def codon_usage(self, feature_ids=False):
if not(feature_ids):
return sequtil.codon_usage(self.orf_sequence)
else:
names = ['%s (%s)' % (c, sequtil.translate(c))
for c in sequtil.codons_unambiguous]
return (sequtil.codons_unambiguous, names)
def codon_usage(self, feature_ids=False):
if not (feature_ids):
return sequtil.codon_usage(self.orf_sequence)
else:
names = [
'%s (%s)' % (c, sequtil.translate(c))
for c in sequtil.codons_unambiguous
]
return (sequtil.codons_unambiguous, names)
def start_example_project(self, project_id, fasta_f, seq_type, labeling_f):
''' Start new project without checking input data
'''
self.set_project(project_id)
# check if user allready has a dir and create one if needed
if not os.path.exists(self.user_dir):
os.mkdir(self.user_dir)
# check if a project with the same name exists, otherwise add number
if(os.path.exists(self.project_dir)):
index = 0
while(os.path.exists(self.project_dir)):
project_id = '%s_%i' % (self.project_id.split('_')[0], index)
self.set_project(project_id)
index += 1
# read data from file
try:
seqs = [s for s in file_io.read_fasta(fasta_f)]
ids = [s[0] for s in seqs]
except Exception as e:
print e
return 'Error in fasta file'
# create sequence feature extraction object
fe = featext.FeatureExtraction()
# set protein data
try:
fe.set_protein_ids(ids)
fe.protein_data_set.set_data_source(seq_type, seqs)
# translate to prot seq if orf provided
if(seq_type == 'orf_seq'):
ids = [s[0] for s in seqs]
prot_seqs = [(sequtil.translate(s[1])) for s in seqs]
# chop off translated stop codons at terminus
prot_seqs = [s[:-1] if s[-1] == '*' else s for s in prot_seqs]
fe.protein_data_set.set_data_source('prot_seq',
zip(ids, prot_seqs))
except ValueError as e:
print(traceback.format_exc())
return str(e)
except:
print(traceback.format_exc())
return 'Error during initiation new project'
# add to feature matrix
try:
labeling_name = os.path.splitext(os.path.basename(labeling_f))[0]
fe.fm_protein.add_labeling_from_file(labeling_name, labeling_f)
except ValueError as e:
return str(e)
# create data directory for this project (just to be sure, check again)
if not(os.path.exists(self.project_dir)):
os.mkdir(self.project_dir)
# and create directories to store job status
os.mkdir(self.job_dir)
os.mkdir(self.job_waiting_dir)
os.mkdir(self.job_running_dir)
os.mkdir(self.job_done_dir)
os.mkdir(self.job_error_dir)
# create classification dir
os.mkdir(self.cl_dir)
else:
return 'A project with the same project id allready exists'
# create project details file
with open(self.project_details_f, 'w') as fout:
fout.write('project_id\t%s\n' % (self.project_id))
fout.write('project_init\t%s\n' % (self.timestamp_str()))
# store feature extraction data
fe.set_root_dir(self.fe_dir)
fe.save()
return ''
def start_new_project(self, project_id, fasta_file, sequence_type,
reference_taxon=None):
'''
TOCHECK: what is fasta_file for type ???
pre: sequence_type is orf_seq or prot_seq
pre: user_id is set
'''
self.set_project(project_id)
# check if user allready has a dir and create one if needed
if not os.path.exists(self.user_dir):
os.mkdir(self.user_dir)
# check if a project with the same name exists
if os.path.exists(self.project_dir):
return 'A project with the same project id allready exists'
# download reference fasta file
ref_seqs = []
if not(reference_taxon is None):
# TODO
if(sequence_type == 'orf_seq'):
return 'Reference set can only be compared to protein' +\
'amino acid sequences, not to ORF sequences.'
# obtain reference proteome sequences
ref_f = os.path.join(self.ref_data_dir,
'%i.fsa' % (reference_taxon))
ref_red_f = os.path.join(self.ref_data_dir,
'%i_reduced.fsa' % (reference_taxon))
# first check local dir
if(os.path.exists(ref_red_f)):
ref_seqs = [s for s in file_io.read_fasta(ref_red_f)]
elif(os.path.exists(ref_f)):
ref_seqs = [s for s in file_io.read_fasta(ref_f)]
# otherwise fetch reference data set
else:
pass
'''
url = 'http://www.uniprot.org/uniref/' +\
'?query=uniprot:(organism:%i+' % (reference_taxon) +\
'keyword:181)+identity:0.5&format=fasta'
response = urllib2.urlopen(url)
try:
ref_seqs = [s for s in file_io.read_fasta(response)]
except Exception:
return 'There appears to be an error in the reference ' +\
'data fasta file'
# check if reference data set is not too large
max_num_seqs = 15000
if(len(ref_seqs) > max_num_seqs):
# randomly select 15000 sequences
indices = random.sample(range(len(ref_seqs)), max_num_seqs)
ref_seqs = [ref_seqs[i] for i in indices]
'''
# estimate reference data set size
size = len(ref_seqs) * 285 # estimate 285 bytes per seq
# check file size
max_size = 5243000 # bytes (5MB)
while True:
data = fasta_file.file.read(8192)
if(size > max_size):
return 'Sequence data exeeds the maximum ' +\
'allowed size (5MB)'
if not(data):
break
size += len(data)
if(size > max_size):
return 'Sequence data exeeds the maximum ' +\
'allowed size (5MB)'
# reset to beginning of fasta file
fasta_file.file.seek(0)
# read sequences from fasta file (to obtain object ids...)
try:
seqs = [s for s in file_io.read_fasta(fasta_file.file)]
seqs.extend(ref_seqs)
ids = [s[0] for s in seqs]
except Exception as e:
return str(e) +\
'Please consult the documentation (<i>file formats</i> ' +\
'section) to learn more about the FASTA file format.'
# reset pointer to begin of file
#fasta_file.file.seek(0)
# close the temporary file, not sure if this is neccesary
fasta_file.file.close()
# create sequence feature extraction object to check input
fe = featext.FeatureExtraction()
try:
fe.set_protein_ids(ids)
fe.protein_data_set.set_data_source(sequence_type, seqs)
# translate to prot seq if orf provided
if(sequence_type == 'orf_seq'):
ids = [s[0] for s in seqs]
prot_seqs = [(sequtil.translate(s[1])) for s in seqs]
# chop off translated stop codons at terminus
prot_seqs = [s[:-1] if s[-1] == '*' else s for s in prot_seqs]
fe.protein_data_set.set_data_source('prot_seq',
zip(ids, prot_seqs))
except ValueError as e:
print(traceback.format_exc())
return str(e)
except:
print(traceback.format_exc())
return 'Error during initiation new project'
# add labeling in case of added reference set
if(len(ref_seqs) > 0):
l = [(s[0], 0) for s in seqs]
l.extend([(s[0], 1) for s in ref_seqs])
class_names = ['dataset', 'taxon%i' % (reference_taxon)]
fe.fm_protein.add_labeling('reference', dict(l), class_names)
# create data directory for this project (just to be sure, check again)
if not(os.path.exists(self.project_dir)):
os.mkdir(self.project_dir)
# and create directories to store job status
os.mkdir(self.job_dir)
os.mkdir(self.job_waiting_dir)
os.mkdir(self.job_running_dir)
os.mkdir(self.job_done_dir)
os.mkdir(self.job_error_dir)
# create classification dir
os.mkdir(self.cl_dir)
else:
return 'A project with the same project id allready exists'
# create project details file
with open(self.project_details_f, 'w') as fout:
fout.write('project_id\t%s\n' % (self.project_id))
fout.write('project_init\t%s\n' % (self.timestamp_str()))
# store feature extraction data
fe.set_root_dir(self.fe_dir)
fe.save()
return ''
def start_example_project(self, project_id, fasta_f, seq_type, labeling_f):
''' Start new project without checking input data
'''
self.set_project(project_id)
# check if user allready has a dir and create one if needed
if not os.path.exists(self.user_dir):
os.mkdir(self.user_dir)
# check if a project with the same name exists, otherwise add number
if (os.path.exists(self.project_dir)):
index = 0
while (os.path.exists(self.project_dir)):
project_id = '%s_%i' % (self.project_id.split('_')[0], index)
self.set_project(project_id)
index += 1
# read data from file
try:
seqs = [s for s in file_io.read_fasta(fasta_f)]
ids = [s[0] for s in seqs]
except Exception as e:
print e
return 'Error in fasta file'
# create sequence feature extraction object
fe = featext.FeatureExtraction()
# set protein data
try:
fe.set_protein_ids(ids)
fe.protein_data_set.set_data_source(seq_type, seqs)
# translate to prot seq if orf provided
if (seq_type == 'orf_seq'):
ids = [s[0] for s in seqs]
prot_seqs = [(sequtil.translate(s[1])) for s in seqs]
# chop off translated stop codons at terminus
prot_seqs = [s[:-1] if s[-1] == '*' else s for s in prot_seqs]
fe.protein_data_set.set_data_source('prot_seq',
zip(ids, prot_seqs))
except ValueError as e:
print(traceback.format_exc())
return str(e)
except:
print(traceback.format_exc())
return 'Error during initiation new project'
# add to feature matrix
try:
labeling_name = os.path.splitext(os.path.basename(labeling_f))[0]
fe.fm_protein.add_labeling_from_file(labeling_name, labeling_f)
except ValueError as e:
return str(e)
# create data directory for this project (just to be sure, check again)
if not (os.path.exists(self.project_dir)):
os.mkdir(self.project_dir)
# and create directories to store job status
os.mkdir(self.job_dir)
os.mkdir(self.job_waiting_dir)
os.mkdir(self.job_running_dir)
os.mkdir(self.job_done_dir)
os.mkdir(self.job_error_dir)
# create classification dir
os.mkdir(self.cl_dir)
else:
return 'A project with the same project id allready exists'
# create project details file
with open(self.project_details_f, 'w') as fout:
fout.write('project_id\t%s\n' % (self.project_id))
fout.write('project_init\t%s\n' % (self.timestamp_str()))
# store feature extraction data
fe.set_root_dir(self.fe_dir)
fe.save()
return ''
def start_new_project(self,
project_id,
fasta_file,
sequence_type,
reference_taxon=None):
'''
TOCHECK: what is fasta_file for type ???
pre: sequence_type is orf_seq or prot_seq
pre: user_id is set
'''
self.set_project(project_id)
# check if user allready has a dir and create one if needed
if not os.path.exists(self.user_dir):
os.mkdir(self.user_dir)
# check if a project with the same name exists
if os.path.exists(self.project_dir):
return 'A project with the same project id allready exists'
# download reference fasta file
ref_seqs = []
if not (reference_taxon is None):
# TODO
if (sequence_type == 'orf_seq'):
return 'Reference set can only be compared to protein' +\
'amino acid sequences, not to ORF sequences.'
# obtain reference proteome sequences
ref_f = os.path.join(self.ref_data_dir,
'%i.fsa' % (reference_taxon))
ref_red_f = os.path.join(self.ref_data_dir,
'%i_reduced.fsa' % (reference_taxon))
# first check local dir
if (os.path.exists(ref_red_f)):
ref_seqs = [s for s in file_io.read_fasta(ref_red_f)]
elif (os.path.exists(ref_f)):
ref_seqs = [s for s in file_io.read_fasta(ref_f)]
# otherwise fetch reference data set
else:
pass
'''
url = 'http://www.uniprot.org/uniref/' +\
'?query=uniprot:(organism:%i+' % (reference_taxon) +\
'keyword:181)+identity:0.5&format=fasta'
response = urllib2.urlopen(url)
try:
ref_seqs = [s for s in file_io.read_fasta(response)]
except Exception:
return 'There appears to be an error in the reference ' +\
'data fasta file'
# check if reference data set is not too large
max_num_seqs = 15000
if(len(ref_seqs) > max_num_seqs):
# randomly select 15000 sequences
indices = random.sample(range(len(ref_seqs)), max_num_seqs)
ref_seqs = [ref_seqs[i] for i in indices]
'''
# estimate reference data set size
size = len(ref_seqs) * 285 # estimate 285 bytes per seq
# check file size
max_size = 5243000 # bytes (5MB)
while True:
data = fasta_file.file.read(8192)
if (size > max_size):
return 'Sequence data exeeds the maximum ' +\
'allowed size (5MB)'
if not (data):
break
size += len(data)
if (size > max_size):
return 'Sequence data exeeds the maximum ' +\
'allowed size (5MB)'
# reset to beginning of fasta file
fasta_file.file.seek(0)
# read sequences from fasta file (to obtain object ids...)
try:
seqs = [s for s in file_io.read_fasta(fasta_file.file)]
seqs.extend(ref_seqs)
ids = [s[0] for s in seqs]
except Exception as e:
return str(e) +\
'Please consult the documentation (<i>file formats</i> ' +\
'section) to learn more about the FASTA file format.'
# reset pointer to begin of file
#fasta_file.file.seek(0)
# close the temporary file, not sure if this is neccesary
fasta_file.file.close()
# create sequence feature extraction object to check input
fe = featext.FeatureExtraction()
try:
fe.set_protein_ids(ids)
fe.protein_data_set.set_data_source(sequence_type, seqs)
# translate to prot seq if orf provided
if (sequence_type == 'orf_seq'):
ids = [s[0] for s in seqs]
prot_seqs = [(sequtil.translate(s[1])) for s in seqs]
# chop off translated stop codons at terminus
prot_seqs = [s[:-1] if s[-1] == '*' else s for s in prot_seqs]
fe.protein_data_set.set_data_source('prot_seq',
zip(ids, prot_seqs))
except ValueError as e:
print(traceback.format_exc())
return str(e)
except:
print(traceback.format_exc())
return 'Error during initiation new project'
# add labeling in case of added reference set
if (len(ref_seqs) > 0):
l = [(s[0], 0) for s in seqs]
l.extend([(s[0], 1) for s in ref_seqs])
class_names = ['dataset', 'taxon%i' % (reference_taxon)]
fe.fm_protein.add_labeling('reference', dict(l), class_names)
# create data directory for this project (just to be sure, check again)
if not (os.path.exists(self.project_dir)):
os.mkdir(self.project_dir)
# and create directories to store job status
os.mkdir(self.job_dir)
os.mkdir(self.job_waiting_dir)
os.mkdir(self.job_running_dir)
os.mkdir(self.job_done_dir)
os.mkdir(self.job_error_dir)
# create classification dir
os.mkdir(self.cl_dir)
else:
return 'A project with the same project id allready exists'
# create project details file
with open(self.project_details_f, 'w') as fout:
fout.write('project_id\t%s\n' % (self.project_id))
fout.write('project_init\t%s\n' % (self.timestamp_str()))
# store feature extraction data
fe.set_root_dir(self.fe_dir)
fe.save()
return ''
