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Python File.call_type方法代码示例

本文整理汇总了Python中synapseclient.File.call_type方法的典型用法代码示例。如果您正苦于以下问题:Python File.call_type方法的具体用法?Python File.call_type怎么用?Python File.call_type使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在synapseclient.File的用法示例。


在下文中一共展示了File.call_type方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: uploadToSynapse

# 需要导入模块: from synapseclient import File [as 别名]
# 或者: from synapseclient.File import call_type [as 别名]
def uploadToSynapse(f):
    """Given a filepath extracts metadata and uploads to Synapse"""
    center, sample_id, workflow_name, date, call_type, dataType, fileType = ['']*7
    url = URLBASE+f
    if   'OICR_BL' in f: center = 'oicr_bl'
    elif 'CRG/clindel/somatic' in f:  center = 'crg_clindel'
    else: center = f.split('/')[4]
    filename =  f.split('/')[-1]
    if center in ('yale', 'wustl', 'LOHcomplete'):
        if filename =='bd829214-f230-4331-b234-def10bbe7938CNV.vcf.gz':
            sample_id, dataType, fileType='bd829214-f230-4331-b234-def10bbe7938', 'cnv', 'vcf'
        else:
            sample_id, dataType = filename.lower().split('.')[:2]
            fileType =  [i for i in filename.split('.')[2:] if i != 'gz'][-1]
    elif center in ('broad', 'BSC', 'oicr_sga', 'mda_kchen', 'MDA_HGSC', 'mcgill_popsv', 'sfu', 'UCSC', 'oicr_bl', 'Synteka_pgm21', 'crg_clindel'):
        sample_id, workflow_name, date, call_type, dataType  =  filename.replace('indels', 'indel', split('.')[:5])
        fileType =  [i for i in filename.split('.')[5:] if i != 'gz'][-1]
    else:
        print 'Not uploading:', f
        return 
    print center, workflow_name, date, call_type, dataType, fileType
    file = File(url, parentId=DIRS[center], synapseStore=False)
    file.center = center.lower()
    file.sample_id = sample_id
    file.workflow_name = workflow_name
    file.date = date
    file.call_type = call_type
    file.dataType = 'DNA'
    file.disease = 'Cancer'
    file.dataSubType = dataType
    file.fileType = fileType
    #file.analysis_id_tumor = ?????
    syn.store(file, forceVersion=False)
开发者ID:larssono,项目名称:synapseICGCSampleTracker,代码行数:35,代码来源:uploadSynapse.py

示例2: Activity

# 需要导入模块: from synapseclient import File [as 别名]
# 或者: from synapseclient.File import call_type [as 别名]
#Create Provenance log
provenance = Activity(name=meta_data['activity'],
                      desciption=meta_data['description'],
                      used = meta_data['used']
                      exectuted = meta_data['used']
                )
#prov = syn.store(prov)

name  = of.path.basename(input_path)
#Add metadata to files to be uploaded
f = File(input_path, name = name, parentId=DST_FOLDER)
f.dataType = meta_data['dataType']
f.fileType = meta_data['dataType']
f.variant_workflow = meta_data['workflow']
f.variant_workflow_version = meta_data['workflowVersion']
f.call_type = call_type
f.reference_build = meta_data['referenceBuild']
f.center_name = meta_data['center_name']
f.file_md5 = synapseclient.utils.md5_for_file(input_path)
f.study = 'PCAWG 2.0'
f.submitter_donor_id = meta_data['donor_id']
f.alignment_workflow_name='Workflow_Bundle_BWA (UCSC Implementation)'
f.alignment_workflow_source_url='https://github.com/kellrott/tcga_realign'
f.alignment_workflow_version='2.6.0'


#Store metadata and file to Synapse
#f = syn.store(f, activity = provenance)

#Add Description
#wiki = synapseclient.Wiki(TITLE, f, DESCRIPTION)
开发者ID:ChristopherWilks,项目名称:pcawg_tools,代码行数:33,代码来源:synapse_vcf_upload.py


注:本文中的synapseclient.File.call_type方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。