def getFastaEntry(self, entryNum, resultFolder):
fastaFile = self.pathToFasta
from Bio import AlignIO, SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped
alignmentIterator = AlignIO.parse(fastaFile,
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(),
"-"))
queryFasta = resultFolder + "/" + "Query_%d.faa" % (entryNum, )
alignment = alignmentIterator.next()
if entryNum > len(alignment):
return None
desiredSeqString = str(alignment[entryNum - 1].seq)
desiredSeqString = desiredSeqString.replace("-", "")
#print desiredSeqString
seqNoGaps = Seq(desiredSeqString,
alphabet=IUPAC.ExtendedIUPACProtein())
seqRecNoGaps = SeqRecord(seq=seqNoGaps, id=alignment[entryNum - 1].id)
#print seqRecNoGaps.seq
#print seqRecNoGaps.id
SeqIO.write(seqRecNoGaps, queryFasta, "fasta")
return queryFasta
def writeNoGaps(self, outputfile):
fastaFile = self.pathToFasta
from Bio import AlignIO, SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped
seqIterator = SeqIO.parse(fastaFile,
"fasta",
alphabet=Gapped(IUPAC.ExtendedIUPACProtein(),
"-"))
outFasta = outputfile
records = list()
for alignment in seqIterator:
desiredSeqString = str(alignment.seq)
desiredSeqString = desiredSeqString.replace("-", "")
#print desiredSeqString
seqNoGaps = Seq(desiredSeqString,
alphabet=IUPAC.ExtendedIUPACProtein())
seqRecNoGaps = SeqRecord(seq=seqNoGaps, id=alignment.id)
#print seqRecNoGaps.seq
#print seqRecNoGaps.id
records.append(seqRecNoGaps)
SeqIO.write(records, outFasta, "fasta")
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':
# Deliberately using a fancy protein alphabet for testing:
nucl = SeqIO.index(i[0][0], 'fasta', alphabet=IUPAC.IUPACUnambiguousDNA())
prot = AlignIO.read(i[0][1], 'clustal', alphabet=Gapped(IUPAC.ExtendedIUPACProtein()))
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 testLimit(self, list_seqs, start):
"""
Extract the aa sequences in the window.
list_seqs is the list of sequence id in the alignment (not the id associated
with the Bio.Seq object).
start is the index of the start of the window.
"""
frame = start % 3
aa_window_length = int(self.window_length / 3)
begin = int((start - frame) / 3)
end = int(begin + aa_window_length)
if frame == 0:
t_align = self.t_align0
elif frame == 1:
t_align = self.t_align1
else:
t_align = self.t_align2
sub_align = MulAlign([], Gapped(IUPAC.ExtendedIUPACProtein(), "N"))
for idx in list_seqs:
sub_align.append(t_align[idx][begin:end])
result = []
for c in range(aa_window_length):
c = Counter(sub_align[:, c])
# count the most common aa
nbr_most_common = c.most_common(1)[0][1]
if nbr_most_common / len(list_seqs) >= self.min_aa_ratio:
result.append(True)
else:
result.append(False)
return result
def generateFastaWithOutEntry(self, entryNumToRemove, resultFolder):
fastaFile = self.pathToFasta
# fastaFileClade = sys.argv[2]
# entryToTest = int(sys.argv[3])
entryToTest = int(entryNumToRemove)
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import MultipleSeqAlignment
alignmentIterator = AlignIO.parse(fastaFile,
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(),
"-"))
alignment = alignmentIterator.next()
pathToNewFile = resultFolder + "/" + "WithOutEntry_%d.faa" % (
entryToTest, )
#print testAlignment[entryToTest].id
#print testAlignment[entryToTest].seq
#print "Number of entries: ",len(testAlignment)
# Here we remove the desired element
newTestAlignment = []
for i in range(len(alignment)):
if i != entryToTest - 1:
newTestAlignment.append(alignment[i])
newAlignment = MultipleSeqAlignment(newTestAlignment)
AlignIO.write(newAlignment, pathToNewFile, "fasta")
#print "Number of entries after: ",len(newTestAlignment)
return pathToNewFile
def writeFastas(self, pathToCompleteFastaAlignment, outputPath):
"""
Writes individual clades as fasta alignments, where the files are stored in the output path
and the name of each file is composed of <clade_name>.fasta . Data is obtained from the complete
fasta alignment provided (pathToCompleteFastaAlignment) and the mappings given to the constructor.
The mappings are a dictionary of fasta ids to clade names. Elements in the alignment not present
in the mappings won't end in any clade fasta file.
:param pathToCompleteFastaAlignment:
:param outputPath:
"""
from Bio import SeqIO, AlignIO
from Bio.Alphabet import IUPAC, Gapped
# create file handles for each clade
for cladeName in list(self._mappings.values()):
self._clade2fileHandle[cladeName] = open(outputPath + "/" +
cladeName + ".fas")
# read complete alignment
alignment = AlignIO.read(pathToCompleteFastaAlignment,
"fasta",
alphabet=Gapped(IUPAC.ExtendedIUPACProtein(),
"-"))
for record in alignment:
handle = self._clade2fileHandle[self._mappings[record.id]]
SeqIO.write(record, handle, "fasta")
for cladeName in self._clade2fileHandle.keys():
self._clade2fileHandle[cladeName].close()
def _guess_consensus_alphabet(self, ambiguous):
"""Pick an (ungapped) alphabet for an alignment consesus sequence (PRIVATE).
This just looks at the sequences we have, checks their type, and
returns as appropriate type which seems to make sense with the
sequences we've got.
"""
# Start with the (un-gapped version of) the alignment alphabet
a = Alphabet._get_base_alphabet(self.alignment._alphabet)
# Now check its compatible with all the rest of the sequences
for record in self.alignment:
# Get the (un-gapped version of) the sequence's alphabet
alt = Alphabet._get_base_alphabet(record.seq.alphabet)
if not isinstance(alt, a.__class__):
raise ValueError(
"Alignment contains a sequence with an incompatible alphabet."
)
# Check the ambiguous character we are going to use in the consensus
# is in the alphabet's list of valid letters (if defined).
if (
hasattr(a, "letters")
and a.letters is not None
and ambiguous not in a.letters
):
# We'll need to pick a more generic alphabet...
if isinstance(a, IUPAC.IUPACUnambiguousDNA):
if ambiguous in IUPAC.IUPACUnambiguousDNA().letters:
a = IUPAC.IUPACUnambiguousDNA()
else:
a = Alphabet.generic_dna
elif isinstance(a, IUPAC.IUPACUnambiguousRNA):
if ambiguous in IUPAC.IUPACUnambiguousRNA().letters:
a = IUPAC.IUPACUnambiguousRNA()
else:
a = Alphabet.generic_rna
elif isinstance(a, IUPAC.IUPACProtein):
if ambiguous in IUPAC.ExtendedIUPACProtein().letters:
a = IUPAC.ExtendedIUPACProtein()
else:
a = Alphabet.generic_protein
else:
a = Alphabet.single_letter_alphabet
return a
def test_translate(self):
"""Test that a dna open reading frame is translated correctly."""
orf = 'ATGTGGAGACGGAAACATCCGAGGACATCCGGAGGAACCCGGGGAGTTCTGAGTGGTAATTAG'
expected_primers = Seq('MWRRKHPRTSGGTRGVLSGN*',
HasStopCodon(IUPAC.ExtendedIUPACProtein(), '*'))
result_primers = translate(orf)
self.assertEqual(result_primers, expected_primers)
self.assertEqual(len(result_primers), 21)
self.assertEqual(isinstance(result_primers, Seq), True)
def translate(self, align, offset):
"""
Translate the alignment according to the selected frame which is set
according to 'offset' value
"""
end = ((align.get_alignment_length() - offset) // 3) * 3 + offset
t_align = MulAlign([], Gapped(IUPAC.ExtendedIUPACProtein(), "N"))
for rec in align:
seq = str(rec.seq).upper().replace("-", "N").replace("n", "N")
new_seq = Seq(seq,
IUPAC.IUPACAmbiguousDNA())[offset:end].translate()
new_rec = SeqRecord(new_seq,
name=rec.name,
id=rec.id,
description="")
t_align.append(new_rec)
return t_align
def process_upload(sequences, format, request):
if format not in ["file", "text"]:
raise InvalidFASTA(
"Invalid format: {}. Must be either 'file' or 'text'.".format(
format))
if format == "text":
seq_file = io.BytesIO()
seq_file.write(sequences)
seq_file.seek(0)
sequences = seq_file
sequences = SeqIO.parse(sequences, "fasta", IUPAC.ExtendedIUPACProtein())
try:
sequence = next(sequences)
except StopIteration:
raise InvalidFASTA("No sequences parsed.")
if not Alphabet._verify_alphabet(sequence.seq):
raise InvalidFASTA("Sequence {} is not a protein.".format(sequence.id))
result = [str(sequence.id)]
classifications, ids, rows = upload_hmmer(sequence)
result.append(classifications[0][1])
secondary_classification = classifications[0][2]
result.append(secondary_classification
if secondary_classification != "Unknown" else None)
result.append(rows)
result.append(upload_blastp(sequence)[0])
result.append(result[-1][0]["id"])
result.append(result[-2][0]["variant"])
request.session["uploaded_sequences"] = [{
"id":
"QUERY", #sequence.id,
"variant":
classifications[0][1],
"sequence":
str(sequence.seq),
"taxonomy":
result[-3][0]["taxonomy"]
}]
return result
#!/usr/bin/env python
import argparse
from Bio import SeqIO
from Bio.Alphabet import IUPAC
import os
import subprocess
parser = argparse.ArgumentParser(
description="Zhiping's indexing solution for counting unique peptides")
parser.parse_args()
aa_letters = IUPAC.ExtendedIUPACProtein().letters
for aa1 in aa_letters:
for aa2 in aa_letters:
# Make indexed directories with first and second amino acids
if not os.path.exists(aa1 + aa2):
os.makedirs(aa1 + aa2)
os.chdir(aa1 + aa2)
# Write script for cluster
SRC = open(aa1 + aa2 + "_hash_count.py", 'w')
SRC.write(
"from Bio import SeqIO\n" + "import sys\n" + "import os\n" +
"# Flush STOUT continuously\n" +
"sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)\n" +
"OUT = open('" + aa1 + aa2 + "_peptides.txt', 'w')\n" +
"counter = 0\n" + "hash_count = {}\n"
"# Loop through records\n" +
"for seq_record in SeqIO.parse('../../nr.fasta', 'fasta'):\n" +
" if counter%1000000 == 0:\n" +
" print 'On seq ' + str(counter) + '\\n'\n" +
" for i in range(len(seq_record.seq) - 14 + 1):\n" +
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import IUPAC, Gapped
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
os.chdir(sys.argv[1])
listing = os.listdir(".")
consensus = {}
genConsensus = ''
pssmGen = ''
consensusThres = 0.7
#generalAlignment = AlignIO.parse(sys.argv[2],"fasta",alphabet=IUPAC.ExtendedIUPACProtein())
generalAlignment = AlignIO.parse(sys.argv[2],
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(), "-"))
lengthGenAl = 0
for genAlignment in generalAlignment:
sumGen = AlignInfo.SummaryInfo(genAlignment)
genConsensus = sumGen.gap_consensus(consensusThres)
#pssmGen = sumGen.pos_specific_score_matrix(genConsensus,chars_to_ignore = ['-'])
pssmGen = sumGen.pos_specific_score_matrix(genConsensus)
lengthGenAl = len(genAlignment)
for item in listing:
if item.endswith(".fas"):
#alignments = AlignIO.parse(item,"fasta",alphabet=IUPAC.ExtendedIUPACProtein())
alignments = AlignIO.parse(item,
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(), "-"))
__author__="pmoreno"
__date__ ="$May 29, 2011 5:16:28 PM$"
if __name__ == "__main__":
#dirOfHMMModels = sys.argv[1]
fastaFileCladeNoGeneralSignal = sys.argv[1]
fastaFileClade = sys.argv[2]
entryToTest = int(sys.argv[3])
resultFolder = sys.argv[4]
from Bio import AlignIO, SeqIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import MultipleSeqAlignment
alignmentNoGenSignalIterator = AlignIO.parse(fastaFileCladeNoGeneralSignal,"fasta",alphabet=Gapped(IUPAC.ExtendedIUPACProtein(),"-"));
alignmentIterator = AlignIO.parse(fastaFileClade,"fasta",alphabet=Gapped(IUPAC.ExtendedIUPACProtein(),"-"));
noGenSignalAlignment = alignmentNoGenSignalIterator.next()
queryFasta = resultFolder+"/"+"Query_%d.faa" % (entryToTest,)
ownCladeProfile = resultFolder+"/"+"ForOwnCladeProfile_%d.faa" % (entryToTest,)
#print testAlignment[entryToTest].id
#print testAlignment[entryToTest].seq
alignmentWithSignal = alignmentIterator.next()
desiredSeqString = str(alignmentWithSignal[entryToTest-1].seq)
desiredSeqString = desiredSeqString.replace("-", "")
#print desiredSeqString
seqNoGaps = Seq(desiredSeqString, alphabet=IUPAC.ExtendedIUPACProtein())
#print seqNoGaps
seqRecNoGaps = SeqRecord(seq=seqNoGaps, id=alignmentWithSignal[entryToTest-1].id)
'TTG': 'L',
'TAC': 'Y',
'TAT': 'Y',
'TAA': '_',
'TAG': 'O',
'TGC': 'C',
'TGT': 'C',
'TGA': 'U',
'TGG': 'W',
}
tt_flip = flip_trans_table(tt_11)
matrix = matlist.blosum62
msa_alphabet = AlphabetEncoder(IUPAC.ExtendedIUPACProtein(), '-.')
alignments = AlignIO.read(align_in, 'fasta', alphabet=msa_alphabet)
# print(len(list(alignments))) # number of orthologs use in final msa
uid_pattern = re.compile(r'uid=(\S+?);')
tax_id_pattern = re.compile(r'tax_id=(\d+)')
# name outfile with uid of gene of interest as has been convention; expects it to be the first gene in the msa
uid = re.search(uid_pattern, alignments[0].id).group(1)
bad_codons = ['...', '---', 'NNN'] # codons that will not receive scores
# get disorder for each sequence in the msa
# make this a function later
disorder_strength = [
] # list of numerical disorder strength score for each aa seq in msa (with gaps)
def run(self, consensusThreshold):
from Bio import AlignIO, SeqIO
from Bio.Align import AlignInfo
# from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import IUPAC, Gapped
# from Bio.Seq import Seq
# from Bio.SeqRecord import SeqRecord
# Directory where files are
# os.chdir(sys.argv[1])
# listing = os.listdir(".")
listing = os.listdir(self.pathToCladesAlignments)
consensus = {}
genConsensus = ''
pssmGen = ''
# this value should be read from the arguments or else use a default
consensusThres = consensusThreshold
# sys.argv[2] holds the path to the general alignment
generalAlignment = AlignIO.parse(self.generalAlignment,
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(),
"-"))
lengthGenAl = 0
positionsToMask = []
for genAlignment in generalAlignment:
sumGen = AlignInfo.SummaryInfo(genAlignment)
genConsensus = sumGen.gap_consensus(consensusThres)
for index, residue in enumerate(genConsensus):
if genConsensus[index] == '-':
continue
if genConsensus[index] == 'X':
continue
positionsToMask.append(index)
#pssmGen = sumGen.pos_specific_score_matrix(genConsensus,chars_to_ignore = ['-'])
pssmGen = sumGen.pos_specific_score_matrix(genConsensus)
lengthGenAl = len(genAlignment)
print positionsToMask
print listing
resultAlignFiles = []
for item in listing:
if item.endswith(".fas"):
#alignments = AlignIO.parse(item,"fasta",alphabet=IUPAC.ExtendedIUPACProtein())
alignments = AlignIO.parse(self.pathToCladesAlignments + item,
"fasta",
alphabet=Gapped(
IUPAC.ExtendedIUPACProtein(),
"-"))
for alignment in alignments:
summ = AlignInfo.SummaryInfo(alignment)
consensus[item] = summ.gap_consensus(consensusThres)
for posToMask in positionsToMask:
if consensus[item][posToMask] == '-':
continue
for alignElement in alignment:
mutSeq = alignElement.seq.tomutable()
mutSeq[posToMask] = 'X'
alignElement.seq = mutSeq.toseq()
SeqIO.write(
alignment, self.outPutPath + item +
"_noPKSsignal_Thres%d.faa" % (consensusThres * 100, ),
"fasta")
resultAlignFiles.append(self.outPutPath + item +
"_noPKSsignal_Thres%d.faa" %
(consensusThres * 100, ))
summ = AlignInfo.SummaryInfo(alignment)
consensus[item] = summ.gap_consensus(consensusThres)
print item, consensus[item]
return resultAlignFiles