Module ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias alias FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Str Str Str Str Str Str Str Str Str Str Str Str Assign NameStore Call NameLoad keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Num Expr Call AttributeLoad NameLoad attr Return AttributeLoad NameLoad attr decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore Call NameLoad Assign NameStore Call AttributeLoad Call NameLoad attr Assign NameStore Call NameLoad Assign NameStore Call NameLoad keyword Str keyword NameLoad keyword Str Expr Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad keyword NameLoad keyword NameLoad keyword Str keyword AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Assign NameStore Call NameLoad For NameStore Call NameLoad NameLoad body Assign NameStore Call AttributeLoad NameLoad attr If Call AttributeLoad NameLoad attr Str body If Call AttributeLoad NameLoad attr Str body Expr Call AttributeLoad NameLoad attr NameLoad orelse Expr Call AttributeLoad NameLoad attr NameLoad orelse Assign NameStore Call NameLoad NameLoad AttributeLoad NameLoad attr Print NameLoad Assign NameStore Call NameLoad NameLoad Assign SubscriptStore NameLoad Index Str NameLoad Assign SubscriptStore NameLoad Index Str Call NameLoad SubscriptLoad NameLoad Index Str Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Assign NameStore ListLoad With Call NameLoad AttributeLoad NameLoad attr Str NameStore body For NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad Call AttributeLoad NameLoad attr attr Str Assert CompareEq SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Str Assert CompareEq SubscriptLoad SubscriptLoad NameLoad Index Num Index Num Str decorator_list
N/A tempfile NamedTemporaryFile multiprocessing Manager collections OrderedDict genmod.utils VariantPrinter genmod.vcf_tools get_variant_dict get_info_dict get_variant_id HeaderParser setup_vcf_file N/A N/A N/A N/A N/A 
    Print some variants to a vcf file and return the filename
     N/A vcf_lines N/A ##fileformat=VCFv4.1
 ##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
 ##contig=<ID=1,length=249250621,assembly=b37>
 ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	father	mother	proband
 1	11900	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/1:60	1/1:60
 1	879585	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/0:60	0/1:60
 1	879586	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/1:60	0/1:60
 1	947378	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
 1	973348	.	G	A	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
 3	879585	.	A	T	100	PASS	MQ=1	GT:GQ	0/1:60	0/0:60	0/1:60
 3	879586	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/1:60	0/1:60
 3	947378	.	A	T	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
 3	973348	.	G	A	100	PASS	MQ=1	GT:GQ	0/0:60	0/0:60	0/1:60
 N/A vcf_file N/A NamedTemporaryFile mode w+t delete False suffix .vcf N/A N/A N/A vcf_file writelines vcf_lines N/A N/A N/A vcf_file seek 0 N/A N/A N/A vcf_file close N/A N/A vcf_file name N/A test_variant_printer N/A N/A N/A N/A N/A Test the variant printer N/A vcf_file N/A setup_vcf_file N/A variant_queue N/A N/A N/A Manager Queue N/A head N/A HeaderParser N/A outfile N/A NamedTemporaryFile mode w+t delete False suffix .vcf N/A N/A N/A outfile close N/A variant_printer N/A VariantPrinter task_queue variant_queue head head mode chromosome outfile N/A outfile name N/A N/A N/A variant_printer start N/A batch N/A OrderedDict N/A line N/A open vcf_file N/A N/A line N/A N/A line rstrip N/A N/A N/A line startswith # N/A N/A N/A N/A line startswith ## N/A N/A N/A N/A head parse_meta_data line N/A N/A N/A N/A head parse_header_line line N/A N/A variant_dict N/A get_variant_dict line N/A head header N/A variant_dict N/A variant_id N/A get_variant_id variant_dict N/A N/A variant_dict N/A variant_id variant_id N/A N/A variant_dict N/A info_dict N/A get_info_dict N/A variant_dict N/A INFO N/A N/A N/A variant_queue put variant_dict N/A N/A N/A variant_queue put None N/A N/A N/A variant_printer join N/A variants N/A N/A N/A open N/A outfile name r f N/A N/A line f N/A N/A N/A N/A variants append N/A N/A N/A N/A line rstrip split N/A N/A N/A N/A variants N/A 0 N/A 0 1 N/A N/A N/A N/A variants N/A 0 N/A 2 11900 N/A