def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
outdir = FS.location
os.system('qsub -v pipeline="jbrowser",bench_id="' + 'F33H7949W0C2FFY' + '",key="' + pipeline_id + '",outdir="' + outdir +
'",name="' + pipeline_id + '_jbrowser"' + ' -N ' + pipeline_id + '_jbrowser /shared/sRNAtoolbox/core/bash_scripts/run_sRNAjbrowser.sh')
return redirect("/srnatoolbox/jobstatus/srnajbrowser/?id=" + pipeline_id)
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
outdir = FS.location
name = pipeline_id + '_gfree'
os.system('qsub -v pipeline="gfree",input="' + "/shared/sRNAtoolbox/testData/Ddent_exo.fa" + '",key="' + pipeline_id + '",minReadLength="' + "19" +
'",maxReadLength="' + "23" + '",microRNA="' + "sja:sma:egr:emu:sme:cel:bta" + '",minRC="' + "10" + '",noMM="' + "0" +
'",outdir="' + outdir + '",name="' + name + '" -N ' + name +
' /shared/sRNAtoolbox/core/bash_scripts/run_sRNAgfree.sh')
return redirect("/srnatoolbox/jobstatus/srnagfree/?id=" + pipeline_id)
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
outdir = FS.location
os.system(
'qsub -v pipeline="dejbrowser",groups="' + "cell#exosome" + '",key="' +
pipeline_id + '",outdir="' + outdir + '",name="' + pipeline_id +
'_dejbrowser",bench_id="' + "RG5TRAJIOOFS7II#F33H7949W0C2FFY" +
'" -N ' + pipeline_id +
'_dejbrowser /shared/sRNAtoolbox/core/bash_scripts/run_sRNAdejbrowser_nolength.sh'
)
return redirect("/srnatoolbox/jobstatus/srnajbrowserde/?id=" + pipeline_id)
def run(request):
if request.POST["bench_id"].replace(" ", "") != "":
pipeline_id = pipeline_utils.generate_uniq_id()
bench_id = request.POST["bench_id"]
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
outdir = FS.location
os.system('qsub -v pipeline="jbrowser",bench_id="' + bench_id + '",key="' + pipeline_id + '",outdir="' + outdir +
'",name="' + pipeline_id + '_jbrowser"' + ' -N ' + pipeline_id + '_jbrowser /shared/sRNAtoolbox/core/bash_scripts/run_sRNAjbrowser.sh')
return redirect("/srnatoolbox/jobstatus/srnajbrowser/?id=" + pipeline_id)
else:
return render(request, "error_page.html", {"errors": ["sRNAbench ID must be provided"]})
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
annotations = ["go"]
go_table = "goa_hsa"
exp = "true"
outdir = FS.location
mir_list = "/shared/sRNAtoolbox/testData/functerms_test_data.txt"
os.system(
'qsub -v pipeline="functerms",annot="' + ",".join(annotations) +
'",outdir="' + outdir + '",go_table="' + go_table + '",exp="' + exp +
'",key="' + pipeline_id + '",name="' + pipeline_id +
'_functerms",input="' + mir_list + '",type="list" -N ' + pipeline_id +
'_functerms /shared/sRNAtoolbox/core/bash_scripts/run_sRNAfuncterms.sh'
)
return redirect("/srnatoolbox/jobstatus/srnafuncterms/?id=" + pipeline_id)
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
outdir = FS.location
program_string = "TS:MIRANDA:PITA"
parameter_string = ":::"
os.system('cp /shared/sRNAtoolbox/testData/rno_miR.fa ' + FS.location)
os.system('cp /shared/sRNAtoolbox/testData/rn5_refSeq_3utr.fa ' + FS.location)
miRNA_file = os.path.join(FS.location, "rno_miR.fa")
utr_file = os.path.join(FS.location, "rn5_refSeq_3utr.fa")
go_table = "goa_hsa"
os.system(
'qsub -v pipeline="mirnafunctargets",program_string="' + program_string + '",parameter_string="' + parameter_string + '",key="' + pipeline_id + '",outdir="' + outdir + '",miRNA_file="' + miRNA_file + '",utr_file="' + utr_file + '",go_table="' + go_table +
'",name="' + pipeline_id + '_mirnafunctargets"' + ' -N ' + pipeline_id + '_mirnafunctargets /shared/sRNAtoolbox/core/bash_scripts/run_mirnafunctargets.sh')
return redirect("/srnatoolbox/jobstatus/mirnafunctargets/?id=" + pipeline_id)
def run(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
input = ""
outdir = FS.location
if len(request.POST["id"].replace(" ", "")) > 0:
input = request.POST["id"]
length = request.POST["length"]
desc = request.POST["desc"]
response = check_ids_param(input, desc, length)
if response is not True:
return render(request, "error_page.html", response)
if len(length.replace(" ", "")) > 0:
os.system(
'qsub -v pipeline="dejbrowser",groups="' + desc + '",key="' +
pipeline_id + '",outdir="' + outdir + '",length="' + length +
'",name="' + pipeline_id + '_dejbrowser",bench_id="' + input +
'" -N ' + pipeline_id +
'_dejbrowser /shared/sRNAtoolbox/core/bash_scripts/run_sRNAdejbrowser.sh'
)
else:
os.system(
'qsub -v pipeline="dejbrowser",groups="' + desc + '",key="' +
pipeline_id + '",outdir="' + outdir + '",name="' +
pipeline_id + '_dejbrowser",bench_id="' + input + '" -N ' +
pipeline_id +
'_dejbrowser /shared/sRNAtoolbox/core/bash_scripts/run_sRNAdejbrowser_nolength.sh'
)
return redirect("/srnatoolbox/jobstatus/srnajbrowserde/?id=" +
pipeline_id)
else:
return render(request, "error_page.html",
{"errors": ["sRNAbench IDs must be provided"]})
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
guess_adapter = None
recursive_adapter_trimming = None
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
id = "4XVGNWRUK0ZCUM1"
file_to_copy = os.path.join("/shared/sRNAtoolbox/webData", id, "reads.fa")
#os.system("head -n 50 " + file_to_copy + " > " + os.path.join(FS.location, "reads.fa"))
#ifile = os.path.join(FS.location, "reads.fa")
ifile = file_to_copy
adapter = None
adapter_minLength = "10"
adapterMM = "1"
newConf = SRNABlastConfig(
"nr",
"/shared/exec/blast/blastn",
FS.location,
"/shared/sRNAbenchDB",
ifile,
"1",
maxReads="10",
minEvalue="10",
adapter=adapter,
recursiveAdapterTrimming=recursive_adapter_trimming,
adapterMinLength=str(adapter_minLength),
adapterMM=str(adapterMM),
guessAdapter=guess_adapter,
local=None)
conf_file_location = os.path.join(FS.location, "conf.txt")
newConf.write_conf_file(conf_file_location)
os.system(
'qsub -v pipeline="blast",configure="' + conf_file_location +
'",key="' + pipeline_id + '",outdir="' + FS.location + '",name="' +
pipeline_id + '_sRNAblast' + '" -N ' + pipeline_id +
'_sRNAblast /shared/sRNAtoolbox/core/bash_scripts/run_sRNAblast.sh')
return redirect("/srnatoolbox/jobstatus/srnablast/?id=" + pipeline_id)
def run(request):
pipeline_id = pipeline_utils.generate_uniq_id()
rc = request.POST["rc"]
rl = "19"
mm = request.POST["mm"]
xrl = "23"
homolog = request.POST["ajax_names"]
name = pipeline_id + '_gfree'
if homolog.replace(" ", "") == "":
homolog = "false"
#return render(request, "error_page.html", {"errors": ["Any species name must be provided. Please check the manual"]})
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
if "reads_file" in request.FILES:
file_to_update = request.FILES['reads_file']
uploaded_file = str(file_to_update)
FS.save(uploaded_file, file_to_update)
input = os.path.join(FS.location, uploaded_file)
outdir = FS.location
os.system('qsub -v pipeline="gfree",input="' + input + '",key="' + pipeline_id + '",minReadLength="' + rl +
'",maxReadLength="' + xrl + '",microRNA="' + homolog + '",minRC="' + rc + '",noMM="' + mm +
'",outdir="' + outdir + '",name="' + name + '" -N ' + name +
' /shared/sRNAtoolbox/core/bash_scripts/run_sRNAgfree.sh')
print ('qsub -v pipeline="gfree",input="' + input + '",key="' + pipeline_id + '",minReadLength="' + rl +'",maxReadLength="' + xrl + '",microRNA="' + homolog + '",minRC="' + rc + '",noMM="' + mm +'",outdir="' + outdir + '",name="' + name + '" -N ' + name +' /shared/sRNAtoolbox/core/bash_scripts/run_sRNAgfree.sh')
return redirect("/srnatoolbox/jobstatus/srnagfree/?id=" + pipeline_id)
else:
return render(request, "error_page.html", {"errors": ["Reads File must be provided"]})
def run(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
miRNA_file = ""
utr_file = ""
program_list = []
parameters_list = []
if "miRNA_file" in request.FILES:
file_to_update = request.FILES['miRNA_file']
uploaded_file = str(file_to_update).replace(" ", "").replace(
")", "").replace("(", "")
if str(file_to_update).split(".")[1] not in [
"fa", "fasta", "mfasta", "mfa", "txt"
]:
return render(
request, "error_page.html", {
"errors": [
'miRNAs file extension must be: fa, fasta, mfasta, mfa or txt. ".'
+ str(file_to_update).split(".")[1] + '" found'
]
})
FS.save(uploaded_file, file_to_update)
miRNA_file = os.path.join(FS.location, uploaded_file)
if "utr_file" in request.FILES:
file_to_update = request.FILES['utr_file']
uploaded_file = str(file_to_update).replace(" ", "").replace(
")", "").replace("(", "")
if str(file_to_update).split(".")[1] not in [
"fa", "fasta", "mfasta", "mfa", "txt"
]:
return render(
request, "error_page.html", {
"errors": [
'UTRs file extension must be: fa, fasta, mfasta, mfa or txt. ".'
+ str(file_to_update).split(".")[1] + '" found'
]
})
FS.save(uploaded_file, file_to_update)
utr_file = os.path.join(FS.location, uploaded_file)
if not ("miRNA_file" in request.FILES and "utr_file" in request.FILES):
return render(
request, "error_page.html",
{"errors": ["miRNAs file and UTR file should be provided"]})
for program in request.POST.getlist("programs"):
program_list.append(program)
program_string = ":".join(program_list)
if len(program_list) < 1:
return render(request, "error_page.html",
{"errors": ["At least one program should be chosen"]})
for i, Parameter in enumerate(request.POST.getlist("Parameters")):
if TOOLS[i] in program_list:
parameters_list.append(Parameter)
parameter_string = ":".join(parameters_list).replace("-", "55-55")
if parameter_string == "":
parameter_string = "".join([":" for i in program_list])
outdir = FS.location
os.system(
'qsub -v pipeline="mirconstarget",program_string="' + program_string +
'",parameter_string="' + parameter_string + '",key="' + pipeline_id +
'",outdir="' + outdir + '",miRNA_file="' + miRNA_file +
'",utr_file="' + utr_file + '",name="' + pipeline_id +
'_mirconstarget"' + ' -N ' + pipeline_id +
'_mirconstarget /shared/sRNAtoolbox/core/bash_scripts/run_mirnatarget.sh'
)
return redirect("/srnatoolbox/jobstatus/mirconstarget/?id=" + pipeline_id)
def generate_id(self):
is_new = True
while is_new:
pipeline_id = generate_uniq_id()
if not JobStatus.objects.filter(pipeline_key=pipeline_id):
return pipeline_id
def run(request):
pipeline_id = pipeline_utils.generate_uniq_id()
guess_adapter = None
recursive_adapter_trimming = None
local = None
ifile = ""
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
if "reads_file" in request.FILES:
file_to_update = request.FILES['reads_file']
uploaded_file = str(file_to_update)
if str(file_to_update).split(".")[1] not in ["fastq", "fa", "rc"]:
return render(
request, "error_page.html", {
"errors": [
'Reads file extension must be: "fastq", "fa", "rc" ".'
+ str(file_to_update).split(".")[1] + '" found'
]
})
FS.save(uploaded_file, file_to_update)
ifile = os.path.join(FS.location, uploaded_file)
elif request.POST["bench_id"].replace(" ", "") != "":
id = request.POST["bench_id"]
file_to_copy = os.path.join("/shared/sRNAtoolbox/webData", id,
"reads.fa")
#os.system("head -n 50 " + file_to_copy + " > " + os.path.join(FS.location, "reads.fa"))
#ifile = os.path.join(FS.location, "reads.fa")
ifile = file_to_copy
elif request.POST["reads_url"].replace(" ", "") != "":
url_input = request.POST["reads_url"]
dest = os.path.join(FS.location, os.path.basename(url_input))
handler = urllib.URLopener()
handler.retrieve(url_input, dest)
ifile = dest
else:
return render(
request, "error_page.html",
{"errors": ["Read File, URL or sRNAbench ID must be provided"]})
if "guessAdapter" in request.POST:
guess_adapter = "true"
adapter = request.POST["adapter"]
maxReads = request.POST["maxReads"]
minEvalue = request.POST["minEvalue"]
if minEvalue.replace(" ", "") != "":
try:
float(minEvalue)
except:
return render(request, "error_page.html", {
"errors": ["Read File, URL or sRNAbench ID must be provided"]
})
else:
minEvalue = "10"
minrc = "1"
alter_adapter = request.POST["alterAdapter"].upper().replace(" ", "")
blastDB = request.POST["blastDB"]
if len(alter_adapter) > 1:
adapter = alter_adapter
if adapter == "XXX":
adapter = None
adapter_minLength = request.POST["adapterMinLength"]
adapterMM = request.POST["adapterMM"]
if "recursiveAdapterTrimming" in request.POST:
recursive_adapter_trimming = "true"
if "local" in request.POST:
blastDB = "/shared/blastDB/nt"
local = "true"
newConf = SRNABlastConfig(
blastDB,
"/shared/exec/blast/blastn",
FS.location,
"/shared/sRNAbenchDB",
ifile,
minrc,
maxReads=maxReads,
minEvalue=minEvalue,
adapter=adapter,
recursiveAdapterTrimming=recursive_adapter_trimming,
adapterMinLength=str(adapter_minLength),
adapterMM=str(adapterMM),
guessAdapter=guess_adapter,
local=local)
conf_file_location = os.path.join(FS.location, "conf.txt")
newConf.write_conf_file(conf_file_location)
os.system(
'qsub -v pipeline="blast",configure="' + conf_file_location +
'",key="' + pipeline_id + '",outdir="' + FS.location + '",name="' +
pipeline_id + '_sRNAblast' + '" -N ' + pipeline_id +
'_sRNAblast /shared/sRNAtoolbox/core/bash_scripts/run_sRNAblast.sh')
return redirect("/srnatoolbox/jobstatus/srnablast/?id=" + pipeline_id)
def run(request, tool):
pipeline_id = pipeline_utils.generate_uniq_id()
species = None
taxonomy = None
ifile = None
string = None
remove = "false"
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
fdw = open(os.path.join(FS.location,"error.txt"),"w")
if tool == "removedup" or tool == "extract":
if "ifile" in request.FILES:
file_to_update = request.FILES['ifile']
uploaded_file = str(file_to_update)
if str(file_to_update).split(".")[1] not in ["fa", "fasta", "gz"]:
return render(request, "error_page.html", {"errors": [
'File extension must be: "fa" or "fasta".' + str(file_to_update).split(".")[
1] + '" found']})
FS.save(uploaded_file, file_to_update)
ifile = os.path.join(FS.location, uploaded_file)
elif request.POST["url"].replace(" ", "") != "":
url_input = request.POST["url"]
dest = os.path.join(FS.location, os.path.basename(url_input))
handler = urllib.URLopener()
handler.retrieve(url_input, dest)
ifile = dest
else:
return render(request, "error_page.html", {"errors": ["URL of file must be provided"]})
string = request.POST["string"]
if tool == "removedup":
if string.replace(" ", "") == "":
return render(request, "error_page.html", {
"errors": ["A string of characters must be provided to be drop out from the sequence names"]})
if "duplicates" in request.POST:
remove = "true"
os.system(
'qsub -v pipeline="helper",mode="rd",key="' + pipeline_id + '",outdir="' + FS.location +
'",inputfile="' + ifile + '",string="' + string + '",remove="' + remove + '",name="'
+ pipeline_id + '_h_rd' + '" -N ' + pipeline_id +
'_h_rd /shared/sRNAtoolbox/core/bash_scripts/run_helper_remove_duplicates.sh')
else:
if string.replace(" ", "") == "":
return render(request, "error_page.html",
{"errors": ["A string of characters must be provided to select the sequences:"]})
os.system(
'qsub -v pipeline="helper",mode="extract",key="' + pipeline_id + '",outdir="' + FS.location +
'",inputfile="' + ifile + '",string="' + string + '",name="'
+ pipeline_id + '_h_extract' + '" -N ' + pipeline_id +
'_h_extract /shared/sRNAtoolbox/core/bash_scripts/run_helper_extract.sh')
fdw.write('qsub -v pipeline="helper",mode="extract",key="' + pipeline_id + '",outdir="' + FS.location +
'",inputfile="' + ifile + '",string="' + string + '",name="'
+ pipeline_id + '_h_extract' + '" -N ' + pipeline_id +
'_h_extract /shared/sRNAtoolbox/core/bash_scripts/run_helper_extract.sh')
if tool == "ncbiparser" or tool == "ensemlparser":
if "ifile" in request.FILES:
file_to_update = request.FILES['ifile']
uploaded_file = str(file_to_update)
FS.save(uploaded_file, file_to_update)
ifile = os.path.join(FS.location, uploaded_file)
elif request.POST["url"].replace(" ", "") != "":
url_input = request.POST["url"]
dest = os.path.join(FS.location, os.path.basename(url_input))
handler = urllib.URLopener()
handler.retrieve(url_input, dest)
ifile = dest
else:
return render(request, "error_page.html", {"errors": ["URL of file must be provided"]})
if tool == "ncbiparser":
os.system(
'qsub -v pipeline="helper",mode="ncbi",key="' + pipeline_id + '",outdir="' + FS.location +
'",inputfile="' + ifile + '",name="' + pipeline_id + '_h_ncbi' + '" -N ' + pipeline_id +
'_h_ncbi /shared/sRNAtoolbox/core/bash_scripts/run_helper_ncbi.sh')
else:
os.system(
'qsub -v pipeline="helper",mode="ensembl",key="' + pipeline_id + '",outdir="' + FS.location +
'",inputfile="' + ifile + '",name="' + pipeline_id + '_h_ens' + '" -N ' + pipeline_id +
'_h_ens /shared/sRNAtoolbox/core/bash_scripts/run_helper_ensembl.sh')
if tool == "rnacentralparser":
species = request.POST["species"]
if species.replace(" ", "") == "":
taxonomy = request.POST["taxonomy"]
taxonomy = taxonomy.replace(" ", "_")
os.system(
'qsub -v pipeline="helper",mode="rnacentral",key="' + pipeline_id + '",outdir="' + FS.location +
'",taxon="' + taxonomy + '",name="' + pipeline_id + '_h_rnac' + '" -N ' + pipeline_id +
'_h_rca /shared/sRNAtoolbox/core/bash_scripts/run_helper_rnacentral_taxon.sh')
else:
species = species.replace(" ", "_")
fdw.write('qsub -v pipeline="helper",mode="rnacentral",key="' + pipeline_id + '",outdir="' + FS.location +
'",species="' + species + '",name="' + pipeline_id + '_h_rnac' + '" -N ' + pipeline_id +
'_h_rca /shared/sRNAtoolbox/core/bash_scripts/run_helper_rnacentral.sh')
os.system(
'qsub -v pipeline="helper",mode="rnacentral",key="' + pipeline_id + '",outdir="' + FS.location +
'",species="' + species + '",name="' + pipeline_id + '_h_rnac' + '" -N ' + pipeline_id +
'_h_rca /shared/sRNAtoolbox/core/bash_scripts/run_helper_rnacentral.sh')
if tool == "trnaparser":
species = request.POST["species"]
if species.replace(" ", "") == "":
return render(request, "error_page.html", {"errors": ['Species can\'t be empty']})
else:
species = species.replace(" ", "_")
os.system(
'qsub -v pipeline="helper",mode="trna",key="' + pipeline_id + '",outdir="' + FS.location +
'",species="' + species + '",name="' + pipeline_id + '_h_trna' + '" -N ' + pipeline_id +
'_h_trna /shared/sRNAtoolbox/core/bash_scripts/run_helper_trna.sh')
#return redirect("/srnatoolbox/jobstatus/helper/?id=" + pipeline_id)
return redirect("/srnatoolbox_dev/")
def run(request):
"""
:rtype : redirect
:param request: posts and gets
:return: redirect to results
"""
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
fdw = file(FS.location + "/error.txt", "w")
annotations = ["go"]
go_table = request.POST["db_table"]
"""
if "go" in request.POST:
annotations.append("go")
if "kegg" in request.POST:
annotations.append("kegg")
if "biocyc" in request.POST:
annotations.append("biocyc")"""
outdir = FS.location
exp = "false"
if "exp" in request.POST:
exp = "true"
if "list" in request.FILES:
# Upload file
file_to_update = request.FILES['list']
uploaded_file = str(file_to_update)
FS.save(uploaded_file, file_to_update)
mir_list = os.path.join(FS.location, uploaded_file)
if not istext(mir_list):
return render(
request, "error_page.html",
{"errors": ["miRNA list file should be a text file"]})
elif request.POST["id"] != "":
try:
new_record = JobStatus.objects.get(pipeline_key=request.POST["id"])
except:
return render(
request, "error_page.html", {
"errors": [
"Job with ID: " + request.POST["id"] +
" does not exist."
]
})
mirna_file = os.path.join("/shared/sRNAtoolbox/webData",
request.POST["id"], "miRBase_main.txt")
if os.path.isfile(mirna_file):
fd = file(mirna_file)
mir_list = os.path.join(FS.location,
"top_10_" + os.path.basename(mirna_file))
fdw = file(mir_list, "w")
fd.readline()
i = 0
while i < 10:
fdw.write(fd.readline().split("\t")[0] + "\n")
i += 1
else:
return render(
request, "error_page.html", {
"errors": [
"Job with ID: " + request.POST["id"] +
" has not the appropriate results to launch sRNAFuncterms"
]
})
elif request.POST["de_id"] != "":
try:
new_record = JobStatus.objects.get(
pipeline_key=request.POST["de_id"])
except:
return render(
request, "error_page.html", {
"errors": [
"Job with ID: " + request.POST["de_id"] +
" does not exist."
]
})
assert isinstance(new_record, JobStatus)
all_consensus = []
if new_record.job_status == "Finished":
for xls in new_record.xls_files:
workbook = xlrd.open_workbook(xls)
names = workbook.sheet_names()
Selection = [name for name in names if "Selection" in name]
if Selection > 0:
parser = SRNAdeParser(xls, "none")
list_d = [obj for obj in parser.get_consensus(*Selection)]
all_consensus = all_consensus + list_d
mir_list = os.path.join(
FS.location, "differential_expression_mirna_all_condition.txt")
fdw = file(mir_list, "w")
for consensus in all_consensus:
fdw.write(consensus.miRNA_Name + "\n")
fdw.close()
else:
return render(
request, "error_page.html", {
"errors": [
"Job with ID: " + request.POST["de_id"] +
" has not the appropriate results to launch sRNAFuncterms"
]
})
else:
return render(
request, "error_page.html", {
"errors": [
"sRNAde ID, sRNAbench ID or miRNA list file should be provided"
]
})
# call qsub
fdw.write(
'qsub -v pipeline="functerms",annot="' + ",".join(annotations) +
'",outdir="' + outdir + '",go_table="' + go_table + '",exp="' + exp +
'",key="' + pipeline_id + '",name="' + pipeline_id +
'_functerms",input="' + mir_list + '",type="list" -N ' + pipeline_id +
'_functerms /shared/sRNAtoolbox/core/bash_scripts/run_sRNAfuncterms.sh'
)
os.system(
'qsub -v pipeline="functerms",annot="' + ",".join(annotations) +
'",outdir="' + outdir + '",go_table="' + go_table + '",exp="' + exp +
'",key="' + pipeline_id + '",name="' + pipeline_id +
'_functerms",input="' + mir_list + '",type="list" -N ' + pipeline_id +
'_functerms /shared/sRNAtoolbox/core/bash_scripts/run_sRNAfuncterms.sh'
)
return redirect("/srnatoolbox/jobstatus/srnafuncterms/?id=" + pipeline_id)
def test(request):
pipeline_id = pipeline_utils.generate_uniq_id()
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
libs_files = []
lib_mode = False
no_libs = False
guess_adapter = None
recursive_adapter_trimming = None
high_conf = False
solid = None
ifile = "/shared/sRNAtoolbox/testData/IK_exo.fastq.gz"
adapter = "TGGAATTCTCGGGTGCCAAGG"
species = ["hg19_5_mp", "NC_007605"]
assemblies = ["hg19", "NC_007605"]
mircro_names = ["hsa", "ebv"]
mir = ":".join(mircro_names)
homolog = ""
adapter_minLength = "10"
adapterMM = "1"
outdir = FS.location
rc = "2"
mm = "0"
seed = "20"
align_type = "n"
remove_barcode = "0"
species_annotation_file = SpeciesAnnotationParser(SPECIES_ANNOTATION_PATH)
species_annotation = species_annotation_file.parse()
newConf = SRNABenchConfig(
species_annotation,
DB,
FS.location,
ifile,
iszip="true",
RNAfold="RNAfold2",
bedGraph="true",
writeGenomeDist="true",
predict="true",
graphics="true",
species=species,
assembly=assemblies,
adapter=adapter,
recursiveAdapterTrimming=recursive_adapter_trimming,
libmode=lib_mode,
nolib=no_libs,
microRNA=mir,
removeBarcode=str(remove_barcode),
adapterMinLength=str(adapter_minLength),
adapterMM=str(adapterMM),
seed=str(seed),
noMM=str(mm),
alignType=str(align_type),
rc=str(rc),
solid=solid,
guessAdapter=guess_adapter,
highconf=high_conf,
homolog=homolog,
user_files=libs_files)
conf_file_location = os.path.join(FS.location, "conf.txt")
newConf.write_conf_file(conf_file_location)
os.system(
'qsub -v pipeline="bench",configure="' + conf_file_location +
'",key="' + pipeline_id + '",outdir="' + outdir + '",name="' +
pipeline_id + '_sRNAbench' + '" -N ' + pipeline_id +
'_sRNAbench /shared/sRNAtoolbox/core/bash_scripts/run_sRNAbench.sh')
return redirect("/srnatoolbox/jobstatus/srnabench/?id=" + pipeline_id)
def run(request):
libs_files = []
pipeline_id = pipeline_utils.generate_uniq_id()
lib_mode = False
no_libs = False
species = []
assemblies = []
guess_adapter = None
recursive_adapter_trimming = None
high_conf = False
solid = None
ifile = ""
mircro_names = []
name_modifier = None
FS.location = os.path.join("/shared/sRNAtoolbox/webData", pipeline_id)
make_dir(FS.location)
if len(request.POST["job_name"].replace(" ", "")) > 1:
name_modifier = request.POST["job_name"].replace(" ", "")
if "reads_file" in request.FILES:
file_to_update = request.FILES['reads_file']
extension = ".".join(str(file_to_update).split(".")[1:])
if extension not in [
"fastq", "fa", "rc", "fastq.gz", "fa.gz", "rc.gz", "txt",
"txt.gz", "sra"
]:
return render(
request, "error_page.html", {
"errors": [
'Reads file extension must be: "fastq", "fa", "rc", "rc.gz", "fa.gz", "fastq.gz" , "txt", "txt.gz", "sra". We have detected: '
+ extension +
' please use one of the supported formats'
]
})
if name_modifier is not None:
uploaded_file = str(name_modifier) + "." + extension
else:
uploaded_file = str(file_to_update).replace(" ", "")
FS.save(uploaded_file, file_to_update)
ifile = os.path.join(FS.location, uploaded_file)
elif request.POST["reads_url"].replace(" ", "") != "":
url_input = request.POST["reads_url"]
extension = ".".join(os.path.basename(url_input).split(".")[1:])
if extension not in [
"fastq", "fa", "rc", "fastq.gz", "fa.gz", "rc.gz", "txt",
"txt.gz", "sra"
]:
return render(
request, "error_page.html", {
"errors": [
'Reads file extension must be: "fastq", "fa", "rc", "rc.gz", "fa.gz", "fastq.gz", "txt", "txt.gz", "sra" ".'
+ extension + '" found'
]
})
if name_modifier is not None:
dest = os.path.join(FS.location,
str(name_modifier) + "." + extension).replace(
" ", "")
else:
dest = os.path.join(FS.location, os.path.basename(url_input))
handler = urllib.URLopener()
handler.retrieve(url_input, dest)
ifile = dest
else:
return render(request, "error_page.html",
{"errors": ["Read File or URL must be provided"]})
if "user_files" in request.FILES:
for i, afile in enumerate(request.FILES.getlist("user_files")):
file_to_update = afile
uploaded_file = str(file_to_update).replace(" ", "")
FS.save(uploaded_file, file_to_update)
libs_files.append(os.path.join(FS.location, uploaded_file))
if "user_urls" in request.POST:
for i, url in enumerate(request.POST.getlist("user_urls")):
if url != "":
libfile = urllib.URLopener()
dest = os.path.join(FS.location,
os.path.basename(url)).replace(" ", "")
libfile.retrieve(url, dest)
libs_files.append(dest)
if "libMode" in request.POST:
lib_mode = True
if "noLibs" in request.POST:
no_libs = True
for specie in request.POST.getlist("species"):
if specie != "":
species.append(specie.split(":")[2])
assemblies.append(specie.split(":")[1])
mircro_names.append(specie.split(":")[0])
if "guessAdapter" in request.POST:
guess_adapter = "true"
adapter = request.POST["adapter"]
alter_adapter = request.POST["alterAdapter"].upper().replace(" ", "")
if len(alter_adapter) > 1:
adapter = alter_adapter
if adapter == "XXX":
adapter = None
adapter_minLength = request.POST["adapterMinLength"]
adapterMM = request.POST["adapterMM"]
if "recursiveAdapterTrimming" in request.POST:
recursive_adapter_trimming = "true"
if "highconf" in request.POST:
high_conf = True
mir = request.POST["miR"]
homolog = request.POST["homolog"]
if len(homolog) < 1:
homolog = None
if "genomeMiR" in request.POST:
mir = ":".join(mircro_names)
if "solid" in request.POST:
solid = "true"
rc = request.POST["rc"]
mm = request.POST["mm"]
seed = request.POST["seed"]
align_type = request.POST["alignType"]
remove_barcode = request.POST["removeBarcode"]
minReadLength = request.POST["minReadLength"]
mBowtie = request.POST["mBowtie"]
if "predict" in request.POST:
predict = "true"
else:
predict = None
species_annotation_file = SpeciesAnnotationParser(SPECIES_ANNOTATION_PATH)
species_annotation = species_annotation_file.parse()
newConf = SRNABenchConfig(
species_annotation,
DB,
FS.location,
ifile,
iszip="true",
RNAfold="RNAfold2",
bedGraph="true",
writeGenomeDist="true",
predict=predict,
graphics="true",
species=species,
assembly=assemblies,
short_names=mircro_names,
adapter=adapter,
recursiveAdapterTrimming=recursive_adapter_trimming,
libmode=lib_mode,
nolib=no_libs,
microRNA=mir,
removeBarcode=str(remove_barcode),
adapterMinLength=str(adapter_minLength),
adapterMM=str(adapterMM),
seed=str(seed),
noMM=str(mm),
alignType=str(align_type),
minRC=str(rc),
solid=solid,
guessAdapter=guess_adapter,
highconf=high_conf,
homolog=homolog,
user_files=libs_files,
minReadLength=minReadLength,
mBowtie=mBowtie)
conf_file_location = os.path.join(FS.location, "conf.txt")
newConf.write_conf_file(conf_file_location)
os.system(
'qsub -v pipeline="bench",configure="' + conf_file_location +
'",key="' + pipeline_id + '",outdir="' + FS.location + '",name="' +
pipeline_id + '_sRNAbench' + '" -N ' + pipeline_id +
'_sRNAbench /shared/sRNAtoolbox/core/bash_scripts/run_sRNAbench.sh')
return redirect("/srnatoolbox/jobstatus/srnabench/?id=" + pipeline_id)
