CODEWITHSUNDEEP
pythondefaultdict
crysis405
crysis405

Reputation: 1131

Search keys and its values using defaultdict

I am new to python, so correct me if this is not the best/fastest way of doing this. I have created a dictionary with multiple values assigned to each key. In codonDict I have included only 1 key with a few of its values (there will be a lot more). Now I have a file which I have called calls here. What I want to do is find the key that corresponds to the #CHROM in the file and then search through the keys values to see if it contains the corresponding POS. 

codonDict = defaultdict(<type 'list'>, {'HE667775': [106690, 106692, 106694, 106696, 106698, 106700, 106702, 106704, 106706, 106708, 106710, 106712, 106714, 106716, 106718, 106720, 106722, 106724, 106726, 106728, 106730, 106732, 106734, 106736, 106738, 106740, 106742, 106744, 106746, 106748, 106750, 106752, 106754, 106756, 106758, 106760, 106762, 106764, 106766, 106768, 106770, 106772, 106774, 106776, 106778, 106780, 106782, 106784, 106786, 106788, 106790, 106792, 106794, 106796, 106798, 106800, 106802, 106804, 106806, 106808, 106810, 106812, 106814, 106816, 106818, 106820, 106822, 106824, 106826, 106828, 106830, 106832, 106834, 106836]})

calls file:

#CHROM      POS
HE667775    106824  
HE667775    24

So from this sample data the desired output would be that HE667775 106824 which gets append to test

What I have tried:

    test = []
    line = calls.readline()

    while len(line) > 1:
    #for line in calls:
        objects = line.split()

        pos = int(objects[1])
        chrom = objects[0]

        #if scaf in codonDict and pos associated with that key

            for scaf, position in codonDict.itervalues():
            if pos == position and chrom in scaf:
                test.append(line)

        print test

Error:

ValueError: too many values to unpack

Edit: This is the complete error traceback, however the lines differ, so line 28 in the above code would be I believe pos = int(objects[1])

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<stdin>", line 28, in main
ValueError: too many values to unpack

Upvotes: 1

Views: 760

Answers (3)

MrLeeh
MrLeeh

Reputation: 5589

To check if chrom is in codonDict just use in like dm03514 wrote before. I could imagine something like this with codonDict as an ordinary dictionary:

def find(chrom, pos):
    if chrom in codonDict:
        values = codonDict[chrom]
        if pos in values:
            print "%i in %s" % (pos, chrom)
        else:
            print "%i not in %s" % (pos, chrom)
    else:
        print "chrom %s not found" % chrom

Upvotes: 0

dm03514
dm03514

Reputation: 55972

To check if the pos from your file is in the condonDict no loop is required, you can use python in to check for membership by:

pos in condonDict[chrom]

Upvotes: 2

MrLeeh
MrLeeh

Reputation: 5589

So i don' t know exactly what your code is doing I' m pretty sure you get the ValueError because of this line of code:

for scaf, position in codonDict.itervalues()

itervalues gives you an iterator over the values of your dictionary. In your case this is a list. But you can' t unpack two variables scaf and position.

Try it this way and there should be no ValueError anymore:

for val in codonDict.itervalues()

Upvotes: 2

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