Python 'Tuple' object has no attribute 'has_key'

Question

I'm running a piece of freely available python code used to detect CNVs in single cell sequencing data:

#!/usr/bin/env python

import sys

def main():

    infilename = sys.argv[1]
    outfilename = sys.argv[2]
    statfilename = sys.argv[3]

    chrominfo = ("/path/hg19.chrom.sizes.txt", 0)
    bins = ("/path/hg19.bin.boundaries.50k.bowtie.k50.sorted.txt", 0)
    INFILE = open(infilename, "r")
    OUTFILE = open(outfilename, "w")
    STATFILE = open(statfilename, "w")

    binCounts = []
    for i in range(len(bins)):
        binCounts.append(0)

    print len(binCounts)
    print len(bins)

    counter = 0
    totalReads = 0
    prevChrompos = ""
    for x in INFILE:
        arow = x.rstrip().split("\t")
        thisChrom = arow[2]
        thisChrompos = arow[3]
        if thisChrom.find("_") > -1:
            #print thisChrom
            continue
        if thisChrom == "chrM":
            #print thisChrom
            continue
        if thisChrom == "":
            continue
        if chrominfo.has_key(thisChrom):
            pass
        else:
            continue

        totalReads += 1

        thisChrominfo = chrominfo[thisChrom]
        thisAbspos = long(thisChrompos) + long(thisChrominfo[2])

        counter += 1

        indexUp = len(bins) - 1
        indexDown = 0
        indexMid = int((indexUp - indexDown) / 2.0)

        while True:
            if thisAbspos >= long(bins[indexMid][2]):
                indexDown = indexMid + 0
                indexMid = int((indexUp - indexDown) / 2.0) + indexMid
            else:
                indexUp = indexMid + 0
                indexMid = int((indexUp - indexDown) / 2.0) + indexDown

            if indexUp - indexDown < 2:
                break

        binCounts[indexDown] += 1
        prevChrompos = thisChrompos

    for i in range(len(binCounts)):
        thisRatio = float(binCounts[i]) / (float(counter) / float(len(bins)))
        OUTFILE.write("\t".join(bins[i][0:3]))
        OUTFILE.write("\t")
        OUTFILE.write(str(binCounts[i]))
        OUTFILE.write("\t")
        OUTFILE.write(str(thisRatio))
        OUTFILE.write("\n")

    binCounts.sort()

    STATFILE.write("TotalReads\tMedianBinCount\n")
    STATFILE.write(str(totalReads))
    STATFILE.write("\t")
    STATFILE.write(str(binCounts[len(bins)/2]))
    STATFILE.write("\n")

    INFILE.close()
    OUTFILE.close()
    STATFILE.close()


def fileToDictionary(inputFile, indexColumn):
    input = open(inputFile, "r")

    rd = dict()
#   input.readline()
    for x in input:
        arow = x.rstrip().split("\t")
        id = arow[indexColumn]
        if rd.has_key(id):
            #rd[id].append(arow)
            print "duplicate knowngene id = " + id
            print "arow =   " + str(arow)
            print "rd[id] = " + str(rd[id])
        else:
            rd[id] = arow

    input.close()
    return(rd)


def fileToArray(inputFile, skipFirst):
    input = open(inputFile, "r")

    ra = []

    for i in range(skipFirst):
        input.readline()

    for x in input:
        arow = x.rstrip().split("\t")
        ra.append(arow)

    input.close()
    return(ra)


if __name__ == "__main__":
    main()

I'm getting an error on line 40:

Traceback (most recent call last):
  File "/path/varbin.50k.sam.py", line 129, in <module>
    main()
  File "/path/varbin.50k.sam.py", line 40, in main
    **if chrominfo.has_key(thisChrom):
AttributeError: 'tuple' object has no attribute 'has_key'**

I don't work regularly in Python, can someone offer a suggestion? Where do I begin?

What do you want to do with this line ? chrominfo is defined at the beginning as a tuple. You can access its elements with chrominfo[0] and chrominfo[1] — Patrick
– Patrick, Commented Jul 9, 2015 at 18:07
I'm not sure why it's hanging in error - what is missing from the 'has_key' call that isn't represented in that first line where it's defined? — mfk534
– mfk534, Commented Jul 9, 2015 at 18:13
should this part : chrominfo = ("/path/hg19.chrom.sizes.txt", 0) be changed to chrominfo = ("/path/hg19.chrom.sizes.txt", thisChrom)? — mfk534
– mfk534, Commented Jul 9, 2015 at 18:20
chrominfo is a tuple. Tuple do not have has_key method. This method is defined for dictionnaries. So my question is : what do you want to achieve with this line of code ? thisChrom is not defined here, so you cannot use it in the definition of chrominfo — Patrick
– Patrick, Commented Jul 9, 2015 at 18:22

SiHa · Accepted Answer · 2015-07-09 18:25:37Z

1

Your code is expecting a dictionary and getting a tuple. I think you've missed a step: You need to change

chrominfo = ("/path/hg19.chrom.sizes.txt", 0)

To

chrominfo = fileToDictionary("/path/hg19.chrom.sizes.txt", 0)

Note also that if dict.has_key(key) has been deprecated in favour of if key in dict.keys()

edited Jul 9, 2015 at 18:25

answered Jul 9, 2015 at 18:20

SiHa

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