def getTemplates(self):
if self.debug:
print(self.seq)
result_handle = NCBIWWW.qblast("blastp",
"pdb",
str(self.seq),
expect=0.01)
blast_records = NCBIXML.parse(result_handle)
if self.debug:
print("BLAST Request Finished")
print()
for record in blast_records:
for alignment in record.alignments:
id = alignment.accession
fasta = self.getFastaFromId(id)
title = alignment.title
length = alignment.length
template = Template(id=id,
fasta=fasta,
sequence=title,
length=length,
alignments=[])
self.templates[id] = template
self.fastas[id] = fasta
for hsp in alignment.hsps:
a = Alignment(id=id,
title=title,
expect=hsp.expect,
score=hsp.score,
identities=hsp.identities,
similarity=(100 * hsp.identities /
len(self.seq)),
target=hsp.query,
targetstart=hsp.query_start,
match=hsp.match,
template=hsp.sbjct,
templatestart=hsp.sbjct_start,
length=length)
targetfront = str(self.seq[:a.targetstart - 1])
targetend = str(self.seq[(a.targetstart + a.length):])
a.target = ''.join(targetfront) + a.target + ''.join(
targetend)
a.length = len(a.target)
templatefront = ['-'] * (a.targetstart - 1)
templateend = ['-'] * (len(self.seq) -
(a.targetstart + a.length))
a.template = ''.join(templatefront) + a.template + ''.join(
templateend)
self.templates[id].alignments.append(a)
self.alignments.append(a)
for id, fasta in self.fastas.items():
fname = '%s/%s.fasta' % (self.fastasfolder, id)
if not os.path.exists(fname):
f = open(fname, 'w')
SeqIO.write(fasta, f, 'fasta')
f.close()
for i, a in enumerate(self.alignments):
fname = '%s/%s-%s.alignment' % (self.alignmentsfolder, a.id,
str(i))
if not os.path.exists(fname):
f = open(fname, 'w')
json.dump(a.toJSON(), f)
f.close()
return self.templates.keys()
def getTemplates(self):
# http://biopython.org/DIST/docs/api/Bio.Blast.NCBIWWW-module.html
if self.debug:
print(self.seq)
# Send BLAST request to server
# Use blastp (protein) for the method
# Use pdb as the database
result_handle = NCBIWWW.qblast("blastp","pdb",str(self.seq),expect=0.01)
# Parse the results into blast records
blast_records = NCBIXML.parse(result_handle)
if self.debug:
print("BLAST Request Finished")
# Read through each blast record
for record in blast_records:
# Grab the alignments from each record
for alignment in record.alignments:
# Use the alignment id as the template key
id = alignment.accession
fasta = self.getFastaFromId(id)
title = alignment.title
length = alignment.length
# Set up the template object for this id
template = Template(
id=id,fasta=fasta,sequence=title,
length=length,alignments=[]
)
# Store the template in the template dict
self.templates[id] = template
"""
self.templates[id] = {"fasta":self.getFastaFromId(id),
'asequence':alignment.title,
'alength':alignment.length,
"alignments":[]}
"""
# Store fasta in dict
self.fastas[id] = fasta
# Get all alignments for this template
for hsp in alignment.hsps:
# Create an alignment object
a = Alignment(
id=id,title=title,expect=hsp.expect,score=hsp.score,
identities=hsp.identities,similarity=(100*hsp.identities/len(self.seq)),
target=hsp.query,targetstart=hsp.query_start,match=hsp.match,
template=hsp.sbjct,templatestart=hsp.sbjct_start,length=length
)
# Alignment isn't necessarily the same size as the sequence
targetfront = str(self.seq[:a.targetstart-1])
targetend = str(self.seq[(a.targetstart+a.length):])
a.target = ''.join(targetfront) + a.target + ''.join(targetend)
a.length = len(a.target)
templatefront = ['-']*(a.targetstart-1)
templateend = ['-']*(len(self.seq)-(a.targetstart+a.length))
a.template = ''.join(templatefront) + a.template + ''.join(templateend)
if self.debug:
print("Seq vs Target Length:",len(self.seq),a.length)
# Append the alignment to the template's alignments
self.templates[id].alignments.append(a)
self.alignments.append(a)
"""
self.templates[id]["alignments"].append({'expect':hsp.expect,
'score':hsp.score,
'identities':hsp.identities,
'similarity':(100*hsp.identities/len(self.seq)),
'target':hsp.query,
'match':hsp.match,
'template':hsp.sbjct})
"""
if self.debug:
print()
print('****ALIGNMENT***')
print('id:',id)
print('sequence:', title)
print('length:',length)
print('e value:', hsp.expect)
print('score:', hsp.score)
print('identities:',(100*hsp.identities/len(self.seq))) # need to print percentage of similarities
print("Target :" + hsp.query[0:75] + '...')
print("Match :" + hsp.match[0:75] + '...')
print("Template:" + hsp.sbjct[0:75] + '...')
print()
# Save off the fasta file
for id,fasta in self.fastas.items():
fname = '%s/%s.fasta' % (self.fastasfolder,id)
if not os.path.exists(fname):
f = open(fname,'w')
SeqIO.write(fasta,f,'fasta')
f.close()
# Save off the alignments
for i,a in enumerate(self.alignments):
fname = '%s/%s-%s.alignment' % (self.alignmentsfolder,a.id,str(i))
if not os.path.exists(fname):
f = open(fname,'w')
json.dump(a.toJSON(),f)
f.close()
return self.templates.keys()
