Hi,
I have a Python script which takes as input a list of SNPs, then calls tabix to retrieve .VCF file and does some stuff with it.
The problem is that i need to manually add (using UCSC genome browser web*) the coordinates of the SNP for tabix to work properly.
Does any one know any simple python API / function / module to easy add this information without having to perform the search manually?
Thanks!
•
written
by
Peixe
3 answers
You could use an external database to find the coordinates of your rs## (not tested, please check the +0/+1 for the coordinates)
for R in rs25 rs26 rs27
do
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Dhg19 -N -e "select concat(chrom,':',chromStart+1,'-',chromEnd) from snp135 where name='$R';" |\
xargs tabix my.vcf.gz
done
•
written
by
Pierre Lindenbaum
ERROR 2013 (HY000): Lost connection to MySQL server at 'reading initial communication packet', system error: 104
open: No such file or directory
[tabix] was bgzip used to compress this file? my.vcf.gz
Pierre Lindenbaum why "from snp135"?
because 11 years ago that was the name of the snpTable.
now for hg38: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp151.sql
You can do this with cruzdb
from cruzdb import Genome
import sys
fname = sys.argv[1]
hg19 = Genome('hg19')
snp135 = hg19.snp135
for rs in (l.split()[0].rstrip() for l in open(fname) if l.startswith("rs")):
print snp135.filter_by(name=rs).first()
which takes a file with the rs id's in the first columns and prints out a bed file with the chromosome locations from dbsnp 135.
hi @brentp, I run into your tool and noted that the following line is giving an error.
snp135 = hg19.snp135
I realized that it's because snp135 is no longer the latest database. How do you determine which version of dbsnp to use without knowing what's currently available? PS: I tried snp141 and it worked..
Have you installed cruzdb first?
Yes I installed it and now get another error:
Traceback (most recent call last):
File "hellowworld.py", line 1, in <module>
from cruzdb import Genome
File "C:\Python34\lib\site-packages\cruzdb\__init__.py", line 5, in <module>
from . import soup
File "C:\Python34\lib\site-packages\cruzdb\soup.py", line 1, in <module>
from . import sqlsoup
File "C:\Python34\lib\site-packages\cruzdb\sqlsoup.py", line 458
except KeyError, ke:
^
SyntaxError: invalid syntax
I guess this synthax error is because you use Python3.4 and the module was written for python2, but that's just my first guess.
You need to save the code as a script and use the input file as a argument when executing the script using your python interpreter.
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