def get_tree():
try:
data = request.get_json()
pid = data["pid"]
uid = data["uid"]
sid = data["sid"]
selval = data["value"]
pipeline = data["pip"]
dbname = data["rid"]
# dbname="isuezrouja"
analysis = "taxonomy"
rf = rootvar.result_files(pid, analysis, pipeline, sid, dbname)
x = sql.SQL(main_db)
samples = x.exe('select * from samples where project_id="' +
pid+'" and sample_id="'+sid+'"')
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
with open(rf.json) as data_file:
data = json.load(data_file)
x.close()
###print data
view = rootvar.ViewSampleResults(
sample, pipeline, dbname, analysis, rf)
return jsonify(tree=[data], range=view.range(selval)[0], pip=pipeline)
except Exception as inst:
return "ERROR: "+str(inst)
def get_taxo_by_name():
data = request.get_json()
pid = data["pid"]
uid = data["uid"]
sid = data["sid"]
tid = data["tid"]
lid = data["lid"]
pip = data["pip"]
dbname = data["rid"]
pipeline = pip
# dbname="isuezrouja"
analysis = "taxonomy"
x = sql.SQL(main_db)
rf = rootvar.result_files(pid, analysis, pip, sid, dbname)
samples = x.exe('select * from samples where project_id="' +
pid+'" and sample_id="'+sid+'"')
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
x.close()
view = rootvar.ViewSampleResults(sample, pipeline, dbname, analysis, rf)
try:
# return jsonify(x=pip)
return jsonify(matrix=view.level(lid, type="matches"))
except Exception as inst:
return "ERROR: "+str(inst)
def functional(data):
pid = data["pid"]
uid = data["uid"]
sids = data["sid"]
pipeline = data["pip"]
rid = data["rid"]
edges = []
FULL_MATRIX = []
#first see if the data set contains taxonomy, function or both annotations
analysis = "function"
#print rid
#
#
os.system("mkdir " + rootvar.__ROOTPRO__ + "/" + pid + "/" + pipeline +
"/RESULTS/ >> " + rootvar.log + " 2>&1")
all_samples_tree_file = rootvar.__ROOTPRO__ + "/" + pid + "/" + pipeline + "/RESULTS/" + rid + ".all_samples_tree.pk"
log = open(
rootvar.__ROOTPRO__ + "/" + pid + "/" + pipeline + "/RESULTS/" + rid +
".log", "w")
#
# if os.path.isfile(all_samples_tree_file):
# x=sql.SQL(all_samples_tree_file+".db")
# val=x.exe("select distinct sample_name from full_matrix")
# stored_samples=len(val)
#
# x=sql.SQL(main_db)
# # load all the samples that have been finalized to run
# sids=x.exe('select c.sample_id from (select * from samples a inner join (select * from sample_status where pip="'+str(pipeline)+'") b on a.sample_id==b.sid) c where c.project_id=="'+pid+'" and c.status="Done" and c.rid="'+rid+'"')
# x.close()
# if os.path.isfile(all_samples_tree_file) and stored_samples == len(sids):
# x=sql.SQL(all_samples_tree_file+".db")
# FULL_MATRIX=x.exe("select * from full_matrix")
# return ["function",FULL_MATRIX,all_samples_tree_file+".json"]
# nodes={}
x = sql.SQL(main_db)
log.write("echo #LOG for Project ID: " + str(pid) + "\n")
for sid in sids:
samples = x.exe('select * from samples where project_id="' + pid +
'" and sample_id="' + sid + '"')
# log.write(str(sid)+"\n")
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
#print sample.name
# log.write(str(samples[0])+"\n")
rf = rootvar.result_files(pid, analysis, pipeline, sample.id, rid)
view = rootvar.ViewSampleResults(sample, pipeline, rid, analysis, rf)
FULL_MATRIX += view.all_func()
#print sample.name
x.close()
# log.write(str(FULL_MATRIX))
#print FULL_MATRIX[0]
#rootvar.full_matrix_function(all_samples_tree_file+".db", FULL_MATRIX)
#print "matrix done"
# tree=["none"]
return ["function", FULL_MATRIX, all_samples_tree_file + ".json"]
def get_childs_of_taxonomy():
data = request.get_json()
pid = data["pid"]
uid = data["uid"]
sid = data["sid"]
tid = data["tid"]
lid = data["lid"]
cond = data["cond"]
pip = data["pip"]
rid = data["rid"]
dbname = data["rid"]
analysis = "taxonomy"
##print cond, pip, rid, pid, uid, sid, tid, lid
if cond == "one": # this is if I am analyzing one or multiple samples
rf = rootvar.result_files(pid, analysis, pip, sid, dbname)
x = sql.SQL(main_db)
samples = x.exe('select * from samples where project_id="' +
pid+'" and sample_id="'+sid+'"')
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
x.close()
view = rootvar.ViewSampleResults(sample, pip, dbname, analysis, rf)
matrix = view.childs_of(tid, 'rpkm')
###print matrix
return jsonify(matrix=matrix)
else:
# load big tree
all_samples_tree_file = rootvar.__ROOTPRO__+"/" + \
pid+"/"+pip+"/RESULTS/"+rid+".all_samples_tree.pk"
G = nx.read_gpickle(all_samples_tree_file)
tree = json_graph.tree_data(G, root='R')
data = []
for i in G.successors(tid):
data.append(i)
x = sql.SQL(all_samples_tree_file+".db")
matrix = rootvar.get_matrix_level_childs(x, data)
samples_sel = list(set([str(i[0]) for i in matrix]))
M, N = rootvar.v2m(matrix, samples_sel, 0, 0)
##print M
heatmap = 'none' # heatmap=iclust.main(M,None)
return jsonify(data=matrix[0], heatmap=heatmap)
def get_functional_counts():
try:
data = request.get_json()
pid = data["pid"]
uid = data["uid"]
sid = data["sid"]
pip = data["pip"]
rid = data["rid"]
pip = data['pip']
analysis = "function"
# lid="assembly"
# file=rootvar.__ROOTPRO__+"/"+pid+"/assembly/idba_ud/"+sid+"/pred.genes."+rid+".matches.function.abundance.results.sqlite3.db"
x = sql.SQL(main_db)
rf = rootvar.result_files(pid, "function", pip, sid, rid)
samples = x.exe('select * from samples where project_id="' +
pid+'" and sample_id="'+sid+'"')
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
x.close()
view = rootvar.ViewSampleResults(sample, pip, rid, analysis, rf)
return jsonify(matrix=view.func_one_sample(), m2=view.func_structure(pid, pip, sid))
except Exception as inst:
return "ERROR: "+str(inst)
def idbaud(projectid,sampleid,db,protocol,reads1, reads2, good_reads):
#db=root.dataset(db)
#1 get project path
x=sql.SQL(root.filedb())
xpath=x.project(projectid)[0][4]
#print 'here------------'
###########################################################################
#2 update the reads on the sql dataset, doit anyway, so if the sample is re run just take the new input, it could be modified.
###########################################################################
val=x.exe('update samples set reads1="'+reads1+'" where project_id="'+projectid+'" and sample_id="'+sampleid+'"')
val=x.exe('update samples set reads2="'+reads2+'" where project_id="'+projectid+'" and sample_id="'+sampleid+'"')
###########################################################################
#3 get the sample full information - load the class samples
###########################################################################
samples=x.exe('select * from samples where project_id="'+projectid+'" and sample_id="'+sampleid+'"')
sample=samples[0]
sample=root.samples(sample,xpath)
root.mkdir(sample.assemblyDir)
###########################################################################
# 4.1 Run fq2fa - this is used by udba_ud program
###########################################################################
idba_ud=root.program('idba_ud',sample,db)
update_status(x,sampleid,db.id,protocol,"Preprocessing")
fq2fa=root.program('fq2fa', sample,db)
if not root.isdir(idba_ud.out): fq2fa.run() #make sure that there is a scaffold.fa file. If not, it computes again the fastq to fasta and the assembly
###########################################################################
# 4.2 Run idba_ud - assembly the samples
###########################################################################
update_status(x,sampleid,db.id,protocol,"Assembling")
idba_ud=root.program('idba_ud',sample,db)
if not root.isdir(idba_ud.out):
idba_ud.run();
os.system(' cd ' + idba_ud.path + ' && rm kmer contig-* align-* graph-* local-contig-* reads.fa')
###########################################################################
# 4.2 Run gene finder - look at the genes over the scaffolds
###########################################################################
prodigal=root.program("prodigal", sample,db)
update_status(x,sampleid,db.id,protocol,"Finding Genes")
if not root.isdir(prodigal.output+".gff"): prodigal.run()
if db.name=="abcdefghij":
print "MetaPlAn2"
update_status(x,sampleid,db.id,protocol,"Processing")
metaphlan=root.program('MetaPhlAn',sample,db)
if not root.isdir(metaphlan.out): metaphlan.run()
#print "Here 2"
G=txp.metaphlan_taxonomy_tree(metaphlan.out)
abn=root.SampleResults(sample,G,protocol, db.name, "taxonomy", metaphlan.out)
abn.start()
update_status(x,sampleid,db.id,protocol,"Done")
if db.name=='MyTaxa':
#print "MyTaxa"
taxa=root.mytaxa(sample,db)
update_status(x,sampleid,db.id,protocol,"Screening")
if not root.isdir(taxa.output+".prot.mytaxa.fa"): taxa.pre()
if not root.isdir(taxa.output+".MyTaxa.matches.daa"): taxa.align()
if not root.isdir(taxa.output+".MyTaxa.align"): taxa.postd()
if not root.isdir(taxa.output+".MyTaxa.input"): taxa.mpre()
if not root.isdir(taxa.output+".MyTaxa.out"): taxa.run()
update_status(x,sampleid,db.id,protocol,"Quantification")
data=taxa.postM()
G=txp.mytaxa_taxonomy_tree(data,taxa.output+".MyTaxa.matches.taxonomy.abundance")
abn=root.SampleResults(sample,G,protocol, "MyTaxa", "taxonomy", taxa.output+".MyTaxa.matches")
abn.start()
update_status(x,sampleid,db.id,protocol,"Done")
if not db.taxo=="none":
print "taxonomy"
###########################################################################
# 4.3 Run bowtie to find matches
###########################################################################
update_status(x,sampleid,db.id,protocol,"Screening")
if db.name=="ryaetguxun":
blastn=root.program('diamond_blastp',sample,db)
else:
blastn=root.program('blastn',sample,db)
blastn.run()
#blastn.run()
###########################################################################
# 4.4 taxonomy abundance
###########################################################################
update_status(x,sampleid,db.id,protocol,"Quantification")
abundance=pb(blastn.out, db.taxo, db.len, db.taxodb, "taxonomy", db.name, "none",good_reads)
###########################################################################
# 4.5 processing Visualization
###########################################################################
G=txp.taxonomy_tree(abundance,blastn.out, protocol, "taxonomy", db.name )
abn=root.SampleResults(sample,G,protocol, db.name, "taxonomy", blastn.out)
abn.start()
root.updateStatus(x,projectid,sampleid,"done")
update_status(x,sampleid,db.id,protocol,"Done")
if not db.func=="none":
print "functional annotation"
update_status(x,sampleid,db.id,protocol,"Screening")
fileso=root.result_files(projectid, "function", protocol, sampleid, db.name)
###########################################################################
# 4.3 Run bowtie to find matches
###########################################################################
root.updateStatus(x,projectid,sampleid,"functional annotation")
blastn=root.program('diamond_blastp',sample,db)
blastn.run()
###########################################################################
# 4.4 taxonomy abundance
###########################################################################
update_status(x,sampleid,db.id,protocol,"Quantification")
abundance=pb(blastn.out, db.func, db.len, db.funcdb, "function", db.name, fileso.GGenes+".rpkm", good_reads)
###########################################################################
# 4.5 processing Visualization
###########################################################################
abn=root.SampleResults(sample,'none',protocol, db.name, "function", blastn.out)
abn.createFuncDb(abundance)
update_status(x,sampleid,db.id,protocol,"Done")
def process(projectid, sampleid, db, protocol, reads1, reads2, good_reads):
#db=root.dataset(db)
x = sql.SQL(root.filedb())
xpath = x.project(projectid)[0][4]
val = x.exe('update samples set reads1="' + reads1 +
'" where project_id="' + projectid + '" and sample_id="' +
sampleid + '"')
val = x.exe('update samples set reads2="' + reads2 +
'" where project_id="' + projectid + '" and sample_id="' +
sampleid + '"')
samples = x.exe('select * from samples where project_id="' + projectid +
'" and sample_id="' + sampleid + '"')
sample = samples[0]
sample = root.samples(sample, xpath)
root.mkdir(sample.matchesDir)
rdir = root.__ROOTPRO__ + "/" + projectid + "/READS/"
if db.name == "abcdefghij":
#print "MetaPhlAnn"
update_status(x, sampleid, db.id, protocol, "Processing")
metaphlan = root.program('MetaPhlAnR', sample, db)
if not root.isdir(metaphlan.out): metaphlan.run()
G = txp.metaphlan_taxonomy_tree(metaphlan.out)
abn = root.SampleResults(sample, G, protocol, db.name, "taxonomy",
metaphlan.out)
abn.start()
update_status(x, sampleid, db.id, protocol, "Done")
if not db.taxo == "none":
# run bowtie using the paired end reads
update_status(x, sampleid, db.id, 'matches', "Screening")
cmd = " ".join([
root.__ROOTEXEDIR__ + 'bowtie2',
'--very-fast-local -p ' + p + ' --no-unal --no-hd --no-sq -x',
db.bowtie, '-1', sample.reads1, '-2', sample.reads2, '-S',
sample.matchesDir + '/alignment.' + db.id + '.matches >>',
root.log, '2>&1'
])
if not root.isdir(sample.matchesDir + '/alignment.' + db.id +
'.matches'):
os.system(cmd)
#process output in sam format to get genes and number of reads per gene.
update_status(x, sampleid, db.id, protocol, "Quantification")
if not root.isdir(sample.matchesDir + '/alignment.' + db.id +
'.matches.taxonomy.abundance.results.sqlite3.db'):
abundance = parse_sam(
sample.matchesDir + '/alignment.' + db.id + '.matches', db,
good_reads)
G = txp.taxonomy_tree(
abundance,
sample.matchesDir + '/alignment.' + db.id + '.matches',
protocol, "taxonomy", db.id)
abn = root.SampleResults(sample, G, protocol, db.id, "taxonomy",
sample.matchesDir + '/alignment.' +
db.id +
'.matches') # Store data in the sql TABLE
abn.start()
update_status(x, sampleid, db.id, protocol, "Done")
return 'success'
if not db.func == "none":
fileso = root.result_files(projectid, "function", protocol, sampleid,
db.name)
#Merge paired ends
update_status(x, sampleid, db.id, protocol, "Merge")
cmd = " ".join([
'python',
root.__ROOTEXEDIR__ + "pairend_join.py -s -p " + p + " -m 8 -o ",
sample.matchesDir + '/merged.reads.fastq', sample.reads1,
sample.reads2
])
#print cmd
root.flog(cmd) #print cmd
if not root.isdir(sample.matchesDir + '/merged.reads.fastq'):
os.system(cmd)
#Get fasta files
cmd = ' '.join([
root.__ROOTEXEDIR__ + '/seqtk seq -a',
sample.matchesDir + '/merged.reads.fastq >',
sample.matchesDir + '/merged.reads.fasta'
])
if not root.isdir(sample.matchesDir + '/merged.reads.fasta'):
os.system(cmd)
#BlastX from diamond
update_status(x, sampleid, db.id, protocol, "Screening")
dout = sample.matchesDir + 'alignment.' + db.id
din = sample.matchesDir + '/merged.reads.fasta'
cmd = ' '.join([
root.__ROOTEXEDIR__ + '/diamond blastx --id 60 -p ' + p +
' -k 1 -e 1e-5 -d', db.diamond, '-a', dout + '.pre', '-q', din,
'>>', root.log, "2>&1"
])
if not root.isdir(dout + '.daa'): os.system(cmd)
cmd = ' '.join([
root.__ROOTEXEDIR__ + '/diamond view -a', dout + '.pre.daa', '-o',
dout + '.matches -f tab', ">>", root.log, "2>&1"
])
if not root.isdir(dout + '.matches'): os.system(cmd)
# parse diamond output
update_status(x, sampleid, db.id, protocol, "Quantification")
if not root.isdir(sample.matchesDir + '/alignment.' + db.id +
'.matches.function.abundance.results.sqlite3.db'):
abundance = pb(dout + '.matches', db.func, db.len, db.funcdb,
"function", db.name, fileso.GGenes + ".rpkm",
good_reads)
#abundance=pdx(dout+'.matches', db, good_reads)
abn = root.SampleResults(sample, 'none', protocol, db.name,
"function", dout + '.matches')
abn.createFuncDb(abundance)
update_status(x, sampleid, db.id, protocol, "Done")
os.system('rm ' + sample.matchesDir + '/merged.reads.fastq >> ' +
root.log + " 2>&1")
os.system('rm ' + sample.matchesDir + '/merged.reads.fasta >> ' +
root.log + " 2>&1")
return 'success'
def taxonomy(data):
pid = data["pid"]
uid = data["uid"]
sids = data["sid"]
pipeline = data["pip"]
rid = data["rid"]
edges = []
FULL_MATRIX = []
#first see if the data set contains taxonomy, function or both annotations
analysis = "taxonomy"
#print '\n\n\n here we goo!!!\n\n\n', pipeline
rootvar.mkdir(rootvar.__ROOTPRO__ + "/" + pid + "/" + pipeline +
"/RESULTS/")
all_samples_tree_file = rootvar.__ROOTPRO__ + "/" + pid + "/" + pipeline + "/RESULTS/" + rid + ".all_samples_tree.pk"
#
stored_samples = 0
if os.path.isfile(all_samples_tree_file):
#print '\n\n\n if the X file has been created'
x = sql.SQL(all_samples_tree_file + ".db")
val = x.exe("select distinct sample_name from full_matrix")
stored_samples = len(val)
#
x = sql.SQL(main_db)
sids = x.exe(
'select c.sample_id from (select * from samples a inner join (select * from sample_status where pip="'
+ str(pipeline) +
'") b on a.sample_id==b.sid) c where c.project_id=="' + pid +
'" and c.status="Done" and c.rid="' + rid + '"')
#
#
#print '\n\n\n\n super important \n', sids
#print '\n\n\n get all the samples from the X file'
#
if os.path.isfile(all_samples_tree_file) and stored_samples == len(sids):
#print 'both have the same length'
G = nx.read_gpickle(all_samples_tree_file)
tree = json_graph.tree_data(G, root='R')
return ["taxonomy", tree]
#section
#print '\n\n\n SO the file has not been created, because the matrix of abundances has not been fetched for those samples'
nodes = {}
#print '\n\n\n So for each sample I get all the information from the sql tables. And create the tree \n\n\n\n\n\n'
#
for sid in sids:
samples = x.exe('select * from samples where project_id="' + pid +
'" and sample_id="' + sid[0] + '"')
xpath = x.project(pid)[0][4]
sample = rootvar.samples(samples[0], xpath)
rf = rootvar.result_files(pid, analysis, pipeline, sample.id, rid)
view = rootvar.ViewSampleResults(sample, pipeline, rid, analysis, rf)
FULL_MATRIX += view.all()
Gp = nx.read_gpickle(rf.pk)
edges += Gp.edges()
for node in Gp.nodes():
if not node in nodes:
nodes[node] = Gp.node[node]['level']
x.close()
rootvar.full_matrix_sql(all_samples_tree_file + ".db", FULL_MATRIX)
G = nx.DiGraph()
for i in edges:
if not i in G.edges():
if not i[1] in G.nodes():
G.add_node(i[1], samples=1, level=nodes[i[1]])
else:
G.node[i[1]]['samples'] += 1
if not i[0] in G.nodes():
G.add_node(i[0], samples=1, level=nodes[i[0]])
else:
G.node[i[0]]['samples'] += 1
if not G.predecessors(i[1]):
G.add_edge(i[0], i[1])
else:
G.node[i[0]]['samples'] += 1
G.node[i[1]]['samples'] += 1
tree = json_graph.tree_data(G, root='R')
nx.write_gpickle(G, all_samples_tree_file)
return ["taxonomy", tree, all_samples_tree_file + ".json"]