'rep2pr1_peaks':
rep2pr1_peaks_subjob.get_output_ref("peaks"),
'rep2pr1_xcor_plot':
rep2pr1_peaks_subjob.get_output_ref("xcor_plot"),
'rep2pr1_xcor_scores':
rep2pr1_peaks_subjob.get_output_ref("xcor_scores"),
'rep2pr2_peaks':
rep2pr2_peaks_subjob.get_output_ref("peaks"),
'rep2pr2_xcor_plot':
rep2pr2_peaks_subjob.get_output_ref("xcor_plot"),
'rep2pr2_xcor_scores':
rep2pr2_peaks_subjob.get_output_ref("xcor_scores"),
'pooledpr1_peaks':
pooledpr1_peaks_subjob.get_output_ref("peaks"),
'pooledpr1_xcor_plot':
pooledpr1_peaks_subjob.get_output_ref("xcor_plot"),
'pooledpr1_xcor_scores':
pooledpr1_peaks_subjob.get_output_ref("xcor_scores"),
'pooledpr2_peaks':
pooledpr2_peaks_subjob.get_output_ref("peaks"),
'pooledpr2_xcor_plot':
pooledpr2_peaks_subjob.get_output_ref("xcor_plot"),
'pooledpr2_xcor_scores':
pooledpr2_peaks_subjob.get_output_ref("xcor_scores"),
})
return output
dxpy.run()
output_prefix = kwargs["output_prefix"]
variant_suffixes = kwargs["variant_suffixes"]
app_output_fn = {}
for subjob_output in subjob_outputs:
for type, id in subjob_output.iteritems():
file_id = id["$dnanexus_link"]
filename = output_prefix + "_" + variant_suffixes[type]
print "Downloading " + str(file_id) + " into " + filename
dxpy.download_dxfile(dxid=file_id, filename=filename, append=True)
app_output_fn[type] = filename
postprocess_outputs = {}
need_to_renumber = ["deletions", "short_inserts", "tandem_duplications", "inversions", "large_inserts"]
for type, fn in app_output_fn.iteritems():
out_fn = fn
if type in need_to_renumber:
out_fn = RenumberMergedOutput(fn, fn+"_renumbered")
print "\nUploading {file} as {fn}".format(file=out_fn, fn=fn)
postprocess_outputs[type] = dxpy.dxlink(dxpy.upload_local_file(out_fn, name=fn))
if kwargs["export_vcf"]:
DownloadRefFasta(kwargs["reference_fasta"])
postprocess_outputs["vcf"] = ExportVCF(kwargs=kwargs, output_path=output_prefix, ref_fn="reference_fasta")
return postprocess_outputs
print dxpy.run()
p.wait()
print p.stdout.read()
print p.stderr.read()
except:
print p.stdout.read()
print p.stderr.read()
# Fill in your application code here.
# The following line(s) use the Python bindings to upload your file outputs
# after you have created them on the local file system. It assumes that you
# have used the output field name for the filename for each output, but you
# can change that behavior to suit your needs.
recalibration_file = dxpy.upload_local_file("%s.recal" % base_name);
tranches_file = dxpy.upload_local_file("%s.tranches" % base_name);
r_plot = dxpy.upload_local_file("%s.plots.R" % base_name);
# The following line fills in some basic dummy output and assumes
# that you have created variables to represent your output with
# the same name as your output fields.
output = {}
output["tranches_file"] = dxpy.dxlink(tranches_file)
output["recalibration_file"] = dxpy.dxlink(recalibration_file)
output["r_plot"] = dxpy.dxlink(r_plot)
return output
dxpy.run()
file_id = id["$dnanexus_link"]
filename = output_prefix + "_" + variant_suffixes[type]
print "Downloading " + str(file_id) + " into " + filename
dxpy.download_dxfile(dxid=file_id, filename=filename, append=True)
app_output_fn[type] = filename
postprocess_outputs = {}
need_to_renumber = [
"deletions", "short_inserts", "tandem_duplications", "inversions",
"large_inserts"
]
for type, fn in app_output_fn.iteritems():
out_fn = fn
if type in need_to_renumber:
out_fn = RenumberMergedOutput(fn, fn + "_renumbered")
print "\nUploading {file} as {fn}".format(file=out_fn, fn=fn)
postprocess_outputs[type] = dxpy.dxlink(
dxpy.upload_local_file(out_fn, name=fn))
if kwargs["export_vcf"]:
DownloadRefFasta(kwargs["reference_fasta"])
postprocess_outputs["vcf"] = ExportVCF(kwargs=kwargs,
output_path=output_prefix,
ref_fn="reference_fasta")
return postprocess_outputs
print dxpy.run()
