Python CGHWSI示例

示例#1

文件： dump_all_metadata.py 项目： akahles/icgc_rnaseq_align

def main():
        if len(sys.argv) < 2:
		sys.stderr.write("must submit a CGHub analysis_id (uuid)\n")
		sys.exit(-1)
	uuid=sys.argv[1]
	sys.stdout.write("Processing uuid: %s\n" % uuid)
	data=CGHWSI.retrieve_analysis_attributes_for_uuid(uuid)
	error=CGHWSI.split_analysis_attributes(data,uuid)

示例#2

文件： create_pawg_metadata.py 项目： syoung/pancancer

def main():
    sys.stdout.write("Processing uuid: %s\n" % ANALYSIS_ID)
    data=CGHWSI.retrieve_analysis_attributes_for_uuid(ANALYSIS_ID)
    error=CGHWSI.split_analysis_attributes(data,ANALYSIS_ID)
    run_command("rsync -av %s/analysis.xml %s/analysis.xml.orig" % (ANALYSIS_ID,ANALYSIS_ID))
    process_analysis_xml(ANALYSIS_ID,FILENAME,CHECKSUM,PATH_TO_BAM)
    run_command("cat %s/analysis.new.xml | egrep -v -e '<!--' > %s/analysis.xml" % (ANALYSIS_ID,ANALYSIS_ID))
    run_command("ln -s %s/%s %s/" % (PATH_TO_BAM,FILENAME,ANALYSIS_ID))

示例#3

文件： dump_all_metadata.py 项目： ICGC-TCGA-PanCancer/pcawg3-rnaseq-align-star

def main():
    if len(sys.argv) < 2:
        sys.stderr.write("must submit a CGHub analysis_id (uuid)\n")
        sys.exit(-1)
    uuid = sys.argv[1]
    sys.stdout.write("Processing uuid: %s\n" % uuid)
    data = CGHWSI.retrieve_analysis_attributes_for_uuid(uuid)
    error = CGHWSI.split_analysis_attributes(data, uuid)