How to use dxpy - 10 common examples

def get_project(project_name):
    '''Try to find the project with the given name or id.'''

    # First, see if the project is a project-id.
    try:
        project = dxpy.DXProject(project_name)
        return project
    except dxpy.DXError:
        pass

    project = dxpy.find_projects(name=project_name, return_handler=True, level="VIEW")
    project = [p for p in project]
    if len(project) == 0:
        print('Did not find project {0}'.format(project_name))
        return None
    elif len(project) == 1:
        return project[0]
    else:
        raise Exception('Found more than 1 project matching {0}'.format(project_name))

#    filePath = filePath.replace("'","").replace('"','').replace("}","").replace("{","")
    try:
        dxlink = json.loads(filePath.strip("'"))
    except:
        dxlink = None

    if project != None:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink,project=project)
            else:
                dxfile = dxpy.get_handler(filePath,project=project)
        except:
            try:
                dxlink = dxpy.dxlink(filePath,project=project)
                dxfile = dxpy.get_handler(dxlink)
            except:
                try:
                    proj_id = env_get_current_project_id()
                    dxfile = dxpy.DXFile(filePath,project=proj_id)
                except:
                    sys.stderr.write('ERROR: unable to find file "' + filePath + '": \n')
                    sys.exit(0)  # Do not error on tool run in dx script

    else:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink)
            else:
                dxfile = dxpy.get_handler(filePath)

if project != None:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink,project=project)
            else:
                dxfile = dxpy.get_handler(filePath,project=project)
        except:
            try:
                dxlink = dxpy.dxlink(filePath,project=project)
                dxfile = dxpy.get_handler(dxlink)
            except:
                try:
                    proj_id = env_get_current_project_id()
                    dxfile = dxpy.DXFile(filePath,project=proj_id)
                except:
                    sys.stderr.write('ERROR: unable to find file "' + filePath + '": \n')
                    sys.exit(0)  # Do not error on tool run in dx script

    else:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink)
            else:
                dxfile = dxpy.get_handler(filePath)
        except:
            try:
                dxlink = dxpy.dxlink(filePath)
                dxfile = dxpy.get_handler(dxlink)
            except:

"\t\tshortLabel %s\n" %(name[:17]) + \
        "\t\tparent %sviewpeaks on\n" %(accession) + \
        "\t\ttype %s\n" %(tracktype) + \
        "\t\tvisibility dense\n" + \
        "\t\tview PK\n" + \
        "\t\tpriority %d\n\n" %(n)
    n_stanzas = 1
    if not lowpass:
        lowpass = []
    if isinstance(lowpass,int):
        lowpass = [lowpass]
    extra_stanza_count = 0
    for (i, cutoff) in enumerate(lowpass,start=1):
        fn = dx.get_id()
        if not os.path.isfile(fn):
            dxpy.download_dxfile(dx.get_id(),fn)
        cutoffstr = '-lt%d' %(cutoff)
        outfn = fn + cutoffstr
        print fn, os.path.getsize(fn), subprocess.check_output('wc -l %s' %(fn), shell=True).split()[0]
        bed_fn = fn + '.bed'
        common.block_on('bigBedToBed %s %s' %(fn, bed_fn))
        common.run_pipe([
            'cat %s' %(bed_fn),
            r"""awk 'BEGIN{FS="\t";OFS="\t"}{if (($3-$2) < %d) {print $0}}'""" %(cutoff)], outfn)
        print outfn, os.path.getsize(outfn), subprocess.check_output('wc -l %s' %(outfn), shell=True).split()[0]
        if tracktype =='bigBed 6 +':
            as_file = 'narrowPeak.as'
        elif tracktype == 'bigBed 12 +':
            as_file = 'gappedPeak.as'
        else:
            print "Cannot match tracktype %s to any .as file" %(tracktype)
        bb_fn = common.bed2bb(outfn,'mm10.chrom.sizes',as_file)

if file_desc['class'] != 'file':
        print("Skipping non-file data object {name} ({id})".format(**file_desc), file=sys.stderr)
        return

    if file_desc['state'] != 'closed':
        print("Skipping file {name} ({id}) because it is not closed".format(**file_desc), file=sys.stderr)
        return

    try:
        show_progress = args.show_progress
    except AttributeError:
        show_progress = False

    try:
        dxpy.download_dxfile(
                            file_desc['id'],
                            dest_filename,
                            show_progress=show_progress,
                            project=project,
                            describe_output=file_desc)
        return
    except:
        err_exit()

"%s sort -@ %d -n %s %s" \
            % (samtools, cpu_count(), input_bam_filename, final_nmsrt_bam_prefix)
        logger.info(command)
        subprocess.check_call(shlex.split(command))

        final_BEDPE_filename = input_bam_basename + ".bedpe.gz"
        out, err = common.run_pipe([
            "bamToBed -bedpe -mate1 -i %s" % (final_nmsrt_bam_filename),
            "gzip -cn"],
            outfile=final_BEDPE_filename)

    subprocess.check_output('ls -l', shell=True)

    tagAlign_file = dxpy.upload_local_file(final_TA_filename)
    if paired_end:
        BEDPE_file = dxpy.upload_local_file(final_BEDPE_filename)

    output = {}
    output["tagAlign_file"] = dxpy.dxlink(tagAlign_file)
    if paired_end:
        output["BEDPE_file"] = dxpy.dxlink(BEDPE_file)

    return output

line_count = wc_output.split()[0]
    n_peaks = int(line_count)

    #TODO batch consistency plot

    # 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 = {}

    EM_fit_output = None
    empirical_curves_output = None
    overlapped_peaks = None
    EM_parameters_log = dxpy.upload_local_file(rep1_vs_rep2_prefix + '.log.txt')
    IDR2_plot = dxpy.upload_local_file(pooled_common_peaks_IDR_filename + '.png')
    output.update({
        "IDR2_plot": dxpy.dxlink(IDR2_plot)
        })

    npeaks_pass = dxpy.upload_local_file(npeaks_pass_filename)
    IDR_output = dxpy.upload_local_file(compress(pooled_common_peaks_IDR_filename))
    IDR_peaks = dxpy.upload_local_file(compress(final_IDR_thresholded_filename))

    #
    # return { "app_output_field": postprocess_job.get_output_ref("answer"), ...}
    #

    subprocess.check_output('ls -l', shell=True, stderr=subprocess.STDOUT)

    output.update({

global args

    if job_input == None:
        temp = vars(parser.parse_args(sys.argv[1:]))
        for key in temp:
            if temp[key] != None:
                if key == 'tags':
                    args[key] = temp[key].split(",")
                    # remove whitespace around tags
                    for i in range(len(args[key])):
                        args[key][i] = args[key][i].rstrip().lstrip()
                elif key == 'properties':
                    try:
                        args[key] = ast.literal_eval(temp[key])
                    except SyntaxError:
                        raise dxpy.AppError("Cannot parse properties: " + temp[key])
                else:
                    args[key] = temp[key]

    else:
        args = job_input

    print(args)
    
    if 'file2' in args:
        paired = True
    else:
        paired = False
   
    is_fasta, is_colorspace, qual_encoding = sniff_fastq(args["file"])
    
    if is_fasta == False and ('qual' in args or 'qual2' in args):

try:
        dxlink = json.loads(filePath.strip("'"))
    except:
        dxlink = None

    if project != None:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink,project=project)
            else:
                dxfile = dxpy.get_handler(filePath,project=project)
        except:
            try:
                dxlink = dxpy.dxlink(filePath,project=project)
                dxfile = dxpy.get_handler(dxlink)
            except:
                try:
                    proj_id = env_get_current_project_id()
                    dxfile = dxpy.DXFile(filePath,project=proj_id)
                except:
                    sys.stderr.write('ERROR: unable to find file "' + filePath + '": \n')
                    sys.exit(0)  # Do not error on tool run in dx script

    else:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink)
            else:
                dxfile = dxpy.get_handler(filePath)
        except:

dxfile = None
    #if filePath.find("$dnanexus_link") != -1:
    #    filePath = filePath.split(' ')[1]
    #    filePath = filePath.replace("'","").replace('"','').replace("}","").replace("{","")
    try:
        dxlink = json.loads(filePath.strip("'"))
    except:
        dxlink = None

    if project != None:

        try:
            if dxlink != None:
                dxfile = dxpy.get_handler(dxlink,project=project)
            else:
                dxfile = dxpy.get_handler(filePath,project=project)
        except:
            try:
                dxlink = dxpy.dxlink(filePath,project=project)
                dxfile = dxpy.get_handler(dxlink)
            except:
                try:
                    proj_id = env_get_current_project_id()
                    dxfile = dxpy.DXFile(filePath,project=proj_id)
                except:
                    sys.stderr.write('ERROR: unable to find file "' + filePath + '": \n')
                    sys.exit(0)  # Do not error on tool run in dx script

    else:

        try:
            if dxlink != None: