Looping through dictionary and comparing values with elements of a separate list.

[Mr_Keystrokes]

Apologies for the long question. Basically I am trying to loop through a dictionary I've constructed and check whether a specific element of the hash is in a given list.

Test script:

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Hash_Isolates={     "1" : ['L02476-16_P_R1', 'AE006468', '873'],     "2" : ['AE006468', 'AE006468', '40'],     "3" : ['AE006468', 'L02476-16_P_R1', '756'],     "4" : ['L00409-17_R1', 'L02476-16_P_R1', '987'],     "5" : ['L00817-17_R1', 'AE006468', '65'] }   new_isolateList=['AE006468', 'L00817-17_R1']   my_Isolates=[]   for i in Hash_Isolates:     if Hash_Isolates[i][0] in new_isolateList and Hash_Isolates[i][1] in new_isolateList:         my_Isolates.append(Hash_Isolates[i])   print(len(my_Isolates))

Strangely, when I run this test script it works, but when I run the proper script it doesn't.
For the test script you get 2 printed out.

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#!/usr/bin/env python2.7   import getpass import sys import re     isolateFile=sys.argv[1] snapper_data=sys.argv[2]   ## Get the user ID ## def get_User():     currentUser = getpass.getuser()     return currentUser     isolatePath='/home/'+get_User()+'/path/to/file/'+isolateFile dataPath='/home/'+get_User()+'/path/to/file/'+snapper_data     # Retrieve isolates from file   isolateList=[] with open(isolatePath, 'r') as file:     isolateList=file.readlines()   new_isolateList=[] for i in isolateList:     try:         x=re.search('(\w.....-?.?.?\d?)', str(i)).group(1)     except:         pass     new_isolateList.append(x)   all_results=[]   with open(dataPath, 'r') as file:     all_results=file.readlines()     # w is the position in the list of the samples being compared from the whole file # x is first sample in comparison # y is the second sample in comparison # z is the SNP distance between the first and second samples Hash_Isolates={} for i in all_results:     w=re.search('(.?.?.?.?.?.?.?),.+,.+,\d+\n', str(i)).group(1)     x=re.search('.?.?.?.?.?.?.?,(.+),.+,\d+\n', str(i)).group(1)     y=re.search('.?.?.?.?.?.?.?,.+,(.+),\d+\n', str(i)).group(1)     z=re.search('.?.?.?.?.?.?.?,.+,.+,(\d+)\n', str(i)).group(1)     Hash_Isolates[w]=[x, y, z]   my_Isolates=[]   for i in Hash_Isolates:     if Hash_Isolates[i][0] in new_isolateList and Hash_Isolates[i][1] in new_isolateList:         my_Isolates.append(Hash_Isolates[i])     print(len(my_Isolates))

So I expect this to work in the same way, but it prints 0. This snapper_data file has 100k + lines.
The data looks like this:
The isolateFile is a text file:

L01121-17_R1
AE006468
L00817-17_R1
L00665-17_R1

The snapper_data file is csv file:

1,L02476-16_P_R1,AE006468,873
2,L02476-16_P_R1,L02888-16_P_R1,2
3,L02476-16_P_R1,L00541-14_P_R1,914
4,L02476-16_P_R1,L02471-16_P_R1,842
5,AE006468,L02888-16_P_R1,832

I'm really desperate to get command of using dictionaries but this is bugging me.

[buran]

well, it looks like you overcomplicate things.

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import csv   with open('isolate_file.txt') as f:     new_isolate = {line.strip() for line in f}   with open('snapper_data.csv') as sd:     rdr = csv.reader(sd)     my_isolates = [line[1:] for line in rdr if len(set(line[1:-1]) & new_isolate)==2]                print(my_isolates)

snapper_data.csv

Output:
1,L02476-16_P_R1,AE006468,873
2,L02476-16_P_R1,L02888-16_P_R1,2
3,L02476-16_P_R1,L00541-14_P_R1,914
4,L02476-16_P_R1,L02471-16_P_R1,842
5,AE006468,L02888-16_P_R1,832
6,L01121-17_R1,AE006468,100

isolate_file.txt

Output:
L01121-17_R1
AE006468
L00817-17_R1
L00665-17_R1

output:

Output:
[['L01121-17_R1', 'AE006468', '100']]

[Mr_Keystrokes]

You see this is why I like Python. So many simpler ways of doing things you just have to know them. Now I've got to decipher what you've written. Thanks.

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1 2	len(set(line[1:-1]) & new_isolate)==2]

Hmm, this doesn't take into account the instances where the 2 elements being compared are the same.

[buran]

Hmm, this doesn't take into account the instances where the 2 elements being compared are the same.

let's take the check in a function

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import csv   def check_line(line, isolate):     my_set = set(line)     return len(my_set & isolate) == len(my_set)   with open('isolate_file.txt') as f:     new_isolate = {line.strip() for line in f}   with open('snapper_data.csv') as sd:     rdr = csv.reader(sd)     my_isolates = [line[1:] for line in rdr if check_line(line[1:-1], new_isolate)]                print(my_isolates)

you can do it also like this

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import csv   with open('isolate_file.txt') as f:     new_isolate = {line.strip() for line in f}   with open('snapper_data.csv') as sd:     rdr = csv.reader(sd)     my_isolates = [line[1:] for line in rdr if line[1] in new_isolate and line[2] in new_isolate]                print(my_isolates)

[Mr_Keystrokes]

Thanks, I like the last solution best. Didn't know about csv reader so that will be useful in the future. And I would never have looked up set(). I have to say it's much simpler than Perl.

[wavic]

I have to say it's much simpler than Perl.

No joking? :D
“Perl – The only language that looks the same before and after RSA encryption.”