Hi,
I'd suggest using different data structure for the intersect of samples
from a program.
data = {
'program1':
{
'sample1': {'TP53', 'ASD'},
'sample2': {'ASD'},
},
'program2': {
'sample1': {'ASD'}
}
}
this way you can do this:
for program in data:
program_genes = []
for sample, value in data[program].iteritems():
program_genes.append(value)
data[program]['intersection'] = set.intersection(*program_genes)
Now you have in each 'programX' sub-dictionary key 'intersection', with
intersection of
all the program genes.
Lukas
On 06/04/2014 12:29 PM, jarod...@libero.it wrote:
Dear all thanks for your suggestion!!!
Thanks to your suggestion I create this structure:with open("prova.csv") as p:
for i in p:
lines =i.rstrip("\n").split("\t")
...: print lines
...:
['programs ', 'sample', 'gene', 'values']
['program1', 'sample1', 'TP53', '2']
['program1', 'sample1', 'TP53', '3']
['program1', 'sample2', 'PRNP', '4']
['program1', 'sample2', 'ATF3', '3']
['program2', 'sample1', 'TP53', '2']
['program2', 'sample1', 'PRNP', '5']
['program2', 'sample2', 'TRIM32', '4']
['program2', 'sample2', 'TLK1', '4']
In [4]: with open("prova.csv") as p:
for i in p:
lines =i.rstrip("\n").split("\t")
dizlines
diz
In [4]: with open("prova.csv") as p:
for i in p:
lines =i.rstrip("\n").split("\t")
line = (lines[0],lines[1])
...: diz.setdefault(line,set()).add(lines[2])
...:
In [5]: diz
Out[5]:
{('program1', 'sample1'): {'TP53'},
('program1', 'sample2'): {'ATF3', 'PRNP'},
('program2', 'sample1'): {'PRNP', 'TP53'},
('program2', 'sample2'): {'TLK1', 'TRIM32'},
('programs ', 'sample'): {'gene'}}
So what I want to do is to use intersect between the keys recursively:
s = diz[('program2', 'sample1']
....:
....:
KeyboardInterrupt
In [14]: s = diz[('program2', 'sample1')]
In [15]: s
Out[15]: {'PRNP', 'TP53'}
In [16]: a
Out[16]: {'ATF3', 'PRNP'}
In [17]: s.inte
s.intersection s.intersection_update
In [17]: s.intersection(a)
Out[17]: {'PRNP'}
How can Have a intersect of all my dictionary and from ('program1', 'sample1')
vs ('program1', 'sample2')...
I want to count how many genes are common
Thanks in advance for your help!
_______________________________________________
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
_______________________________________________
Tutor maillist - Tutor@python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
