def get_features_in_aln(alignment, variant, save_dir="", save_gff=True):
#Let's extract consensus
a=SummaryInfo(alignment)
cons=a.dumb_consensus(threshold=0.1, ambiguous='X')
seq = Sequence(id="Consensus", variant_id=variant, taxonomy_id=1, sequence=cons.tostring())
updated_features = get_variant_features(seq, save_dir=save_dir, save_gff=save_gff)
return updated_features
def test_proteins(self):
a = MultipleSeqAlignment([
SeqRecord(Seq("MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-"), id="ID001"),
SeqRecord(Seq("MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*"), id="ID002"),
SeqRecord(Seq("MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*"), id="ID003")
])
self.assertEqual(32, a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
self.assertEqual(str(c), "MHQAIFIYQIGYXXLKSGYIQSIRSPEYDNW*")
c = s.gap_consensus(ambiguous="X")
self.assertEqual(str(c), "MHXXIFIYQIGYXXLKSGYIQSIRSPEYXNWX")
m = s.pos_specific_score_matrix(chars_to_ignore=["-", "*"], axis_seq=c)
self.assertEqual(
str(m),
""" A D E F G H I K L M N P Q R S W Y
M 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
H 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0
X 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
F 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0
L 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
K 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
R 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0
E 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 0.0 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0
W 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
""")
letters = IUPACData.protein_letters
base_freq = 1.0 / len(letters)
e_freq_table = {letter: base_freq for letter in letters}
ic = s.information_content(e_freq_table=e_freq_table,
chars_to_ignore=["-", "*"])
self.assertAlmostEqual(ic, 133.061475107, places=6)
def trim_aln_to_seq_length(alignment,sequence):
"""Trim alignment to a sequence, i.e. leave only postions that correspond to this sequence span"""
n1=str(uuid.uuid4())
n2=str(uuid.uuid4())
#Get consensus
a=SummaryInfo(alignment)
cons=a.dumb_consensus(threshold=0.1, ambiguous='X')
#Needle it
SeqIO.write([SeqRecord(cons,id='CONS',name='CONS')],n1+'.fasta','fasta')
SeqIO.write([SeqRecord(sequence,id='KEY',name='KEY')],n2+'.fasta','fasta')
#Now we will redo it with Needlman Wunsh - the global alignment
needle_cline = NeedleCommandline(asequence=n1+".fasta", bsequence=n2+".fasta",gapopen=10, gapextend=0.5, outfile=n1+".txt")
stdout, stderr = needle_cline()
# print('Needle alignment')
align = AlignIO.read(n1+".txt", "emboss")
os.system('rm %s.fasta %s.fasta %s.txt'%(n1,n2,n1))
# print align
# print alignment
#first seq is consensus, we need to get borders useing second one.
seq=str(align[1,:].seq)
# print seq
begin=seq.index(str(sequence[0]))
end=len(seq)-seq[::-1].index(str(sequence[-1]))
print begin
print end
return alignment[:,begin:end]
def trim_hist_aln_to_core(msa):
"""Trims hist alignment to core"""
templ_H3 = Seq(
"ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA",
IUPAC.protein,
)
templ_H4 = Seq(
"SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG",
IUPAC.protein,
)
templ_H2A = Seq(
"SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSKSK",
IUPAC.protein,
)
templ_H2B = Seq(
"AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK",
IUPAC.protein,
)
templ_core_H3 = templ_H3[43:114]
templ_core_H4 = templ_H4[23:93]
templ_core_H2A = templ_H2A[15:119]
templ_core_H2B = templ_H2B[33:120]
templ = {"H3": templ_core_H3, "H4": templ_core_H4, "H2A": templ_core_H2A, "H2B": templ_core_H2B}
a = SummaryInfo(msa)
cons = a.dumb_consensus(threshold=0.1, ambiguous="X")
return trim_aln_to_seq_length(msa, templ[identify_hist_type(cons)])
def trim_aln_to_seq(alignment,sequence):
"""Trim alignment to a sequence, i.e. leave only postions that correspond to this sequence
Note that seqeuence should be incorportatable into alignment without additional gaps in alignment.
"""
n1=str(uuid.uuid4())
n2=str(uuid.uuid4())
#Get consensus
a=SummaryInfo(alignment)
cons=a.dumb_consensus(threshold=0.1, ambiguous='X')
#Needle it
SeqIO.write([SeqRecord(cons,id='CONS',name='CONS')],n1+'.fasta','fasta')
SeqIO.write([SeqRecord(sequence,id='KEY',name='KEY')],n2+'.fasta','fasta')
#Now we will redo it with Needlman Wunsh - the global alignment
needle_cline = NeedleCommandline(asequence=n1+".fasta", bsequence=n2+".fasta",gapopen=10, gapextend=0.5, outfile=n1+".txt")
stdout, stderr = needle_cline()
# print('Needle alignment')
align = AlignIO.read(n1+".txt", "emboss")
os.system('rm %s.fasta %s.fasta %s.txt'%(n1,n2,n1))
# print align
# print alignment
align.extend(alignment)
a=align[1:,:]
return trim_aln_to_key_seq(a,sequence)[1:,:]
def test_nucleotides(self):
filename = "GFF/multi.fna"
format = "fasta"
alignment = AlignIO.read(filename, format, alphabet=unambiguous_dna)
summary = SummaryInfo(alignment)
c = summary.dumb_consensus(ambiguous="N")
self.assertEqual(str(c), "NNNNNNNN")
c = summary.gap_consensus(ambiguous="N")
self.assertEqual(str(c), "NNNNNNNN")
expected = {"A": 0.25, "G": 0.25, "T": 0.25, "C": 0.25}
m = summary.pos_specific_score_matrix(chars_to_ignore=["-"],
axis_seq=c)
self.assertEqual(
str(m), """ A C G T
N 2.0 0.0 1.0 0.0
N 1.0 1.0 1.0 0.0
N 1.0 0.0 2.0 0.0
N 0.0 1.0 1.0 1.0
N 1.0 2.0 0.0 0.0
N 0.0 2.0 1.0 0.0
N 1.0 2.0 0.0 0.0
N 0.0 2.0 1.0 0.0
""")
# Have a generic alphabet, without a declared gap char, so must tell
# provide the frequencies and chars to ignore explicitly.
ic = summary.information_content(e_freq_table=expected,
chars_to_ignore=["-"])
self.assertAlmostEqual(ic, 7.32029999423075, places=6)
def calcAbundance(alignmentFile, consensusFile, abundanceFile, abundancePercentFile, verbose):
print('Calculating the abundance matrix...')
alignment = AlignIO.read(alignmentFile, "fasta")
summary = SummaryInfo(alignment)
consensusSeq = SeqIO.read(consensusFile, 'fasta')
if (len(consensusSeq) == alignment.get_alignment_length()):
abundanceMatrix = summary.pos_specific_score_matrix(consensusSeq)
else:
with open(consensusFile, "w") as f:
SeqIO.write(SeqRecord( summary.dumb_consensus(), id='consensus'), f, "fasta")
abundanceMatrix = summary.pos_specific_score_matrix()
if verbose:
print("Abundance matrix (absolute values):")
print(str(abundanceMatrix))
with open(abundanceFile, 'w') as f:
f.write(str(abundanceMatrix))
for pos, abundance in enumerate(abundanceMatrix):
for res, value in abundance.items():
abundanceMatrix[pos][res] = 100.0 * float(value) / float(len(alignment))
if verbose:
print("Abundance matrix (percentages):")
print(str(abundanceMatrix))
with open(abundancePercentFile, 'w') as f:
f.write(str(abundanceMatrix))
print('OK')
def trim_aln_to_seq_length(alignment, sequence):
"""Trim alignment to a sequence, i.e. leave only postions that correspond to this sequence span"""
n1 = str(uuid.uuid4())
n2 = str(uuid.uuid4())
#Get consensus
a = SummaryInfo(alignment)
cons = a.dumb_consensus(threshold=0.1, ambiguous='X')
#Needle it
SeqIO.write([SeqRecord(cons, id='CONS', name='CONS')], n1 + '.fasta',
'fasta')
SeqIO.write([SeqRecord(sequence, id='KEY', name='KEY')], n2 + '.fasta',
'fasta')
#Now we will redo it with Needlman Wunsh - the global alignment
needle_cline = NeedleCommandline(asequence=n1 + ".fasta",
bsequence=n2 + ".fasta",
gapopen=10,
gapextend=0.5,
outfile=n1 + ".txt")
stdout, stderr = needle_cline()
# print('Needle alignment')
align = AlignIO.read(n1 + ".txt", "emboss")
os.system('rm %s.fasta %s.fasta %s.txt' % (n1, n2, n1))
# print align
# print alignment
#first seq is consensus, we need to get borders useing second one.
seq = str(align[1, :].seq)
# print seq
begin = seq.index(str(sequence[0]))
end = len(seq) - seq[::-1].index(str(sequence[-1]))
print begin
print end
return alignment[:, begin:end]
def trim_aln_to_seq(alignment, sequence):
"""Trim alignment to a sequence, i.e. leave only postions that correspond to this sequence
Note that seqeuence should be incorportatable into alignment without additional gaps in alignment.
"""
n1 = str(uuid.uuid4())
n2 = str(uuid.uuid4())
#Get consensus
a = SummaryInfo(alignment)
cons = a.dumb_consensus(threshold=0.1, ambiguous='X')
#Needle it
SeqIO.write([SeqRecord(cons, id='CONS', name='CONS')], n1 + '.fasta',
'fasta')
SeqIO.write([SeqRecord(sequence, id='KEY', name='KEY')], n2 + '.fasta',
'fasta')
#Now we will redo it with Needlman Wunsh - the global alignment
needle_cline = NeedleCommandline(asequence=n1 + ".fasta",
bsequence=n2 + ".fasta",
gapopen=10,
gapextend=0.5,
outfile=n1 + ".txt")
stdout, stderr = needle_cline()
# print('Needle alignment')
align = AlignIO.read(n1 + ".txt", "emboss")
os.system('rm %s.fasta %s.fasta %s.txt' % (n1, n2, n1))
# print align
# print alignment
align.extend(alignment)
a = align[1:, :]
return trim_aln_to_key_seq(a, sequence)[1:, :]
def test_proteins(self):
alpha = HasStopCodon(Gapped(generic_protein, "-"), "*")
a = MultipleSeqAlignment([
SeqRecord(Seq("MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-", alpha),
id="ID001"),
SeqRecord(Seq("MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*", alpha),
id="ID002"),
SeqRecord(Seq("MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*", alpha),
id="ID003")
])
self.assertEqual(32, a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
self.assertEqual(str(c), "MHQAIFIYQIGYXXLKSGYIQSIRSPEYDNW*")
c = s.gap_consensus(ambiguous="X")
self.assertEqual(str(c), "MHXXIFIYQIGYXXLKSGYIQSIRSPEYXNWX")
m = s.pos_specific_score_matrix(chars_to_ignore=['-', '*'], axis_seq=c)
self.assertEqual(
str(m),
""" A D E F G H I K L M N P Q R S W Y
M 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
H 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0
X 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
F 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0
L 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
K 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
R 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0
E 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 0.0 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0
W 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
""")
ic = s.information_content(chars_to_ignore=['-', '*'])
self.assertAlmostEqual(ic, 133.061475107, places=6)
def test_proteins(self):
alpha = HasStopCodon(Gapped(generic_protein, "-"), "*")
a = MultipleSeqAlignment([
SeqRecord(Seq("MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-", alpha), id="ID001"),
SeqRecord(Seq("MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*", alpha), id="ID002"),
SeqRecord(Seq("MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*", alpha), id="ID003")])
self.assertEqual(32, a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
self.assertEqual(str(c), "MHQAIFIYQIGYXXLKSGYIQSIRSPEYDNW*")
c = s.gap_consensus(ambiguous="X")
self.assertEqual(str(c), "MHXXIFIYQIGYXXLKSGYIQSIRSPEYXNWX")
m = s.pos_specific_score_matrix(chars_to_ignore=['-', '*'], axis_seq=c)
self.assertEqual(str(m), """ A D E F G H I K L M N P Q R S W Y
M 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
H 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0
X 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
F 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0 0.0 0.0 0.0 0.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 2.0
L 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
K 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
G 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Q 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
I 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
R 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0
S 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0
P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0
E 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
Y 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0
X 0.0 2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
N 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0 0.0 0.0 0.0 0.0 0.0
W 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.0 0.0
X 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
""")
ic = s.information_content(chars_to_ignore=['-', '*'])
self.assertAlmostEqual(ic, 133.061475107, places=6)
def get_aln_and_features(request, ids=None):
from tools.hist_ss import templ, get_hist_ss_in_aln
import subprocess
import StringIO
from Bio.Align import MultipleSeqAlignment
from Bio.Align.AlignInfo import SummaryInfo
if ids is None and request.method == "GET" and "id" in request.GET:
ids = request.GET.getlist("id")
else:
#Returning 'false' stops Bootstrap table
return "false"
sequences = Sequence.objects.filter(id__in=ids[:50])
if len(sequences) == 0:
return None, None
elif len(sequences) == 1:
#Already aligned to core histone
canonical = {"name":"canonical{}".format(sequences.first().variant.core_type), "seq":str(templ[sequences.first().variant.core_type].seq)}
sequences = [canonical, sequences.first().sequence.to_dict()]
features = sequences.first().features
else:
try:
hist_type = max(
[(hist, sequences.filter(variant__core_type_id=hist).count()) for hist in ["H2A", "H2B", "H3", "H4", "H1"]],
key=lambda x:x[1]
)[0]
except ValueError:
hist_type = "Unknown"
muscle = os.path.join(os.path.dirname(sys.executable), "muscle")
process = subprocess.Popen([muscle], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
sequences = "\n".join([s.format() for s in sequences])
aln, error = process.communicate(sequences)
seqFile = StringIO.StringIO()
seqFile.write(aln)
seqFile.seek(0)
sequences = list(SeqIO.parse(seqFile, "fasta")) #Not in same order, but does it matter?
msa = MultipleSeqAlignment(sequences)
save_dir = os.path.join(os.path.sep, "tmp", "HistoneDB")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
hv,ss = get_hist_ss_in_aln(msa, hist_type=hist_type, save_dir=save_dir, debug=False)
a = SummaryInfo(msa)
cons = Sequence(id="consensus", sequence=a.dumb_consensus(threshold=0.1, ambiguous='X').tostring())
features = Features.from_dict(cons, ss)
sequences = [{"name":s.id, "seq":s.seq.tostring()} for s in sequences]
sequences.insert(0, cons.to_dict())
result = {"seqs":sequences, "features":features.full_gff()}
return JsonResponse(result, safe=False)
def lymphocyte_factory( self ):
num_lymphocytes = self.num_lymphocytes
self.lymphocytes = []
summary_info = SummaryInfo( self.friendly )
consensus = summary_info.dumb_consensus()
self.consensus = consensus
for j in range( 0, num_lymphocytes ):
lymphocyte = self.guess_gaps( consensus.data )
lymphocyte = self.scramble( lymphocyte )
self.lymphocytes.append( Lymphocyte( lymphocyte ) )
self.compute_accum_weight()
def get_features_in_aln(alignment, variant, save_dir="", save_gff=True):
#Let's extract consensus
a = SummaryInfo(alignment)
cons = a.dumb_consensus(threshold=0.1, ambiguous='X')
seq = Sequence(id="Consensus",
variant_id=variant,
taxonomy_id=1,
sequence=str(cons))
updated_features = get_variant_features(seq,
save_dir=save_dir,
save_gff=save_gff)
return updated_features
def get_hist_ss_in_aln(alignment, hist_type='Unknown', save_dir="", debug=True, save_censesus=False):
"""Returns sequence elements in histone alignment, all numbers assume first element in seq has number 0!!! Not like in PDB"""
#Let's extract consensus
if(debug):
print alignment
a=SummaryInfo(alignment)
cons=a.dumb_consensus(threshold=0.1, ambiguous='X')
if(debug):
print "Consensus"
print cons
hv, ss = get_hist_ss(cons,hist_type,save_dir,True)
if save_censesus:
return hv,ss,cons
return hv,ss
def annotate_hist_msa(msa, htype, variant=None):
"""Adds to the MSA lines from features.json"""
# read json
with open("inp_data/features.json") as ff:
f = json.load(ff)
f = f[htype]
genseq = f["General" + htype]["sequence"]
genf = f["General" + htype]["feature1"]
a = SummaryInfo(msa)
cons = a.dumb_consensus(threshold=0.1, ambiguous="X")
sr_c = SeqRecord(id="consensus", seq=cons)
sr_genseq = SeqRecord(id="template", seq=Seq(genseq))
auxmsa = muscle_aln([sr_c, sr_genseq])
auxmsa.sort()
gapped_template = str(auxmsa[1].seq)
gapped_cons = str(auxmsa[0].seq)
s = list()
for c, i in zip(gapped_cons, range(len(gapped_template))):
if c != "-":
s.append(gapped_template[i])
newgapped_template = "".join(s)
# now we need to gap feature
gapped_genf = list()
k = 0
for c, i in zip(newgapped_template, range(len(newgapped_template))):
if c != "-":
gapped_genf.append(genf[i - k])
else:
k = k + 1
gapped_genf.append("-")
gapped_genf = "".join(gapped_genf)
newmsa = MultipleSeqAlignment([SeqRecord(id="gi|features|id", description=htype, seq=Seq(gapped_genf))])
newmsa.extend(msa)
# print newmsa
return newmsa
def test_nucleotides(self):
filename = "GFF/multi.fna"
format = "fasta"
alignment = AlignIO.read(filename, format, alphabet=unambiguous_dna)
summary = SummaryInfo(alignment)
c = summary.dumb_consensus(ambiguous="N")
self.assertEqual(str(c), 'NNNNNNNN')
self.assertNotEqual(c.alphabet, unambiguous_dna)
self.assertTrue(isinstance(c.alphabet, DNAAlphabet))
c = summary.gap_consensus(ambiguous="N")
self.assertEqual(str(c), 'NNNNNNNN')
self.assertNotEqual(c.alphabet, unambiguous_dna)
self.assertTrue(isinstance(c.alphabet, DNAAlphabet))
expected = FreqTable({"A": 0.25, "G": 0.25, "T": 0.25, "C": 0.25},
FREQ, unambiguous_dna)
m = summary.pos_specific_score_matrix(chars_to_ignore=['-'],
axis_seq=c)
self.assertEqual(str(m), """ A C G T
N 2.0 0.0 1.0 0.0
N 1.0 1.0 1.0 0.0
N 1.0 0.0 2.0 0.0
N 0.0 1.0 1.0 1.0
N 1.0 2.0 0.0 0.0
N 0.0 2.0 1.0 0.0
N 1.0 2.0 0.0 0.0
N 0.0 2.0 1.0 0.0
""")
# Have a generic alphabet, without a declared gap char, so must tell
# provide the frequencies and chars to ignore explicitly.
ic = summary.information_content(e_freq_table=expected,
chars_to_ignore=['-'])
self.assertAlmostEqual(ic, 7.32029999423075, places=6)
def get_seed_aln_and_features(request, seed):
from Bio.Align import MultipleSeqAlignment
from Bio.Align.AlignInfo import SummaryInfo
seed_file = os.path.join(settings.STATIC_ROOT_AUX, "browse", "seeds")
try:
histone = Histone.objects.get(id=seed)
seed_file = os.path.join(seed_file, "{}".format(histone.id))
except Histone.DoesNotExist:
try:
variant = Variant.objects.get(id=seed)
seed_file = os.path.join(seed_file, variant.hist_type.id, "{}".format(variant.id))
# the default names for canonical are with underscores, so we do not need to convert back. ALEXEY, 30/12/15
# seed_file = os.path.join(seed_file, variant.hist_type.id, "{}".format(variant.id.replace("canonical", "canonical_")))
except Variant.DoesNotExist:
return HttpResponseNotFound('<h1>No histone variant with name {}</h1>'.format(seed))
download = request.GET.get("download", False) == "true"
format = request.GET.get("format", "json")
try:
limit = int(request.GET.get("limit", 0))
except ValueError:
limit = 0
consensus = request.GET.get("consensus", False)
if not consensus in ["limit", "all", False]:
consensus = "all"
response = HttpResponse(content_type='text')
if download:
response['Content-Disposition'] = 'attachment; filename="{}.{}"'.format(seed, format)
sequences = SeqIO.parse("{}.fasta".format(seed_file), "fasta")
if consensus:
sequences = [s for i, s in enumerate(sequences) if consensus == "all" or (consensus == "limit" and i < limit)]
msa = MultipleSeqAlignment(sequences)
a = SummaryInfo(msa)
sequences.insert(0, SeqRecord(id="Consensus", description="", seq=a.dumb_consensus(threshold=0.1, ambiguous='X')))
limit = limit+1 if limit > 0 else 0
def limited_seqs():
for i, seq in enumerate(sequences):
if not consensus or consensus == "limit" or (limit > 0 and i < limit):
yield seq
with open("{}.gff".format(seed_file)) as feature_file:
features = feature_file.read()
if format == "fasta":
SeqIO.write(limited_seqs(), response, "fasta")
elif format == "gff":
response.write(features)
elif format == "pdf":
with open("{}.pdf".format(seed_file)) as pdf:
response.write(pdf.read())
else:
#Default format is json
sequences = [{"name":seq.id, "seq":seq.seq.tostring()} for seq in limited_seqs()]
result = {"seqs":sequences, "features":features}
response.write(json.dumps(result))
return response
def get_aln_and_features(request, ids=None):
from tools.hist_ss import get_variant_features
from tools.L_shade_hist_aln import write_alignments
import subprocess
import StringIO
from Bio.Align import MultipleSeqAlignment
from Bio.Align.AlignInfo import SummaryInfo
from Bio.SeqRecord import SeqRecord
save_dir = os.path.join(os.path.sep, "tmp", "HistoneDB")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
os.chmod(save_dir,0o777)
if ids is None and request.method == "GET" and "id" in request.GET:
ids = request.GET.getlist("id")
sequences = Sequence.objects.filter(id__in=ids[:50])
download = False
upload = False
elif request.GET.get("download", False) == "true":
download = True
upload = False
else:
#Returning 'false' stops Bootstrap table
return "false"
if request.GET.get("upload", False) == "true":
uploaded_sequence = request.session.get("uploaded_sequences", [])
if len(uploaded_sequence) > 0:
try:
variant = Variant.objects.get(id=uploaded_sequence[0]["variant"])
except:
if len(sequences) > 0:
variant = sequences[0].variant
else:
return "false"
uploaded_sequence = Sequence(
id=uploaded_sequence[0]["id"],
variant=variant,
sequence=uploaded_sequence[0]["sequence"],
taxonomy=Taxonomy.objects.get(name=uploaded_sequence[0]["taxonomy"]))
upload = True
download = False
if not download:
if len(sequences) == 0:
return None, None
elif len(sequences) == 1:
#Already aligned to core histone
seq = sequences[0]
hist_type = seq.variant.hist_type.id
variants = [seq.variant]
if upload:
sequences = [uploaded_sequence, seq]
else:
#let's load the corresponding canonical
try:
if(("canonical" in str(seq.variant)) or ("generic" in str(seq.variant))):
canonical=seq
elif(str(seq.variant.hist_type)=="H1"):
canonical=Sequence.objects.filter(variant_id='generic_'+str(seq.variant.hist_type),reviewed=True,taxonomy=seq.taxonomy)[0]
else:
canonical=Sequence.objects.filter(variant_id='canonical_'+str(seq.variant.hist_type),reviewed=True,taxonomy=seq.taxonomy)[0]
except:
try: #try H2A.X as a substitute for canonical
if(str(seq.variant.hist_type)=='H2A'):
canonical=Sequence.objects.filter(variant_id='H2A.X',reviewed=True,taxonomy=seq.taxonomy)[0]
elif(str(seq.variant.hist_type)=='H3'): #Try H3.3
canonical=Sequence.objects.filter(variant_id='H3.3',reviewed=True,taxonomy=seq.taxonomy)[0]
elif(str(seq.variant.id)=='scH1'):
canonical=seq
else:
raise
except:
canonical=seq #we here default not to show the sequence by simply suppling itslef - only one line will be displayed
#default Xenopus
# if(str(seq.variant.hist_type)=="H1"):
# canonical = Sequence(id="0000|xenopus|generic{}".format(hist_type), sequence=str(TemplateSequence.objects.get(variant="General{}".format(hist_type)).get_sequence().seq))
# else:
# canonical = Sequence(id="0000|xenopus|canonical{}".format(hist_type), sequence=str(TemplateSequence.objects.get(variant="General{}".format(hist_type)).get_sequence().seq))
sequences = [canonical, seq]
sequence_label = seq.short_description
else:
seq = sequences[0]
variants = list(Variant.objects.filter(id__in=sequences.values_list("variant", flat=True).distinct()))
sequence_label = "Consensus"
muscle = os.path.join(os.path.dirname(sys.executable), "muscle")
process = subprocess.Popen([muscle], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
sequences = "\n".join([s.format() for s in sequences])
aln, error = process.communicate(sequences)
seqFile = StringIO.StringIO()
seqFile.write(aln)
seqFile.seek(0)
sequences = list(SeqIO.parse(seqFile, "fasta")) #Not in same order, but does it matter?
msa = MultipleSeqAlignment(sequences)
a = SummaryInfo(msa)
cons = Sequence(id=sequence_label, variant_id=variants[0].id, taxonomy_id=1, sequence=a.dumb_consensus(threshold=0.1, ambiguous='X').tostring())
save_dir = os.path.join(os.path.sep, "tmp", "HistoneDB")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
features = get_variant_features(cons, variants=variants, save_dir=save_dir)
#A hack to avoid two canonical seqs
unique_sequences = [sequences[0]] if len(sequences) == 2 and sequences[0].id == sequences[1].id else sequences
# doing the Sequence.short_description work
#Note that the gffs are also generated with the short description not
sequences = [{"name":"QUERY" if "QUERY" in s.id else Sequence.long_to_short_description(s.id), "seq":s.seq.tostring()} for s in unique_sequences]
# sequences = [{"name":s.id, "seq":s.seq.tostring()} for s in sequences]
if sequence_label == "Consensus":
sequences.insert(0, cons.to_dict(id=True))
request.session["calculated_msa_seqs"] = sequences
request.session["calculated_msa_features"] = features#.to_ict() if features else {}
result = {"seqs":sequences, "features":features} #.full_gff() if features else ""}
return JsonResponse(result, safe=False)
else:
format = request.GET.get("format", "json")
response = HttpResponse(content_type='text')
response['Content-Disposition'] = 'attachment; filename="sequences.{}"'.format(format)
sequences = request.session.get("calculated_msa_seqs", [])
features = request.session.get("calculated_msa_features", "")
#features = Features.from_dict(Sequence("Consensus"), features_dict) if features_dict else None
if format == "fasta":
for s in sequences:
print >> response, ">{}\n{}".format(s["name"], s["seq"])
elif format == "gff":
response.write(features) #.full_gff() if features else "")
elif format == "pdf":
aln = MultipleSeqAlignment([SeqRecord(Seq(s["seq"]), id=s["name"]) for s in sequences[1:]])
result_pdf = write_alignments(
[aln],
save_dir = save_dir
)
with open(result_pdf) as pdf:
response.write(pdf.read())
#Cleanup
os.remove(result_pdf)
else:
#Default format is json
result = {"seqs":sequences, "features":features} #.full_gff() if features else ""}
response.write(json.dumps(result))
return response
def get_seed_aln_and_features(request, seed):
from Bio.Align import MultipleSeqAlignment
from Bio.Align.AlignInfo import SummaryInfo
seed_file = os.path.join(settings.STATIC_ROOT_AUX, "browse", "seeds")
try:
histone = Histone.objects.get(id=seed)
seed_file = os.path.join(seed_file, "{}".format(histone.id))
except Histone.DoesNotExist:
try:
variant = Variant.objects.get(id=seed)
seed_file = os.path.join(seed_file, variant.hist_type.id, "{}".format(variant.id))
# the default names for canonical are with underscores, so we do not need to convert back. ALEXEY, 30/12/15
# seed_file = os.path.join(seed_file, variant.hist_type.id, "{}".format(variant.id.replace("canonical", "canonical_")))
except Variant.DoesNotExist:
return HttpResponseNotFound('<h1>No histone variant with name {}</h1>'.format(seed))
download = request.GET.get("download", False) == "true"
format = request.GET.get("format", "json")
try:
limit = int(request.GET.get("limit", 0))
except ValueError:
limit = 0
consensus = request.GET.get("consensus", False)
if not consensus in ["limit", "all", False]:
consensus = "all"
response = HttpResponse(content_type='text')
if download:
response['Content-Disposition'] = 'attachment; filename="{}.{}"'.format(seed, format)
sequences = SeqIO.parse("{}.fasta".format(seed_file), "fasta")
if consensus:
sequences = [s for i, s in enumerate(sequences) if consensus == "all" or (consensus == "limit" and i < limit)]
msa = MultipleSeqAlignment(sequences)
a = SummaryInfo(msa)
sequences.insert(0, SeqRecord(id="Consensus", description="", seq=a.dumb_consensus(threshold=0.1, ambiguous='X')))
limit = limit+1 if limit > 0 else 0
def limited_seqs():
for i, seq in enumerate(sequences):
if not consensus or consensus == "limit" or (limit > 0 and i < limit):
yield seq
with open("{}.gff".format(seed_file)) as feature_file:
features = feature_file.read()
if format == "fasta":
SeqIO.write(limited_seqs(), response, "fasta")
elif format == "gff":
response.write(features)
elif format == "pdf":
with open("{}.pdf".format(seed_file)) as pdf:
response.write(pdf.read())
else:
#Default format is json
sequences = [{"name":seq.id, "seq":seq.seq.tostring()} for seq in limited_seqs()]
result = {"seqs":sequences, "features":features}
response.write(json.dumps(result))
return response
def get_aln_and_features(request, ids=None):
from tools.hist_ss import get_variant_features
from tools.L_shade_hist_aln import write_alignments
import subprocess
import StringIO
from Bio.Align import MultipleSeqAlignment
from Bio.Align.AlignInfo import SummaryInfo
from Bio.SeqRecord import SeqRecord
save_dir = os.path.join(os.path.sep, "tmp", "HistoneDB")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
os.chmod(save_dir,0o777)
if ids is None and request.method == "GET" and "id" in request.GET:
ids = request.GET.getlist("id")
sequences = Sequence.objects.filter(id__in=ids)
download = False
upload = False
elif request.GET.get("download", False) == "true":
download = True
upload = False
else:
#Returning 'false' stops Bootstrap table
return "false"
if request.GET.get("upload", False) == "true":
uploaded_sequence = request.session.get("uploaded_sequences", [])
if len(uploaded_sequence) > 0:
try:
variant = Variant.objects.get(id=uploaded_sequence[0]["variant"])
except:
if len(sequences) > 0:
variant = sequences[0].variant
else:
return "false"
uploaded_sequence = Sequence(
id=uploaded_sequence[0]["id"],
variant=variant,
sequence=uploaded_sequence[0]["sequence"],
taxonomy=Taxonomy.objects.get(name=uploaded_sequence[0]["taxonomy"]))
upload = True
download = False
if not download:
if len(sequences) == 0:
return None, None
elif len(sequences) == 1:
#Already aligned to core histone
seq = sequences[0]
hist_type = seq.variant.hist_type.id
variants = [seq.variant]
if upload:
sequences = [uploaded_sequence, seq]
else:
#let's load the corresponding canonical
try:
if(("canonical" in str(seq.variant)) or ("generic" in str(seq.variant))):
canonical=seq
elif(str(seq.variant.hist_type)=="H1"):
canonical=Sequence.objects.filter(variant_id='generic_'+str(seq.variant.hist_type),reviewed=True,taxonomy=seq.taxonomy)[0]
else:
canonical=Sequence.objects.filter(variant_id='canonical_'+str(seq.variant.hist_type),reviewed=True,taxonomy=seq.taxonomy)[0]
except:
try: #try H2A.X as a substitute for canonical
if(str(seq.variant.hist_type)=='H2A'):
canonical=Sequence.objects.filter(variant_id='H2A.X',reviewed=True,taxonomy=seq.taxonomy)[0]
elif(str(seq.variant.hist_type)=='H3'): #Try H3.3
canonical=Sequence.objects.filter(variant_id='H3.3',reviewed=True,taxonomy=seq.taxonomy)[0]
elif(str(seq.variant.id)=='scH1'):
canonical=seq
else:
raise
except:
canonical=seq #we here default not to show the sequence by simply suppling itslef - only one line will be displayed
#default Xenopus
# if(str(seq.variant.hist_type)=="H1"):
# canonical = Sequence(id="0000|xenopus|generic{}".format(hist_type), sequence=str(TemplateSequence.objects.get(variant="General{}".format(hist_type)).get_sequence().seq))
# else:
# canonical = Sequence(id="0000|xenopus|canonical{}".format(hist_type), sequence=str(TemplateSequence.objects.get(variant="General{}".format(hist_type)).get_sequence().seq))
sequences = [canonical, seq]
sequence_label = seq.short_description
else:
seq = sequences[0]
variants = list(Variant.objects.filter(id__in=sequences.values_list("variant", flat=True).distinct()))
sequence_label = "Consensus"
muscle = os.path.join(os.path.dirname(sys.executable), "muscle")
process = subprocess.Popen([muscle], stdin=subprocess.PIPE, stdout=subprocess.PIPE)
sequences = "\n".join([s.format() for s in sequences])
aln, error = process.communicate(sequences)
seqFile = StringIO.StringIO()
seqFile.write(aln)
seqFile.seek(0)
sequences = list(SeqIO.parse(seqFile, "fasta")) #Not in same order, but does it matter?
msa = MultipleSeqAlignment(sequences)
a = SummaryInfo(msa)
cons = Sequence(id=sequence_label, variant_id=variants[0].id, taxonomy_id=1, sequence=a.dumb_consensus(threshold=0.1, ambiguous='X').tostring())
save_dir = os.path.join(os.path.sep, "tmp", "HistoneDB")
if not os.path.exists(save_dir):
os.makedirs(save_dir)
features = get_variant_features(cons, variants=variants, save_dir=save_dir)
#A hack to avoid two canonical seqs
unique_sequences = [sequences[0]] if len(sequences) == 2 and sequences[0].id == sequences[1].id else sequences
# doing the Sequence.short_description work
#Note that the gffs are also generated with the short description not
sequences = [{"name":"QUERY" if "QUERY" in s.id else Sequence.long_to_short_description(s.id), "seq":s.seq.tostring()} for s in unique_sequences]
# sequences = [{"name":s.id, "seq":s.seq.tostring()} for s in sequences]
if sequence_label == "Consensus":
sequences.insert(0, cons.to_dict(id=True))
request.session["calculated_msa_seqs"] = sequences
request.session["calculated_msa_features"] = features#.to_ict() if features else {}
result = {"seqs":sequences, "features":features} #.full_gff() if features else ""}
return JsonResponse(result, safe=False)
else:
format = request.GET.get("format", "json")
response = HttpResponse(content_type='text')
response['Content-Disposition'] = 'attachment; filename="sequences.{}"'.format(format)
sequences = request.session.get("calculated_msa_seqs", [])
features = request.session.get("calculated_msa_features", "")
#features = Features.from_dict(Sequence("Consensus"), features_dict) if features_dict else None
if format == "fasta":
for s in sequences:
print >> response, ">{}\n{}".format(s["name"], s["seq"])
elif format == "gff":
response.write(features) #.full_gff() if features else "")
elif format == "pdf":
aln = MultipleSeqAlignment([SeqRecord(Seq(s["seq"]), id=s["name"]) for s in sequences[1:]])
result_pdf = write_alignments(
[aln],
save_dir = save_dir
)
with open(result_pdf) as pdf:
response.write(pdf.read())
#Cleanup
os.remove(result_pdf)
else:
#Default format is json
result = {"seqs":sequences, "features":features} #.full_gff() if features else ""}
response.write(json.dumps(result))
return response
