>>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf', 'r')) #fsock >>> vcf_reader = vcf.Reader(filename=r'D:\test\example.hc.vcf.gz') #filename 头文件信息主要保存在Reader对象的属性中,包括alts,contigs,filters,formats,infos,metadata。 alts使用实例: >>> vcf_reader = vcf....
>>>importvcf>>>vcf_reader=vcf.Reader(filename=r'D:\test\example.hc.vcf.gz')>>>forrecordinvcf_reader:printrecordRecord(CHROM=chr1,POS=10146,REF=AC,ALT=[A])Record(CHROM=chr1,POS=10347,REF=AACCCT,ALT=[A])Record(CHROM=chr1,POS=10439,REF=AC,ALT=[A])Record(CHROM=chr1,POS=10492,RE...
>>> vcf_reader = vcf.Reader(open('vcf/test/example-4.0.vcf','r'))#fsock >>> vcf_reader = vcf.Reader(filename=r'D:\test\example.hc.vcf.gz')#filename 头文件信息主要保存在Reader对象的属性中,包括alts,contigs,filters,formats,infos,metadata。 alts使用实例: >>> vcf_reader = vcf.Reader...
>>> vcf_reader = vcf.Reader(filename=r'D:\test\example.hc.vcf.gz') #filename 头文件信息主要保存在Reader对象的属性中,包括alts,contigs,filters,formats,infos,metadata。 alts使用实例:>>> vcf_reader = vcf.Reader(filename=r'D:\test\example.hc.vcf.gz')>>> vcf_reader.altsOrderedDict([('N...
importpysamimportvcfforrecordinvcf_reader.fetch('20',1110695,1230237):print(record) 关于杂合度的详细参考:http://www.uwyo.edu/dbmcd/molmark/lect04/lect4.html 关于pyvcf的介绍: https://pyvcf.readthedocs.io/en/latest/INTRO.html pyvcf的详细用法示例如下: ...
vcf_reader = vcf.Reader(filename=r'/mnt/X500/farmers/zhengtian/NA12878/delly_compare_giab/fp.vcf') for sample in vcf_reader: print(sample.INFO) vcf2tensor pyvcf官方手册: A VCFv4.0 and 4.1 parser for Python. Online version of PyVCF documentation is available athttp://pyvcf.rtfd.org/ ...
>>> vcf_reader.fetch('4', 10, 20) # doctest: +SKIP would include all records overlapping a 10 base pair region from the 11th base of through the 20th base (which is at index 19) of chromosome 4. It would not include the 21st base (at index 20). (Seehttp://genomewiki.ucsc.edu...
The Reader supports retrieval of records within designated regions for files with tabix indexes via the fetch method. This requires the pysam module as a dependency. Pass in a chromosome, and, optionally, start and end coordinates, for the regions of interest:...
bcf_srs_t *files; // using the synced reader only for -r option bcf_hdr_t *hdr; cmpals_t cmpals_in, cmpals_out; faidx_t *fai; struct { int tot, set, swap; } nref; char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets; int argc, rmdup, ou...
endswith('.gz') vcf_r = Reader(filename=vcf_infile, compressed=compressed) vcf_r.fetch('1', 1) # call a dummy fetch to initialize vcf_r._tabix if tabix_params: vcf_r.reader = vcf_r._tabix.fetch(**tabix_params) cnt_1, cnt_2, cnt_3 = 0, 0, 0 for rec in vcf_r: doc ...