Question

I am new to python (well to coding in general) and am trying to use it to analyze some data at work. I have a file like this:

    HWI-ST591_0064:5:1101:1228:2111#0/1 +   7included   11  A>G -   -
    HWI-ST591_0064:5:1101:1205:2125#0/1 +   genomic 17  A>G -   -
    HWI-ST591_0064:5:1101:1178:2129#0/1 +   7included   6   A>C 8   A>T
    HWI-ST591_0064:5:1101:1176:2164#0/1 +   7included   6   A>T 8   A>G
    HWI-ST591_0064:5:1101:1199:2234#0/1 +   7included   14  T>C 21  G>A
    HWI-ST591_0064:5:1101:1208:2249#0/1 +   7included   32  C>T -   -

Tab delimited. I am trying to create a dictionary that contains the first value of the line (a unique identifier) as a list of values that matches the joined last 4 values as the key, like this:

     {'32C>T--': ['HWI-ST591_0064:5:1101:1208:2249#0/1'], 
    '6A>C8A>C': ['HWI-ST591_0064:5:1101:1318:2090#0/1'], 
    '36A>G--': ['HWI-ST591_0064:5:1101:1425:2093#0/1'], 
     '----': ['HWI-ST591_0064:5:1101:1222:2225#0/1'], 
    '6A>C8A>T': ['HWI-ST591_0064:5:1101:1178:2129#0/1','HWIST591_0064:5:1101:1176:2164#0/1']}

This way I can then get a list of the unique identifies and count or sort or do the other things I need to do. I can get the dictionary made, but when I try to output it to a file I get an error. I think the problem is because this is a list, I keep getting the error

File “trial.py”, line 33, in
outFile.write(“%s\t%s\n” % (‘\t’ .join(key, mutReadDict[key])))
TypeError: unhashable type: ‘list’

Is there a way to make this work so I can have it in a file? I tried .iteritems() on the for loop making the dictionary but that didn’t seem to work. Thanks and here is my code:

inFile = open('path', 'rU')
outFile = open('path', 'w')

from collections import defaultdict

mutReadDict = defaultdict(list)

 for line in inFile:
entry               = line.strip('\n').split('\t')
fastQ_ID            = entry[0]
strand              = entry[1]
chromosome          = entry[2]
mut1pos             = entry[3]
mut1base            = entry[4]
mut2pos             = entry[5]
mut2base            = entry[6]

mutKey = mut1pos + mut1base + mut2pos + mut2base

if chromosome == '7included':
    mutReadDict[mutKey].append(fastQ_ID)
else:
    pass

keyList = [mutReadDict.keys()]
keyList.sort()

for key in keyList:
outFile.write("%s\t%s\n" % ('\t' .join(key, mutReadDict[key])))

outFile.close()

Answer 1

I think you want:

keyList = mutReadDict.keys()

instead of

keyList = [mutReadDict.keys()]

You probably mean this too:

for key in keyList:
    outFile.write("%s\t%s\n" % (key, '\t'.join(mutReadDict[key])))