The snpy from superbobry

snpy's Introduction

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An easy to use wrapper-library for working with openSNP data. The current implementation only supports local or downloaded files, but JSON API interaction is planned.

All you need to remember at this point is a single function:

>>> import sn
>>> snps = sn.parse("72.ftdna-illumina.36")
>>> sns
>>> snps[:1]
[_SNP(name='rs3094315', variation=None, chromosome='1', position=742429, strand=None, genotype='AA')]

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snpy's Issues

VCF Files

HI ,

I downloaded the last version of the bulk of openSNP.
It's actually 4700 files of raw data from various companies.
I tested your library with all the openSNP file and they're is some file with
I tested them with python 3.7.

user6020_file4548_yearofbirth_unknown_sex_unknown.ancestry.txt

I also installed pyVCF parser

Here the Traceback outputed by python using a file of one user:


user6020_file4548_yearofbirth_unknown_sex_unknown.ancestry.txt

Traceback (most recent call last):
  File "/home/yoan/Bureau/ADN/openSNP_rawdata/opensnp_datadump.current/parser.py", line 13, in <module>
    for i in snps:
  File "/usr/local/lib/python3.7/dist-packages/sn.py", line 78, in _23andme_ancestry
    for row in handle:
  File "/usr/lib/python3.7/csv.py", line 112, in __next__
    row = next(self.reader)
  File "/usr/lib/python3.7/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xbb in position 12: invalid start byte

the code:

import sn
import os

folder_content = os.listdir(os.getcwd())
for i in folder_content:
    print(i)
    if os.path.isfile(i):
        #try:
        snps = sn.parse(i)
        cpt = 0
        for i in snps:
            print(i)
            cpt += 1
            if cpt == 10:
                break

Thanks in advance for our help !

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