def split_file(file2, ncpu, min_num_lines=100):
print 'splitting [%s] into %d pieces' % (file2, ncpu)
D, fname, fbase, fext = lib_utils.separateDirFn2(file2)
out_prefix = '%s/%s_parts' % (D, fbase)
#compute the number of lines per a splitted file
N = lib_utils.count_num_lines(file2)
L = round(1. * N / ncpu) + 1
if L <= min_num_lines:
file2b = '%s_00' % out_prefix
print 'the input file size is too small to split.'
shutil.copyfile(file2, file2b)
return [file2b]
else:
cmd = 'split -d -l %d %s %s' % (L, file2, out_prefix)
lib_utils.gen_msg_time('cmd', cmd, 'split_file') #debug
upair_fns = []
for j in range(ncpu):
part_fn = '%s%02d' % (out_prefix, j)
if lib_utils.check_if_file_valid(part_fn):
upair_fns.append(part_fn)
else:
lib_utils.gen_msg_time('error',
'file[%s] does not exist' % part_fn,
'split_file')
print 'done.'
return upair_fns
def __init__(self,resource_dir,work_dir='/tmp',go_bin=os.path.join(os.environ['DIVINE'],'python_libs','bin','fastsemsim'),debug=False):
self.resource_dir = resource_dir
self.obo_fn = '%s/go.obo'%self.resource_dir
if not lib_utils.check_if_file_valid(self.obo_fn):
lib_utils.gen_msg_time('error','check if the file[%s] exists'%self.obo_fn,'lib_geneontology.py')
self.goa_fn = '%s/gene_association.goa_human'%self.resource_dir
if not lib_utils.check_if_file_valid(self.goa_fn):
lib_utils.gen_msg_time('error','check if the file[%s] exists'%self.goa_fn,'lib_geneontology.py')
self.work_dir = work_dir
#rfix = random.randint(1,1e7)
#rfix = 0
#to prepare input_fn
self.query_fn = None
self.gobin = go_bin
self.go_categories = ['biological_process','molecular_function','cellular_component']
self.gosim_fns = {}
self.uniprot2RefGenes = {}
self.debug = debug
def gen_all_pairs_file(self,upair_file):
uniprot_list_fn = '%s/go_%d.tmp'%(self.work_dir,random.randint(1,1e7))
cmd = "cut -f2 %s | grep -vP '^!' | sort | uniq > %s"%(self.goa_fn,uniprot_list_fn)
lib_utils.gen_msg_time('cmd',cmd,'lib_geneontology.run_sim')
Uniprot = lib_utils.file2list(uniprot_list_fn)
fp2 = lib_utils.open2(upair_file,'w')
U = len(Uniprot)
print 'total number of queries[%d]'%U
for i,u1 in enumerate(Uniprot):
print '[%d/%d]'%(i,U)
for u2 in Uniprot[i+1:]:
fp2.write('%s\t%s\n'%(u1,u2))
fp2.close()
print 'done.'
def run_sim(self,out_dir,sim_method='SimRel'):
for root_node in self.go_categories:
gocmd = self.gobin
gocmd += " --ontology_file %s"%self.obo_fn
gocmd += " --ontology_file_format obo"
gocmd += " --ac_file %s"%self.goa_fn
gocmd += " --ac_sep '\\t'"
gocmd += " --task SS"
gocmd += " -o GeneOntology"
if root_node not in self.go_categories:
lib_utils.gen_msg_time('error','%s not defined'%root_node,'lib_geneontology.py')
gocmd += " --root %s"%root_node
gocmd += " --ac fly"
gocmd += " --tss %s"%sim_method
gocmd += " --tmix max"
gocmd += " --remove_nan"
gocmd += " --ignore_EC TAS"
gocmd += " --query_ss_type obj"
gocmd += " --query_mode pairs"
gocmd += " --query_input file"
gocmd += " --query_file %s" % self.query_fn
gosim_fn = "%s/%s_%s.tsv" % (out_dir,self.query_fn.split('/')[-1],root_node)
gocmd += " --output_file %s"%gosim_fn
if self.debug and lib_utils.check_if_file_valid(gosim_fn):
lib_utils.gen_msg_time('notice','reuse %s'%gosim_fn,'lib_geneontology.run_sim')
else:
lib_utils.gen_msg_time('cmd',gocmd,'lib_geneontology.run_sim')
#print 'reuse...' #debug
self.gosim_fns[root_node]=gosim_fn
def map_uniprot_to_refgene(self):
tmp_fn = '%s_tmp%d'%(self.query_fn,random.randint(1,1e7))
cmd = 'cut -f1 %s | sort | uniq > %s'%(self.query_fn,tmp_fn)
lib_utils.gen_msg_time('cmd',cmd,'map_uniprot_to_refgene')
Query = lib_utils.file2list(tmp_fn,False)
os.unlink(tmp_fn)
tmp_fn = '%s_tmp%d'%(self.query_fn,random.randint(1,1e7))
cmd = 'cut -f2 %s | sort | uniq > %s'%(self.query_fn,tmp_fn)
lib_utils.gen_msg_time('cmd',cmd,'map_uniprot_to_refgene')
Query.extend(lib_utils.file2list(tmp_fn,False))
os.unlink(tmp_fn)
fp = lib_utils.open2(self.goa_fn,'r')
for i in fp:
if i[0]=='!':continue
j=i.split('\t')
refGene = j[2]
uniprot = j[1]
if uniprot in Query:
if refGene not in self.uniprot2RefGenes:
self.uniprot2RefGenes[uniprot]=refGene
fp.close()