def process(scattered_input, dme_ix, ncpus, reads_root):
# Fill in code here to process the input and create output.
if DEBUG:
logger.setLevel(logging.DEBUG)
else:
logger.setLevel(logging.INFO)
dme_ix = dxpy.DXFile(dme_ix)
# The following line(s) download your file inputs to the local file system
# using variable names for the filenames.
dxpy.download_dxfile(dme_ix.get_id(), "index.tgz")
fq = dxpy.DXFile(scattered_input)
name = fq.describe()['name']
dxpy.download_dxfile(fq.get_id(), name)
bam_root = name + '_techrep'
logger.info("* === Calling DNAnexus and ENCODE independent script... ===")
logger.debug("** DIR: %s" % os.listdir('./'))
logger.debug(subprocess.check_output(shlex.split('head %s' % name)))
if os.path.isfile(ALIGN_SCRIPT):
logger.debug("** Executable %s exists" % ALIGN_SCRIPT)
else:
logger.debug("** Executable %s DOES NOT exist" % ALIGN_SCRIPT)
exit(1)
align_cmd = '%s index.tgz %s %s %s no_stats' % (ALIGN_SCRIPT, name,
str(ncpus), bam_root)
logger.debug('** command line: %s' % align_cmd)
map_out = subprocess.check_output(shlex.split(align_cmd))
logger.info("* === Returned from dname_align_se ===")
# As always, you can choose not to return output if the
# "postprocess" stage does not require any input, e.g. rows have
# been added to a GTable that has been created in advance. Just
# make sure that the "postprocess" job does not run until all
# "process" jobs have finished by making it wait for "map" to
# finish using the depends_on argument (this is already done for
# you in the invocation of the "postprocess" job in "main").
logger.debug("** DIR: %s" % os.listdir('./'))
logger.debug("** OUTPUT DIR: %s" % os.listdir('output/'))
os.rename(bam_root + '_bismark.bam', bam_root + '.bam')
return {
"bam_file":
dxpy.dxlink(dxpy.upload_local_file(bam_root + '.bam')),
"report_file":
dxpy.dxlink(
dxpy.upload_local_file(bam_root + '_bismark_map_report.txt'))
}
def download_qc_report(self, download_dir):
"""
Downloads the QC report from the DNAnexus sequencing results project.
Args:
download_dir: `str` - The local directory path to download the QC report to.
Returns:
`str`. The filepath to the downloaded QC report.
"""
if not os.path.isdir(download_dir):
os.makedirs(download_dir)
res = dxpy.find_one_data_object(project=self.dx_project_id,
folder=self.DX_QC_REPORT_FOLDER,
name="*_QC_Report.pdf",
name_mode="glob")
#res will be something like {u'project': u'project-BzqVkxj08kVZbPXk54X0P2JY', u'id': u'file-BzqVkg800Fb0z4437GXJfGY6'}
#dxpy.find_one_data_object() raises a dxpy.exceptions.DXSearchError() if nothing is found.
dx_file = dxpy.DXFile(dxid=res["id"], project=res["project"])
download_file_name = os.path.join(download_dir, dx_file.name)
msg = "{filename} to {download_dir}.".format(filename=dx_file.name,
download_dir=download_dir)
debug_logger.debug("Downloading " + msg)
dxpy.bindings.dxfile_functions.download_dxfile(
dxid=dx_file, filename=download_file_name)
success_logger.info("Downloaded " + msg)
return download_file_name
def main(input_bam, paired=True, params=''):
# The following line(s) initialize your data object inputs on the platform
# into dxpy.DXDataObject instances that you can start using immediately.
input_bam = dxpy.DXFile(input_bam)
base_name = remove_extensions(input_bam.describe()['name'],
[".bam", ".BAM", ".sam", ".SAM"])
# The following line(s) download your file inputs to the local file system
# using variable names for the filenames.
dxpy.download_dxfile(input_bam.get_id(), "input.bam")
# Fill in your application code here.
command = "java -Xmx6g -jar /opt/jar/SamToFastq.jar INPUT=input.bam F=%s_1.fastq" % base_name
if paired:
command += " F2=%s_2.fastq" % base_name
subprocess.check_call(command, shell=True)
# 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.
output = {}
fastq_file = dxpy.upload_local_file("%s_1.fastq" % base_name)
output["fastq_file"] = dxpy.dxlink(fastq_file)
if paired:
paired_fastq_file = dxpy.upload_local_file("%s_2.fastq" % base_name)
output["paired_fastq_file"] = dxpy.dxlink(paired_fastq_file)
return output
def calc_mismatch_per_cycle_stats(bam_file,
aligner,
output_project,
output_folder,
properties={}):
logger = []
misc_subfolder = output_folder + '/miscellany'
bam_file = dxpy.DXFile(bam_file)
bam_filename = bam_file.describe()['name']
dxpy.download_dxfile(bam_file.get_id(), bam_filename)
ofn = os.path.splitext(bam_filename)[0] + '.mm_stats'
# Change permissions
cmd = 'chmod +x /bwa_mismatches'
run_cmd(cmd, logger)
cmd = '/bwa_mismatches -o {0} -m {1} {2}'.format(ofn, ALIGNERS[aligner],
bam_filename)
run_cmd(cmd, logger)
properties['file_type'] = 'mismatch_stats'
mismatch_per_cycle_stats = dxpy.upload_local_file(filename=ofn,
project=output_project,
folder=misc_subfolder,
properties=properties,
parents=True)
return {
'mismatch_per_cycle_stats': mismatch_per_cycle_stats,
"tools_used": logger
}
def main(inputs):
# The following line(s) initialize your data object inputs on the platform
# into dxpy.DXDataObject instances that you can start using immediately.
input_filenames = []
for input_file in inputs:
dxf = dxpy.DXFile(input_file)
input_filenames.append(dxf.name)
dxpy.download_dxfile(dxf.get_id(), dxf.name)
extension = splitext(splitext(input_filenames[-1])[0])[
1] #uses last extension - presumably they are all the same
pooled_filename = '-'.join(
[splitext(splitext(fn)[0])[0]
for fn in input_filenames]) + "_pooled%s.gz" % (extension)
out, err = run_pipe(
['gzip -dc %s' % (' '.join(input_filenames)), 'gzip -c'],
outfile=pooled_filename)
pooled = dxpy.upload_local_file(pooled_filename)
# 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["pooled"] = dxpy.dxlink(pooled)
return output
def test_upload_download_remove(self):
num_test_objs = 10
min_obj_size = 50
with NamedTemporaryDirectory(change_dir=True) as tmp_d:
self.create_dataset(tmp_d, num_test_objs, min_obj_size)
self.test_dir.upload(['.'])
which_obj = self.get_dataset_obj_names(num_test_objs)[-1]
dx_p = self.test_dir / which_obj
file_h = dxpy.DXFile(dxid=dx_p.canonical_resource,
project=dx_p.canonical_project)
file_h.wait_on_close(20) # wait for file to go to closed state
for which_obj in self.get_dataset_obj_names(num_test_objs):
self.assertTrue((self.test_dir / which_obj).exists())
with NamedTemporaryDirectory(change_dir=True) as tmp_d:
self.test_dir.download(tmp_d)
for which_obj in self.get_dataset_obj_names(num_test_objs):
self.assertCorrectObjectContents(which_obj, which_obj,
min_obj_size)
(self.test_dir / which_obj).remove()
# consistency check
while (self.test_dir / which_obj).exists():
time.sleep(.5)
self.assertFalse((self.test_dir / which_obj).exists())
def _download_symbolic_link(dxid, md5digest, project, dest_filename):
dxfile = dxpy.DXFile(dxid)
url, _headers = dxfile.get_download_url(preauthenticated=True,
duration=6 * 3600,
project=project)
# Follow the redirection
print('Following redirect for ' + url)
wget_exe = _which("wget")
if wget_exe is None:
err_exit("wget is not installed on this system")
cmd = ["wget", "--tries=5", "--quiet"]
if os.path.isfile(dxid):
# file already exists, resume upload.
cmd += ["--continue"]
cmd += ["-O", dest_filename, url]
try:
print("Downloading symbolic link with wget")
subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
msg = ""
if e and e.output:
msg = e.output.strip()
err_exit("Failed to call wget: {cmd}\n{msg}\n".format(cmd=str(cmd),
msg=msg))
if md5digest is not None:
_verify(dest_filename, md5digest)
def flagstat_parse(dxlink):
desc = dxpy.describe(dxlink)
with dxpy.DXFile(desc['id'], mode='r') as flagstat_file:
if not flagstat_file:
return None
qc_dict = { #values are regular expressions, will be replaced with scores [hiq, lowq]
'in_total': 'in total',
'duplicates': 'duplicates',
'mapped': 'mapped',
'paired_in_sequencing': 'paired in sequencing',
'read1': 'read1',
'read2': 'read2',
'properly_paired': 'properly paired',
'with_self_mate_mapped': 'with itself and mate mapped',
'singletons': 'singletons',
'mate_mapped_different_chr': 'with mate mapped to a different chr$', #i.e. at the end of the line
'mate_mapped_different_chr_hiQ': 'with mate mapped to a different chr \(mapQ>=5\)' #RE so must escape
}
flagstat_lines = flagstat_file.read().splitlines()
for (qc_key, qc_pattern) in qc_dict.items():
qc_metrics = next(re.split(qc_pattern, line) for line in flagstat_lines if re.search(qc_pattern, line))
(hiq, lowq) = qc_metrics[0].split(' + ')
qc_dict[qc_key] = [int(hiq.rstrip()), int(lowq.rstrip())]
return qc_dict
def group_files_by_read(fastq_files):
"""
Function : Groups a list of FASTQ files by the values of their Read property that indicates the read number.
Returns a dict mapping each observed value of the property (or 'none' if a file does not have a value
for the property) to a list of the files with that value. Within each group, the files are sorted by their
value of the Chunk property (to ensure that left and right reads of a given chunk are handled together.
Args : fastq_files - a list of dxpy.DXFile objects representing FASTQ files.
Returns : dict.
"""
#print("Grouping Fastq files by read number")
fastq_dxfiles = [dxpy.DXFile(item) for item in fastq_files]
read_dict = {}
for fastq_dxfile in fastq_dxfiles:
props = fastq_dxfile.get_properties()
read_num = props["read"]
if read_num not in ["1", "2", "none"]:
raise dxpy.AppError("%s has invalid Read property: %s" %
(fastq_dxfile.get_id(), read_num))
if read_num not in read_dict:
read_dict[read_num] = []
fastq_dxlink = dxpy.dxlink(fastq_dxfile)
read_dict[read_num].append(fastq_dxlink)
#for read_num in read_dict:
# read_dict[read_num] = sorted(read_dict[read_num], key=chunk_property)
return read_dict
def main():
inputs_file = open("inputs_stats.txt", 'w')
print sys.argv[2]
workflow = dxpy.DXWorkflow(sys.argv[2].split(":")[-1])
fh = dxpy.DXFile(sys.argv[1].split(":")[-1])
if "/Results" in fh.describe()['folder']:
return
app_id = sys.argv[3]
if "applet" in app_id:
app = dxpy.DXApplet(app_id)
else:
app = dxpy.DXApp(app_id)
w_id = sys.argv[1].split(":")[1]
existing_inputs = []
for item in workflow.describe()['stages'][0]['input']:
existing_inputs.append(item)
print existing_inputs
for x in app.describe()['inputSpec']:
print x
if x['class'] == 'file' and x['name'] not in existing_inputs:
inputs_file.write(x['name'] + "\n")
inputs_file.close()
def test_alignment_count(applet_id, project_id, folder, tmpdir):
"""Run BWA on a FASTQ file and verify that the number of
alignments produced is correct.
"""
# Recall that applet_id is set in the associated conftest.py, which either
# gets it from the command line or builds the applet and retrieves its id.
# And tmpdir is some pytest magic. It's type is py.path.local.LocalPath.
# It's strpath property just returns a string.
applet = dxpy.DXApplet(applet_id)
input_dict = {
"fastq": dxpy.dxlink(SAMPLE_FASTQ),
"genomeindex_targz": dxpy.dxlink(HS37D5_BWA_INDEX)
}
job = applet.run(input_dict,
instance_type="mem1_ssd1_x16",
folder=folder,
project=project_id)
job.wait_on_done()
output_bam_dxfile = dxpy.DXFile(job.describe()["output"]["bam"])
local_filename = os.path.join(tmpdir.strpath, "test.bam")
dxpy.download_dxfile(output_bam_dxfile.get_id(), local_filename)
count_alignments_cmd = "samtools view {bam} | wc -l".format(
bam=local_filename)
num_alignments = int(
subprocess.check_output(count_alignments_cmd, shell=True))
assert num_alignments == 1951476
def main(input_file):
# The following line(s) initialize your data object inputs on the platform
# into dxpy.DXDataObject instances that you can start using immediately.
input_file = dxpy.DXFile(input_file)
# The following line(s) download your file inputs to the local file system
# using variable names for the filenames.
dxpy.download_dxfile(input_file.get_id(), "input_file")
# Fill in your application code here.
subprocess.check_call(
"fastq_quality_trimmer -t 20 -Q 33 -i input_file -o output_file",
shell=True)
# 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.
output_file = dxpy.upload_local_file("output_file")
# 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["output_file"] = dxpy.dxlink(output_file)
return output
def download_url_create_symlink(self, url, sym_name):
print("url = {}".format(url))
tmp_file = "localfile"
# download [url]
cmd = ["wget", "--tries=5", "--quiet", "-O", tmp_file, url]
try:
print("Downloading original link with wget")
subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError as e:
msg = ""
if e and e.output:
msg = e.output.strip()
err_exit("Failed to download with wget: {cmd}\n{msg}\n".format(
cmd=str(cmd), msg=msg))
# calculate its md5 checksum
digest = md5_checksum(tmp_file)
os.remove(tmp_file)
# create a symlink on the platform, with the correct checksum
input_params = {
'name': sym_name,
'project': self.proj_id,
'drive': "drive-PUBLISHED",
'md5sum': digest,
'symlinkPath': {
'object': url
}
}
result = dxpy.api.file_new(input_params=input_params)
return dxpy.DXFile(dxid=result["id"], project=self.proj_id)
def combine_files(countDXlinks, resultfn):
"""The 'gather' subjob of the applet.
Arguments:
countDXlinks (list[dict]): list of DXlinks to process job output files.
resultfn (str): Filename to use for job output file.
Returns:
DXLink for the main function to return as the job output.
Note: Only the DXLinks are passed as parameters.
Subjobs work on a fresh instance so files must be downloaded to the machine
"""
if resultfn.endswith(".bam"):
resultfn = resultfn[:-4] + '.txt'
sum_reads = 0
with open(resultfn, 'w') as f:
for i, dxlink in enumerate(countDXlinks):
dxfile = dxpy.DXFile(dxlink)
filename = "countfile{0}".format(i)
dxpy.download_dxfile(dxfile, filename)
with open(filename, 'r') as fsub:
for line in fsub:
sum_reads += parse_line_for_readcount(line)
f.write(line)
f.write('Total Reads: {0}'.format(sum_reads))
countDXFile = dxpy.upload_local_file(resultfn)
countDXlink = dxpy.dxlink(countDXFile.get_id())
return {"countDXLink": countDXlink}
def main(**job_inputs):
# If we weren't provided a mmi index for the reference, generate it.
if 'genome_mmi' not in job_inputs:
mmi_input = {'genome_fastagz': job_inputs['genome_fastagz']}
minimap_index_job = dxpy.new_dxjob(mmi_input, 'run_minimap_index')
job_inputs['genome_mmi'] = minimap_index_job.get_output_ref(
'genome_mmi')
output = {'genome_mmi': job_inputs['genome_mmi']}
# check if we're dealing with pacbio or ONT reads and what the filetype is
datatype = job_inputs['datatype']
one_reads_file = dxpy.DXFile(job_inputs['reads'][0]).describe()['name']
try:
file_ext = re.search("(fastq|fasta|fa|fq){1}(.gz)?$",
one_reads_file,
flags=re.I).group(1).lower()
except AttributeError:
raise dxpy.AppError("Invalid filetype extension supplied.")
# for fasta and fastq inputs, run jobs using native minimap2
jobs = run_minimap2_subjobs(job_inputs)
output['bam_files'] = [j.get_output_ref('mapped_reads') for j in jobs]
output['bai_files'] = [
j.get_output_ref('mapped_reads_index') for j in jobs
]
return output
def _move(self, dest):
"""Moves the data object to a different folder within project.
Args:
dest (Path): The destination file/folder path within same project
Raises:
ValueError: When attempting to move projects
DNAnexusError: If attempting to move across projects
"""
if not self.resource:
raise ValueError('Cannot move project ({})'.format(self))
if dest.canonical_project != self.canonical_project:
# This can be implemented by clone and remove original
raise DNAnexusError('Cannot move across different projects')
if self == dest:
return
file_handler = dxpy.DXFile(dxid=self.canonical_resource,
project=self.canonical_project)
target_dest, should_rename = self._prep_for_copy(dest)
with _wrap_dx_calls():
file_handler.move('/' + (target_dest.parent.resource or ''))
if should_rename:
file_handler.rename(dest.name)
self.clear_cached_properties()
def _clone(self, dest):
"""Clones the data object into the destination path.
The original file is retained.
Args:
dest (Path): The destination file/folder path in a different project
Raises:
ValueError: If attempting to clone a project
DNAnexusError: If cloning within same project
"""
if not self.resource:
raise ValueError('Cannot clone project ({})'.format(self))
if dest.canonical_project == self.canonical_project:
raise DNAnexusError('Cannot clone within same project')
file_handler = dxpy.DXFile(dxid=self.canonical_resource,
project=self.canonical_project)
target_dest, should_rename = self._prep_for_copy(dest)
with _wrap_dx_calls():
new_file_h = file_handler.clone(
project=dest.canonical_project,
folder='/' + (target_dest.parent.resource or ''))
# no need to rename if we changed destination to include original name
if should_rename:
new_file_h.rename(dest.name)
def main(inputs, prefix=None):
input_filenames = []
for input_file in inputs:
dxf = dxpy.DXFile(input_file)
input_filenames.append(dxf.name)
dxpy.download_dxfile(dxf.get_id(), dxf.name)
# uses last extension - presumably they are all the same
extension = splitext(splitext(input_filenames[-1])[0])[1]
if prefix:
pooled_filename = prefix + "_pooled%s.gz" % (extension)
else:
pooled_filename = \
'-'.join([splitext(splitext(fn)[0])[0] for fn in input_filenames]) + "_pooled%s.gz" % (extension)
out, err = common.run_pipe([
'gzip -dc %s' % (' '.join(input_filenames)),
'gzip -cn'],
outfile=pooled_filename)
pooled = dxpy.upload_local_file(pooled_filename)
output = {
"pooled": dxpy.dxlink(pooled)
}
return output
def download_and_gunzip_file(input_file, skip_decompress=False, additional_pipe=None, create_named_pipe=False, input_filename=None):
input_file = dxpy.DXFile(input_file)
if input_filename is None:
input_filename = input_file.describe()['name']
ofn = input_filename
cmd = 'dx download ' + input_file.get_id() + ' -o - '
if input_filename.endswith('.tar.gz'):
ofn = 'tar_output_{0}'.format(ofn.replace('.tar.gz', ''))
cmd += '| tar -zxvf - '
elif (os.path.splitext(input_filename)[-1] == '.gz') and not skip_decompress:
cmd += '| gunzip '
ofn = os.path.splitext(ofn)[0]
if additional_pipe is not None:
cmd += '| ' + additional_pipe
cmd += ' > "{0}"'.format(ofn)
if create_named_pipe:
named_pipe_cmd = 'mkfifo {0}'.format(ofn)
run_cmd(named_pipe_cmd)
cmd += '&'
run_cmd(cmd)
return ofn
def merge_bams(bam_files, bam_root, use_cat, use_sort, nthreads):
fnames = []
for bam in bam_files:
dxbam = dxpy.DXFile(bam)
dxfn = dxbam.describe()['name']
logger.info("* Downloading %s... *" % dxfn)
dxpy.download_dxfile(bam, dxfn)
fnames.append(dxfn)
outfile_name = bam_root
logger.info("* Merged alignments file will be: %s *" %
(outfile_name + '.bam'))
if len(fnames) == 1:
# UNTESTED
rep_outfile_name = bam_root + '_bismark_biorep'
logger.info("* Only one input file (%s), no merging required." %
fnames[0])
os.rename(fnames[0], outfile_name + '.bam')
else:
if use_cat:
for fn in fnames:
if not os.path.isfile('sofar.bam'):
os.rename(fn, 'sofar.bam')
else:
logger.info("* Merging...")
# NOTE: keeps the first header
cat_cmd = 'samtools cat sofar.bam %s' % fn
subprocess.check_call(shlex.split(cat_cmd),
stdout=open('merging.bam', 'a'))
os.rename('merging.bam', 'sofar.bam')
# At this point there is a 'sofar.bam' with one or more input bams
logger.info("* Files merged into %s (via cat) *" %
(outfile_name + '.bam'))
else:
# use samtools merge
# UNTESTED
filelist = " ".join(fnames)
merge_cmd = 'samtools merge sofar.bam ' + filelist
logger.info("Merging via merge: %s " % merge_cmd)
mergeout = subprocess.check_output(shlex.split(merge_cmd))
# this gets renamed later
logger.info(mergeout)
if use_sort:
# sorting needed due to samtools cat
# UNTESTED
sort_cmd = 'samtools sort -@ %s -m 6G -f sofar.bam sorted.bam' % nthreads
logger.info("* Sorting merged bam: %s" % sort_cmd)
sortout = subprocess.check_output(shlex.split(sort_cmd))
logger.info(sortout)
os.rename('sorted.bam', outfile_name + '.bam')
else:
os.rename('sofar.bam', outfile_name + '.bam')
return outfile_name + '.bam'
def main(quants_a, quants_b, annotations):
# tool_versions.py --applet $script_name --appver $script_ver
sw_versions = subprocess.check_output(['tool_versions.py', '--dxjson', 'dnanexus-executable.json'])
dxfile_a = dxpy.DXFile(quants_a)
dxfile_b = dxpy.DXFile(quants_b)
dxfile_anno = dxpy.DXFile(annotations)
print "* Downloading files..."
dxpy.download_dxfile(dxfile_a.get_id(), "quants_a.tsv")
dxpy.download_dxfile(dxfile_b.get_id(), "quants_b.tsv")
dxpy.download_dxfile(dxfile_anno.get_id(), "annotations.gtf.gz")
# Create and appropriate name for output files
out_root = root_name_from_pair(dxfile_a.name.split('.')[0],dxfile_b.name.split('.')[0])
print "* Expecting output: '"+out_root+"_srna_mad_plot.png'"
# Must move sub-scripts into current dir so they will be found by srna-mad-qc.sh
subprocess.check_call(['mv', "/usr/bin/extract_gene_ids.awk", '.'])
subprocess.check_call(['mv', "/usr/bin/sum_srna_expression.awk", '.'])
subprocess.check_call(['mv', "/usr/bin/MAD.R", '.'])
# DX/ENCODE independent script is found in resources/usr/bin
print "* ===== Calling DNAnexus and ENCODE independent script... ====="
subprocess.check_call(['srna_mad_qc.sh','annotations.gtf.gz','quants_a.tsv','quants_b.tsv',out_root])
print "* ===== Returned from dnanexus and encodeD independent script ====="
mad_plot_file = out_root + '_mad_plot.png'
mad_qc_file = out_root + '_mad_qc.txt'
print "* package properties..."
qc_metrics = {}
f_qc = open(mad_qc_file, 'r')
mad_output = f_qc.read()
f_qc.close()
mad_output = mad_output.replace("NA","-1")
qc_metrics["MAD.R"] = json.loads(mad_output)
meta_string = json.dumps(qc_metrics)
print json.dumps(qc_metrics,indent=4)
props = {}
props["SW"] = sw_versions
print "* Upload Plot..."
plot_dxfile = dxpy.upload_local_file(mad_plot_file,properties=props,details=qc_metrics)
return { "metadata": meta_string, "mad_plot": plot_dxfile }
def main(quants_a, quants_b):
# tool_versions.py --applet $script_name --appver $script_ver
sw_versions = subprocess.check_output(
['tool_versions.py', '--dxjson', 'dnanexus-executable.json'])
dxfile_a = dxpy.DXFile(quants_a)
dxfile_b = dxpy.DXFile(quants_b)
print "* Downloading files..."
dxpy.download_dxfile(dxfile_a.get_id(), "quants_a.tsv")
dxpy.download_dxfile(dxfile_b.get_id(), "quants_b.tsv")
# Create and appropriate name for output files
out_root = root_name_from_pair(
dxfile_a.name.split('.')[0],
dxfile_b.name.split('.')[0])
out_root += '_mad'
mad_plot_file = out_root + '_plot.png'
# DX/ENCODE independent script is found in resources/usr/bin
print "* Runnning MAD.R..."
subprocess.check_call(["ls", "-l"])
#mad_output = subprocess.check_output(['Rscript', '/usr/bin/MAD.R', 'quants_a.tsv', 'quants_b.tsv'])
#subprocess.check_call(['mv', "MAplot.png", mad_plot_file ])
subprocess.check_call(
['rampage_mad_qc.sh', 'quants_a.tsv', 'quants_b.tsv', out_root])
mad_json_file = out_root + '.json'
print "* package properties..."
qc_metrics = {}
#qc_metrics["MAD.R"] = json.loads(mad_output)
fileH = open(mad_json_file, 'r')
qc_metrics["MAD.R"] = json.load(fileH)
fileH.close()
meta_string = json.dumps(qc_metrics)
print json.dumps(qc_metrics, indent=4)
props = {}
props["SW"] = sw_versions
print "* Upload Plot..."
plot_dxfile = dxpy.upload_local_file(mad_plot_file,
properties=props,
details=qc_metrics)
return {"metadata": meta_string, "mad_plot": plot_dxfile}
def file_get_details(fid, dxfile=None, proj_id=None):
'''Returns dx file's details as json.'''
if dxfile == None:
if proj_id != None:
dxfile = dxpy.DXFile(fid, project=proj_id)
else:
dxfile = file_handler_from_fid(fid)
return dxfile.get_details()
def main(bam_file,
ref_vcf_file,
eval_vcf_file,
qual_cutoff,
depth_cutoff,
bed_file=None):
# The following line(s) initialize your data object inputs on the platform
# into dxpy.DXDataObject instances that you can start using immediately.
bam_file = dxpy.DXFile(bam_file)
if bed_file is not None:
bed_file = dxpy.DXFile(bed_file)
ref_vcf_file = dxpy.DXFile(vcf_file)
eval_vcf_file = dxpy.DXFile(eval_vcf_file)
# The following line(s) download your file inputs to the local file system
# using variable names for the filenames.
dxpy.download_dxfile(bam_file.get_id(), "bam_file")
dxpy.download_dxfile(vcf_file.get_id(), "vcf_file")
if bed_file is not None:
dxpy.download_dxfile(bed_file.get_id(), "bed_file")
# 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.
sites_for_manual_review = dxpy.upload_local_file("sites_for_manual_review")
# 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["sites_for_manual_review"] = dxpy.dxlink(sites_for_manual_review)
output["number_of_missed_sites"] = number_of_missed_sites
output["found_sites"] = found_sites
output["Sensitivity"] = Sensitivity
output["specificity"] = specificity
return output
def main(childbam, fatherbam, motherbam, reference, outputbase=None, targetbed=None):
inputbams = [dxpy.DXFile(item) for item in (childbam, fatherbam, motherbam)]
if len(inputbams) != 3:
raise dxpy.exceptions.AppError("A trio must consist of three files (%d bam files were provided)"%len(inputbams))
scc("dx download '%s' -o - --no-progress | zcat > reference.fa"%dxpy.DXFile(reference).get_id(), shell=True)
scc(["samtools", "faidx", "reference.fa"])
targetopt = ''
if not targetbed is None:
dxpy.download_dxfile(targetbed, "target.bed")
targetopt = '-l target.bed'
if outbase is None:
outbase = inputbams[0].get_properties()['SAMPLE_NAME'] + '.trio'
# order in trioconfig must be child, father, mother
trioconfig = open('trioconfig', 'w')
inputfiles = []
for i in range(len(inputbams)):
dxpy.download_dxfile(inputbams[i].get_id(), "inputbams-%d.bam"%i)
inputfiles.append("inputbams-%d.bam"%i)
trioconfig.write(str(inputbams[i].get_properties()['SAMPLE_NAME']) + "\n")
trioconfig.close()
# could tee to an output bcf file if desired
# FIXME - need to specify child's gender for non-PAR on X
# trioxd for female child, trioxs for male child
command = """samtools mpileup -uf reference.fa -D -V -C 50 %s %s | \
bcftools view -s trioconfig -T trioauto -vg - > %s.vcf \
"""%(targetopt, ' '.join(inputfiles), outputbase)
print "::: command is:\n\t" + command
scc(command, shell=True)
#bcfout = dxpy.upload_local_file("bcfout");
vcfout = dxpy.upload_local_file("%s.vcf"%outputbase);
output = {}
#output["bcfout"] = dxpy.dxlink(bcfout)
output["vcfout"] = dxpy.dxlink(vcfout)
return output
def file_get_properties(fid, dxfile=None, proj_id=None):
'''Returns dx file's properties.'''
if dxfile == None:
if proj_id != None:
dxfile = dxpy.DXFile(fid, project=proj_id)
else:
dxfile = file_handler_from_fid(fid)
return dxfile.get_properties()
def test_AAA_DownloadResultResults(self):
job_hash = self.job.describe()
output_hash = job_hash["output"]["rds"]
self.assertTrue(len(output_hash) == 1)
f = dxpy.DXFile(output_hash.values()[0], project=job_hash["project"])
print "TestCase: Downloading %s" % f.name
dxpy.download_dxfile(f.id, f.name, project=job_hash["project"])
self.assertTrue(os.path.isfile(f.name))
def main(**kwargs):
dxpy.download_folder(DCC_CREDENTIALS_PROJECT,
'.',
folder=DCC_CREDENTIALS_FOLDER)
if 'key' in kwargs:
key = '-'.join([dxpy.api.system_whoami()['id'], kwargs.pop('key')])
else:
key = dxpy.api.system_whoami()['id']
key_tuple = common.processkey(key, KEYFILE)
if not key_tuple:
logger.error("Key %s is not found in the keyfile %s" % (key, KEYFILE))
raise PortalCredentialsError("Supply a valid keypair ID")
authid, authpw, server = key_tuple
if 'url' in kwargs:
server = kwargs.pop('url')
keypair = (authid, authpw)
tokens = ['python3 checkfiles.py']
for k, v in kwargs.iteritems():
if isinstance(v, bool):
if v:
tokens.append("--" + k.replace('_', '-'))
continue
if isinstance(v, str) or isinstance(v, unicode) or isinstance(v, int):
tokens.append(' '.join(["--" + k.replace('_', '-'), str(v)]))
if 'dx_file' in kwargs:
dxfile = dxpy.DXFile(kwargs.get('dx_file'))
local_file = dxpy.download_dxfile(dxfile, dxfile.name)
tokens.append("--local-file %s" % (dxfile.name))
# this is just to get a command string to print that has no secrets
tokens_safe = deepcopy(tokens)
tokens_safe.append("--username %s --password %s" %
("." * len(authid), "." * len(authpw)))
tokens_safe.append(server)
logger.info(' '.join(tokens_safe))
tokens.append("--username %s --password %s" % (authid, authpw))
# this needs to be the last token
tokens.append(server)
checkfiles_command = ' '.join(tokens)
subprocess.check_call(shlex.split(checkfiles_command))
output = {}
outfilename = kwargs.get('out')
errfilename = kwargs.get('err')
if outfilename:
out = dxpy.upload_local_file(outfilename)
output.update({'out': dxpy.dxlink(out)})
if errfilename:
err = dxpy.upload_local_file(errfilename)
output.update({'err': dxpy.dxlink(err)})
return output
def download_file(file_dxid):
"""
Args : dx_file - a file object ID on DNAnexus to the current working directory.
Returns : str. Path to downloaded file.
"""
dx_file = dxpy.DXFile(file_dxid)
filename = dx_file.describe()['name']
dxpy.download_dxfile(dxid=dx_file.get_id(), filename=filename)
return filename
def main ( fastq1_gz, fastq2_gz, bowtie_index ):
input_fastq_file1 = dxpy.DXFile(fastq1_gz)
input_fastq_file1_name = input_fastq_file1.describe()['name']
if input_fastq_file1_name.endswith('.gz'):
dxpy.download_dxfile(fastq1_gz, "fastq1.gz")
subprocess.call("gunzip -q fastq1.gz", shell=True)
else:
dxpy.download_dxfile(fastq1_gz, "fastq1")
input_fastq_file2 = dxpy.DXFile(fastq2_gz)
input_fastq_file2_name = input_fastq_file2.describe()['name']
if input_fastq_file2_name.endswith('.gz'):
dxpy.download_dxfile(fastq2_gz, "fastq2.gz")
subprocess.call("gunzip -q fastq2.gz", shell=True)
else:
dxpy.download_dxfile(fastq2_gz, "fastq2")
dxpy.download_dxfile(bowtie_index, "bowtie_index.tgz")
command1 = "tar -xzf bowtie_index.tgz"
subprocess.call(command1, shell=True)
command4 = "ls -1 *bt2 | head -1 | sed 's/.1.bt2//g' > file_containing_bowtie_index_name"
subprocess.call(command4, shell=True)
subprocess.call("ls",shell=True)
subprocess.call("cat file_containing_bowtie_index_name",shell=True)
outprefix='out'
command5 = "cat file_containing_bowtie_index_name | xargs -i sh -c 'preprocessing.sh {{}} fastq1 fastq2 . {outprefix}'".format(outprefix=outprefix)
subprocess.call(command5, shell=True)
print(command5)
sorted_bam_pe_filename = "{outprefix}_noDup.sort.bam".format(outprefix=outprefix)
split_bam1_filename = "{outprefix}_pair1.bam".format(outprefix=outprefix)
split_bam2_filename = "{outprefix}_pair2.bam".format(outprefix=outprefix)
sorted_bam_pe_file = dxpy.upload_local_file(sorted_bam_pe_filename)
split_bam1_file = dxpy.upload_local_file(split_bam1_filename)
split_bam2_file = dxpy.upload_local_file(split_bam2_filename)
return { "sorted_bam_pe": sorted_bam_pe_file, "split_bam1": split_bam1_file, "split_bam2": split_bam2_file }
