def blast_against_genome(self, ctx, params):
# ctx is the context object
# return variables are: returnVal
#BEGIN blast_against_genome
if len(params['query']) > 5:
sequence = params['query']
else:
#error message: your sequence are too short
print "error"
#else:
#sequence=script_util.get_seq(params['gene_id'])
#sequence=(params['gene_id'])
genome_id = 'Bifidobacterium_animalis_subsp._lactis_AD011'
workspaceid = 'plane83:1436884411390'
#print "generate input file\n"
target = open('tmp_seq', 'w')
target.write(">")
target.write("input_seq\n")
target.write(sequence)
target.close()
#print "downloading genome object from workspace\n"
genome = script_util.get_genome('genome_id', 'workspaceid',
ctx['token'])
#print "finished downloading\n";
#extract sequences from the genome object
with open('tmp_data', 'w') as outfile:
json.dump(genome, outfile)
res1 = open('tmp_data').read()
res = json.loads(res1)
os.remove('tmp_data')
#print "making dir\n"
if os.path.exists('blast_db'):
files = glob.glob('blast_db/*')
for f in files:
os.remove(f)
if not os.path.exists('blast_db'): os.makedirs('blast_db')
target = open('blast_db/tmp_genome_fasta', 'w')
for gene in res['data']['features']:
if 'protein_translation' in gene.keys():
target.write(">")
target.write(gene['id'])
target.write("\n")
target.write(gene['protein_translation'])
target.write("\n")
target.close()
#print "formatdb..\n"
#format database for blast
os.system("formatdb -i blast_db/tmp_genome_fasta -p T")
os.system(
"blastall -p blastp -i tmp_seq -m 9 -o tmp_out -d blast_db/tmp_genome_fasta"
)
os.remove('tmp_seq')
print "test"
res = script_util.extract_blast_output('tmp_out')
os.remove(tmp_out)
os.remove(input_seq)
returnVal = res
#END blast_against_genome
# At some point might do deeper type checking...
if not isinstance(returnVal, basestring):
raise ValueError('Method blast_against_genome return value ' +
'returnVal is not type basestring as required.')
# return the results
return [returnVal]
def blast_against_genome(self, ctx, params):
# ctx is the context object
# return variables are: returnVal
#BEGIN blast_against_genome
if len(params['query']) > 5:
sequence=params['query']
else:
#error message: your sequence are too short
print "error"
#else:
#sequence=script_util.get_seq(params['gene_id'])
#sequence=(params['gene_id'])
genome_id='Bifidobacterium_animalis_subsp._lactis_AD011'
workspaceid='plane83:1436884411390'
#print "generate input file\n"
target=open('tmp_seq','w')
target.write(">")
target.write("input_seq\n")
target.write(sequence)
target.close()
#print "downloading genome object from workspace\n"
genome=script_util.get_genome('genome_id','workspaceid',ctx['token'])
#print "finished downloading\n";
#extract sequences from the genome object
with open('tmp_data','w') as outfile:
json.dump(genome, outfile)
res1=open('tmp_data').read()
res=json.loads(res1)
os.remove('tmp_data')
#print "making dir\n"
if os.path.exists('blast_db'):
files=glob.glob('blast_db/*')
for f in files: os.remove(f)
if not os.path.exists('blast_db'): os.makedirs('blast_db')
target=open('blast_db/tmp_genome_fasta','w')
for gene in res['data']['features']:
if 'protein_translation' in gene.keys():
target.write(">")
target.write(gene['id'])
target.write("\n")
target.write(gene['protein_translation'])
target.write("\n")
target.close()
#print "formatdb..\n"
#format database for blast
os.system("formatdb -i blast_db/tmp_genome_fasta -p T")
os.system("blastall -p blastp -i tmp_seq -m 9 -o tmp_out -d blast_db/tmp_genome_fasta")
os.remove('tmp_seq')
print "test"
res=script_util.extract_blast_output('tmp_out')
os.remove(tmp_out)
os.remove(input_seq)
returnVal = res
#END blast_against_genome
# At some point might do deeper type checking...
if not isinstance(returnVal, basestring):
raise ValueError('Method blast_against_genome return value ' +
'returnVal is not type basestring as required.')
# return the results
return [returnVal]
def blast_against_genome(self, ctx, params):
# ctx is the context object
# return variables are: returnVal
#BEGIN blast_against_genome
print "start"
if len(params['query']) > 5:
sequence=params['query']
else:
#error message: your sequence are too short
print "error"
#else:
#sequence=script_util.get_seq(params['gene_id'])
#sequence=(params['gene_id'])
genome_id='Bifidobacterium_animalis_subsp._lactis_AD011'
workspaceid='plane83:1436884411390'
#print "generate input file for query sequence\n"
target=open('tmp_seq','w')
target.write(">")
target.write("input_seq\n")
target.write(sequence)
target.close()
#print "downloading genome object from workspace\n"
#genome=script_util.get_genome('genome_id','workspaceid',ctx['token'])
#print "finished downloading\n";
if os.path.exists('blast_db'):
files=glob.glob('blast_db/*')
for f in files: os.remove(f)
if not os.path.exists('blast_db'): os.makedirs('blast_db')
#with open('tmp_data','w') as outfile:
# json.dump(genome, outfile)
if(params['blast_program'] == 'blastp'):
formatdb_type='T'
#extract protein sequences from the genome object
res1=open('tmp_data').read()
res=json.loads(res1)
target=open('blast_db/tmp_genome_fasta','w')
for gene in res['data']['features']:
if 'protein_translation' in gene.keys():
target.write(">" + gene['id'] + "\n" + gene['protein_translation'] + "\n")
target.close()
if(params['blast_program'] == 'blastn'):
formatdb_type='F'
#extract dna sequence from the genome object
res1=open('tmp_data').read()
res=json.loads(res1)
target=open('blast_db/tmp_genome_fasta','w')
for gene in res['data']['features']:
if 'dna_sequence' in gene.keys():
target.write(">" + gene['id'] + "\n" + gene['dna_sequence'] + "\n")
target.close()
#os.remove('tmp_data')
#print "formatdb..\n"
#format database for blast
cmdstring="formatdb -i blast_db/tmp_genome_fasta -p %s" %(formatdb_type)
os.system(cmdstring)
#blast search
cmdstring="blastall -p %s -i tmp_seq -m 9 -o tmp_out -d blast_db/tmp_genome_fasta -e %s" % (params['blast_program'], params['e-value'])
os.system(cmdstring)
os.remove('tmp_seq')
#extract the blast output
res=script_util.extract_blast_output('tmp_out')
os.remove('tmp_out')
res1=json.loads(res)
print "finished"
returnVal = res1
#END blast_against_genome
# At some point might do deeper type checking...
if not isinstance(returnVal, list):
raise ValueError('Method blast_against_genome return value ' +
'returnVal is not type list as required.')
# return the results
return [returnVal]
