def preprocess(self,buildAnnotations=True):
# print "Preprocessing"
# if buildAnnotations:
# annotation.go(self.rootdir, self.annotated_genes) #changed to annotation - Nafiz
# intergene.go(self.rootdir, self.intergenes)
print "Preprocessing"
#Combine all genome files into a single genome fasta file
#https://github.com/mortonjt/Boa/blob/master/src/format/fasta.py
fasta.go(self.genome_dir,
self.all_fasta,
self.all_faidx,
self.six_fasta,
self.six_faidx)
indexer = fasta.Indexer(self.all_fasta,self.all_faidx) #a class at fasta.py
indexer.index()
indexer.load()
#https://github.com/mortonjt/Boa/blob/master/src/genome/intergene.py
intergene.go(self.genome_dir,self.intergenes)
#https://github.com/mortonjt/Boa/blob/master/src/annotation/annotation.py
annotation.go(self.genome_dir,self.annotated_genes,index_obj=indexer)
#Combine all gff files together
outhandle = open(self.gff,'w')
for root, subFolders, files in os.walk(self.genome_dir):
for fname in files:
genome_dir = []
organism,ext = os.path.splitext(os.path.basename(fname))
absfile=os.path.join(root,fname)
if ext==".gff":
shutil.copyfileobj(open(absfile),outhandle)
outhandle.close()
tmpfile = "tmp%d.faa"%(os.getpid())
outhandle = open(tmpfile,'w')
for root, subFolders, files in os.walk(self.genome_dir):
for fname in files:
genome_dir = []
organism,ext = os.path.splitext(os.path.basename(fname))
absfile=os.path.join(root,fname)
if ext==".fna":
shutil.copyfileobj(open(absfile),outhandle)
outhandle.close()
faa.reformat(tmpfile,self.faa)
os.remove(tmpfile)
faaindex = fasta.Indexer(self.faa,self.faaidx)
faaindex.index()
def test(self):
tmpfile = "tmp%d.faa"%(os.getpid())
faa.reformat(self.faa,tmpfile)
os.rename(tmpfile,self.faa)
faaindex = fasta.Indexer(self.faa,self.faaidx)
faaindex.index()
faaindex.load()
gff = GFF(self.gff,self.outfasta,self.fasta,self.faidx,False)
#gff.indextree()
gff.indexdb()
hits = gff.call_orfs(self.queries,faaindex)
print hits
ids,seqs = zip(*hits)
correct_queries = [('CP002279.1','toxin.fa.cluster2.fa',0,0,1,51,100,
'Mesorhizobium opportunistum WSM2075, complete genome'),
('CP002279.1','transport.fa.cluster2.fa',0,0,1,1551,2000,
'Mesorhizobium opportunistum WSM2075, complete genome'),
('CP002279.1','transport.fa.cluster2.fa',0,0,1,3551,4000,
'Mesorhizobium opportunistum WSM2075, complete genome')]
self.assertItemsEqual(ids,correct_queries)
def preprocess(self):
print "Preprocessing"
#Combine all genome files into a single genome fasta file
fasta.go(self.genome_dir,
self.all_fasta,
self.all_faidx,
self.six_fasta,
self.six_faidx)
indexer = fasta.Indexer(self.all_fasta,self.all_faidx)
indexer.index()
indexer.load()
intergene.go(self.genome_dir,self.intergenes)
annotation.go(self.genome_dir,self.annotated_genes,index_obj=indexer)
#Combine all gff files together
outhandle = open(self.gff,'w')
for root, subFolders, files in os.walk(self.genome_dir):
for fname in files:
genome_files = []
organism,ext = os.path.splitext(os.path.basename(fname))
absfile=os.path.join(root,fname)
if ext==".gff":
shutil.copyfileobj(open(absfile),outhandle)
outhandle.close()
tmpfile = "tmp%d.faa"%(os.getpid())
outhandle = open(tmpfile,'w')
for root, subFolders, files in os.walk(self.genome_dir):
for fname in files:
genome_files = []
organism,ext = os.path.splitext(os.path.basename(fname))
absfile=os.path.join(root,fname)
if ext==".faa":
shutil.copyfileobj(open(absfile),outhandle)
outhandle.close()
faa.reformat(tmpfile,self.faa)
os.remove(tmpfile)
faaindex = fasta.Indexer(self.faa,self.faaidx)
faaindex.index()