【8.2】基因组坐标转基因名(pyensembl)

坐标转基因

一、pyensembl

1.1 安装pyensembl

activate3
pip install pyensembl 

下载gtf注释文件

cd /data/database/genome
wget -c https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.refGene.gtf.gz
gzip -d hg38.refGene.gtf.gz


grep -v fix /data/database/genome/hg38/gtf/hg38.refGene.gtf >/data/database/genome/hg38/gtf/hg38.refGene_remove_fix.gtf

grep -v alt /data/database/genome/hg38/gtf/hg38.refGene_remove_fix.gtf >/data/database/genome/hg38/gtf/hg38.refGene_remove.gtf

grep -v MIR /data/database/genome/hg38/gtf/hg38.refGene_remove.gtf >/data/database/genome/hg38/gtf/hg38.refGene_remove_3.gtf

1.2 python使用示例

import os
import sys
import pyensembl
import sqlite3
from pyensembl import EnsemblRelease
from pyensembl.genome import Genome


from bpkit.utils import safe_mkdir

os.environ['PYENSEMBL_CACHE_DIR'] = '/data/tmp'

print(sys.modules['pyensembl'])
def get_genname_by_loc():

  data = Genome(
      reference_name='hg38',
      annotation_name='features',
      gtf_path_or_url='/data/database/genome/hg38/gtf/hg38.refGene_remove_3.gtf') # gtf_path_or_url用来指定gtf的路径
  # parse GTF and construct database of genomic features
  data.index()  # 建立index，其实就是建立sqlite的书哭哭

  gene_names = data.gene_ids_at_locus(contig='chr12', position=25245365 )
  # gene_names = data.gene_names_at_locus(contig='chr12', position=2524)
  # exon_ids = data.exon_ids_of_gene_name('KRAS')

  print(gene_names)
  # print(exon_ids)

三、讨论

3.1 多个版本的参考基因组

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/

• hg38.ensGene.gtf.gz
• hg38.knownGene.gtf.gz
• hg38.ncbiRefSeq.gtf.gz
• hg38.refGene.gtf.gz

OR4F16 在refGene中，在5号染色体和1号染色体中都存在；但是在ncbiRefSeq中只存在与1号染色体。

不同版本对应关系 hg19，GRCH37和Ensembl75是三种国际生物信息学数据库资源收集存储单位，即NCBI，UCSC和ENSEMBL各自发布的基因组信息。

hg系列，hg18/19/38来自UCSC，也是目前使用频率最高的基因组。从出道至今我就只看过hg19了，但是建议大家都转为hg38，因为它是目前的最新版本。

基因组各种版本对应关系综合来看如下所示：

GRCh36 (hg18): ENSEMBL release_52.
GRCh37 (hg19): ENSEMBL release_59/61/64/68/69/75.
GRCh38 (hg38): ENSEMBL release_76/77/78/80/81/82.

3.2 网页版基于坐标或者基于基因名查看信息

http://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr5%3A180794288%2D180795226&hgsid=247670514_vk8YPfdCWBFKBtwS92U56yT3Y0c0

http://genome-euro.ucsc.edu/cgi-bin/hgTracks?hgtgroup_map_close=1&hgtgroup_genes_close=0&hgtgroup_phenDis_close=0&hgtgroup_covid_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_neandertal_close=1&hgtgroup_denisova_close=1&hgtgroup_varRep_close=0&hgtgroup_rep_close=0&hgsid=247668439_ssYg9GY6cp3l9lqlzOhvhrjbSaKX&position=OR4F16&hgt.positionInput=OR4F16&goButton=go&hgt.suggestTrack=knownGene&db=hg19&c=chr21&l=22656839&r=22657040&pix=950&dinkL=2.0&dinkR=2.0

参考资料

• https://github.com/openvax/pyensembl
• https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/
• https://blog.csdn.net/jiangpeng59/article/details/83147236
• https://cloud.tencent.com/developer/article/1054968