barcode]ACGACGTACGACGT[cleavage]
"""
iBase_edit_event = 0
for i, tRef_Query_base in enumerate(
zip(sRef_needle[iTarget_start:iTarget_end],
sQuery_needle[iTarget_start:iTarget_end])):
sRef_base = tRef_Query_base[0]
sQuery_base = tRef_Query_base[1]
if sRef_base == '-' or sQuery_base == '-': continue
if sRef_base != sQuery_base and sQuery_base != 'N':
iBase_edit_event = 1
lBaseEdit[i][sQuery_base] += 1
# print(sQuery_needle)
dResult[sBarcode][9].append(lBaseEdit)
if iBase_edit_event == 1:
dResult[sBarcode][10].append([
sRef, sQuery_seq_raw, lTarget_indel_result,
[
list(orderedDict.values())
for orderedDict in lBaseEdit
], sRef_needle_ori, sQuery_needle_ori
])
# dResult[sBarcode] = [0, 0, 0, 0, [], [], [], [], [], [BaseEdit_freq_data]]
iBarcode_matched = 0
iInsert_count = 0
iDelete_count = 0
iComplex_count = 0
# end: for sBarcode, lCol_ref
# end: for lCol_FASTQ
return dResult
def __init__(self, root_dir, *args, **kwargs):
# set the default configurations
self._build_tree = False
self._infer_gtr = True
self._root = None
self._mutation_rate = None
self._relaxed_clock = None
self._Tc = None
# set the directory, containing files for the session
self._root_dir = root_dir
self._nwk = os.path.join(self._root_dir, in_tree)
self._aln = os.path.join(self._root_dir, in_aln)
self._meta = os.path.join(self._root_dir, in_meta)
self._cfg = os.path.join(self._root_dir, in_cfg)
# some parameters for the logger function should be set explicitly,
# because we might need them before super.__init__(...) is called
self.verbose = 5
self.t_start = time.time()
self._log_file = os.path.join(self._root_dir, log_filename)
# read the JSON configuration file
with open(self._cfg) as ff:
config_dic = json.load(ff)
# Compose the list of steps to perform,
# # save this as dictionary to session_state.json file (used to update
# web browser state)
self._init_session_state(config_dic)
# build tree if necessary
# build tree if necessary
if self._build_tree:
try:
self.logger("Building phylogenetic tree...", 1)
self._advance_session_progress()
res = build_tree(self._root_dir)
if (res != 0):
raise RuntimeError(
"Error in tree builder FastTree. The method returned: "
+ str(res))
except Exception as e:
s = str(e)
self._session_error(
"Error occurred when building phylogenetic tree."
" Exception description: " + s)
raise
try:
tree = Phylo.read(self._nwk, 'newick')
aln = AlignIO.read(self._aln, 'fasta')
# read the metadata
dates, metadata = self._read_metadata_from_file(self._meta)
super(TreeTime, self).__init__(dates=dates,
tree=tree,
aln=aln,
gtr=self._gtr,
*args,
**kwargs)
except Exception as e:
s = str(e)
self._session_error("Error in TreeTime object initialization. "
" Exception description: " + s)
raise
self._metadata = metadata
def simulate_missing(path_to_align, spp_info, prop_n):
# Set path to alignment
alignment_path = str(path_to_align)
full_path = os.path.abspath(alignment_path)
base_name = os.path.basename(full_path)
dir_name = os.path.dirname(full_path)
# Get species list
spp_list = str(spp_info).split(",")
# Get N proportions
n_percents = [float(x) for x in str(prop_n).split(",")]
# Read in alignment and prune to desired species if requested
try:
formats = {
'nex': 'nexus',
'nexus': 'nexus',
'phy': 'phylip',
'phylip-relaxed': 'phylip-relaxed',
'phylip': 'phylip',
'fa': 'fasta',
'fasta': 'fasta'
}
fformat = formats[alignment_path.split('.')[-1]]
raw_alignment = AlignIO.read(alignment_path, fformat)
# If alignment cannot be read in, raise exception
except:
sys.exit("ERROR: Cannot process " + os.path.basename(alignment_path))
# Get species from raw alignment
raw_spp = []
for seq_record in raw_alignment:
raw_spp.append(str(seq_record.id))
if all(elem in spp_list for elem in raw_spp):
# Create dummy alignment
global pruned_alignment
pruned_alignment = raw_alignment[0:0]
# Populate alignment by adding taxa sorted by taxon ID
for i in range(0, len(spp_list)):
spp_to_add = spp_list[i]
spp_n_percent = n_percents[i]
raw_index = raw_spp.index(spp_to_add)
raw_id = raw_alignment[raw_index].id
raw_seq = raw_alignment[raw_index].seq
new_seq = add_n(raw_seq, spp_n_percent)
pruned_alignment.add_sequence(str(raw_id), new_seq)
# If resulting alignment is empty, raise exception
if int(pruned_alignment.get_alignment_length()) == 0:
sys.exit(
"ERROR: Alignment processed, but appears to have no bases...")
else:
with open(
dir_name + '\\' + base_name.replace(
"." + alignment_path.split('.')[-1],
"_SimN." + alignment_path.split('.')[-1]),
"w") as handle:
SeqIO.write(pruned_alignment, handle, "phylip")
else:
sys.exit("ERROR: Requested species not found in " +
os.path.basename(alignment_path) + "...")
def ali_parser(alignment_file):
# optional parameter use score or hmmemit to choose seed sequence #args.ali
if args.mode == 'con':
subprocess.check_output([hmmbuild_exe, '--symfrac', '0', args.output_path+args.file_name+'.hmm', args.ali])
subprocess.check_output([hmmemit_exe, '-c', '-o', args.output_path+'temp_seed_seq.fasta', args.output_path+args.file_name+'.hmm'])
seed_seq_record = AlignIO.read(args.output_path+'temp_seed_seq.fasta', 'fasta')
seed_seq_record = str(seed_seq_record[0].seq)
seed_seq_record = SeqRecord(Seq(seed_seq_record), id=args.file_name+'-consensus')
seed_to_ali_mapping = [x+1 for x in range(len(seed_seq_record))]
elif args.mode == 'rep':
full_ali_obj = AlignIO.read(alignment_file, "fasta")
for record in full_ali_obj:
record.seq = str(record.seq).replace('X','-') # in case of 'X', replacing it with '-'
raw_array = np.array([list(rec) for rec in full_ali_obj], order="F") # Convert alignment object to np_array object
col_array = np.transpose(raw_array) # align_columns.shape == (#col, #raw), i.e. (#site, #seq)
# compute the columne scores (as the proxy for seq coverage percentage)
col_scores = []
for col in col_array:
unique, counts = np.unique(col, return_counts=True)
if '-' in unique:
col_scores.append(1.0 - float(dict(zip(unique, counts))['-'])/float(len(col)))
# obtain the seq with the highest coverage in the alignment
array_score = np.copy(raw_array).astype(object)
j = 0 # seq count
while j < len(array_score):
i = 0 # col count
while i < len(col_scores):
if array_score[j][i] == '-': array_score[j][i] = 0.0
else:
array_score[j][i] = float(col_scores[i])
i += 1
j += 1
seq_score=np.zeros( j )
#np_sum
j = 0 # seq count
while j < len(array_score):
i = 0 # col count
while i < len(col_scores):
seq_score[j]=seq_score[j]+array_score[j][i]
i += 1
j += 1
#obtaining seed_seq related info
seed_seq_array = raw_array[np.argmax(seq_score)]
seed_seq = "".join(seed_seq_array)
for record in full_ali_obj:
if str(record.seq) == seed_seq:
seed_id = str(record.id)
seed_to_ali_mapping = [0 if x == '-' else 1 for x in seed_seq_array] # constructing a mapping list of '-'== 0 & amino acids == 1,2,3,... seed_seq indicating position in the original alignment)
i = 0 # track the alignment position
j = 1 # track the seed_seq position
#print len(seed_seq)
while i < len(seed_seq):
if seed_to_ali_mapping[i] == 1:
seed_to_ali_mapping[i] = j
i += 1
j += 1
else:
i += 1
#print '%d \n%s %s\n%s' % (np.amax(seq_score), seed_id, seed_seq, seed_to_ali_mapping) # check
seed_seq_record = SeqRecord(Seq(seed_seq.replace("-","")), id=seed_id) # remove the 'gap' so it won't affect hmm_aa_freq mapping in the Main Processes
SeqIO.write(seed_seq_record, args.output_path+"temp_seed_seq.fasta", "fasta")
# run hmmscan
domain_threshold = args.profile_threshold
profile_threshold = args.domain_threshold
subprocess.check_output([hmmscan_exe, '-o', args.output_path+'temp_hmmscan.out', '-E', profile_threshold ,'--domE', domain_threshold, args.database, args.output_path+'temp_seed_seq.fasta'])
return (seed_seq_record, seed_to_ali_mapping)
import Bio
from Bio.Phylo import PhyloXML, NewickIO
import argparse
from Bio import Phylo
from Bio import AlignIO
from Bio.Phylo.Consensus import *
from Bio.Phylo.TreeConstruction import DistanceCalculator
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
parser = argparse.ArgumentParser(description="")
parser.add_argument("multSeqAln", help="", type=str)
#parser.add_argument("out",help="")
args = parser.parse_args()
msa = AlignIO.read(args.multSeqAln, "fasta")
#tree = Phylo.read(args.multSeqAln, "newick")
#msas = bootstrap(msa, 100)
calculator = DistanceCalculator('blosum62')
constructor = DistanceTreeConstructor(calculator)
#trees = bootstrap_trees(msa, 100, constructor)
print "start bootstrap"
consensus_tree = bootstrap_consensus(msa, 2, constructor,
majority_consensus)
print "bootstrap done"
print consensus_tree
consensus_tree.root_with_outgroup("Tamandua")
Phylo.draw(consensus_tree)
lists[start]=1
start+=1
return lists
###################################################################################
############################### MAIN PROCESSES ################################
###################################################################################
seed_seq, seed_to_ali_mapping = ali_parser(args.ali)[0], ali_parser(args.ali)[1]
domains = hmmscan_parser(args.output_path+'temp_hmmscan.out', seed_seq.id)
hmm_database = {}
for key, value in domains.items():
#hmm_database = HMM(args.database, seed_seq.id).hmm_database # Storing target hmm profile into a HMM Class which is structured as a dictionary
hmm_database = HMM(args.database, key,hmm_database )
alimentObj = AlignIO.read(args.ali, "fasta")
aligmentObjLen=len(alimentObj[0])
local_seed_seq_master = [[]]*(aligmentObjLen+int(0.1*aligmentObjLen))
max_seed_seq_master = [[]]*aligmentObjLen
seed_seq_master = [[]]*(aligmentObjLen+int(0.1*aligmentObjLen)) #The master list storing aa_freqs for the entire seed_seq
domain_position_check=[0 for x in range(aligmentObjLen)]
##### LET HMM_database order as score
'''
domains_order = {}
dom_key=(domains.keys())
for i in dom_key[::-1]:
domains_order[i]=domains[i]
aln_gen, aln_nat, score, _, _ = alignments[0]
match_count = 0
for i in range(len(aln_gen)):
if aln_gen[i] != '-':
if aln_gen[i] == aln_nat[i]:
match_count += 1
print(aln_gen)
print(aln_nat)
percent_identity = match_count / actual_length
print(match_count, actual_length,
f"{percent_identity*100:0.2f} % identity")
# Export alignments
# aln = AlignIO.read('alns/sample_aln.fasta','fasta')
aln = AlignIO.read(aln_filename, 'fasta')
p = view_alignment(aln, plot_width=800)
export_svgs(p, filename="figs/" + sample_sp + ".svg")
# export_png(p, filename="figs/" + sample_sp + ".png")
# pn.pane.Bokeh(p)
# export_svgs(p, filename="figs/" + sample_sp + ".svg")
closest_matches.append(aln_nat.replace('-', ''))
closest_identities.append(percent_identity)
# write final file
df_func['closest_match'] = closest_matches
df_func['percent_identity'] = closest_identities
df_func.to_csv('alns/func_sps_matches.csv')
def remove_low_cov_and_consensus_columns(alignment_file_in, minimal_cov,
min_consensus, alignment_file_out):
def remove_single_columns_from_msa(alignment_in, column_to_remove):
alignment_column_l = alignment_in[:, :column_to_remove - 1]
alignment_column_r = alignment_in[:, column_to_remove:]
alignment_new = alignment_column_l + alignment_column_r
return alignment_new
def remove_multi_columns_from_msa(alignment_in, column_list):
alignment_new = alignment_in
removed_col_num = 0
for column in sorted(column_list):
alignment_new = remove_single_columns_from_msa(
alignment_new, column - removed_col_num)
removed_col_num += 1
return alignment_new
def remove_low_cov_columns(alignment, min_cov):
# get columns with low coverage
sequence_number = len(alignment)
total_col_num = alignment.get_alignment_length()
low_cov_columns = []
n = 0
while n < total_col_num:
current_column = alignment[:, n]
dash_number = current_column.count('-')
gap_percent = (dash_number / sequence_number) * 100
if gap_percent > min_cov:
low_cov_columns.append(n + 1)
n += 1
# remove identified columns
alignment_new = remove_multi_columns_from_msa(alignment,
low_cov_columns)
#alignment_new = slice_string(alignment, low_cov_columns)
return alignment_new
def remove_low_consensus_columns(alignment, min_consensus):
# get columns with low coverage
sequence_number = len(alignment)
total_col_num = alignment.get_alignment_length()
low_css_columns = []
n = 0
while n < total_col_num:
current_column = alignment[:, n]
# get all aa in current column
aa_list = set()
for aa in current_column:
aa_list.add(aa)
# get maximum aa percent
most_abundant_aa_percent = 0
for each_aa in aa_list:
each_aa_percent = (current_column.count(each_aa) /
sequence_number) * 100
if each_aa_percent > most_abundant_aa_percent:
most_abundant_aa_percent = each_aa_percent
# if maximum percent lower than provided cutoff, add current column to low consensus column list
if most_abundant_aa_percent < min_consensus:
low_css_columns.append(n + 1)
n += 1
# remove identified columns
alignment_new = remove_multi_columns_from_msa(alignment,
low_css_columns)
#alignment_new = slice_string(alignment, low_css_columns)
return alignment_new
# read in alignment
alignment = AlignIO.read(alignment_file_in, "fasta")
# remove_low_cov_columns
alignment_cov = remove_low_cov_columns(alignment, minimal_cov)
# remove_low_consensus_columns
alignment_cov_css = remove_low_consensus_columns(alignment_cov,
min_consensus)
# write filtered alignment
alignment_file_out_handle = open(alignment_file_out, 'w')
for each_seq in alignment_cov_css:
alignment_file_out_handle.write('>%s\n' % str(each_seq.id))
alignment_file_out_handle.write('%s\n' % str(each_seq.seq))
alignment_file_out_handle.close()
