Entering edit mode
3.9 years ago
nayeona.hi
▴
60
I am practicing with the book "bioinformatics with python cookbook".
In the part of POPULATION GENETICS with PLINK files,
I am using colab instead of jupyter notebook and find some errors.
'hapmap01.map' file is not generated.
So, the function "get_non_auto_SNPs" doesn't work.
Plink is usable on colab?
How could I solve this problem?
Thanks in advance.
Sub-sampling
In [5]:
os.system('plink --recode --file hapmap3_r2_b36_fwd.consensus.qc.poly --noweb --out hapmap10 --thin 0.1 --geno 0.1')
os.system('plink --recode --file hapmap3_r2_b36_fwd.consensus.qc.poly --noweb --out hapmap1 --thin 0.01 --geno 0.1')
Getting only autosomal data
In [6]:
def get_non_auto_SNPs(map_file, exclude_file):
f = open(map_file)
w = open(exclude_file, 'w')
for l in f:
toks = l.rstrip().split('\t')
chrom = int(toks[0])
rs = toks[1]
if chrom > 22:
w.write('%s\n' % rs)
w.close()
In [7]:
get_non_auto_SNPs('hapmap10.map', 'exclude10.txt')
get_non_auto_SNPs('hapmap1.map', 'exclude1.txt')
#get_non_auto_SNPs('hapmap3_r2_b36_fwd.consensus.qc.poly.map', 'exclude.txt')
In [8]:
!plink --recode --file hapmap10 --noweb --out hapmap10_auto --exclude exclude10.txt
!plink --recode --file hapmap1 --noweb --out hapmap1_auto --exclude exclude1.txt
#geno!!!
#!plink --recode --file hapmap3_r2_b36_fwd.consensus.qc.poly --noweb --out hapmap_auto --exclude exclude.txt