Question: how to rectify python AttributeError: 'NoneType' object has no attribute 'strip'
0
gravatar for stafnymd
3.3 years ago by
stafnymd10
stafnymd10 wrote:

Hi. I am a beginner in Bioinformatics. I am coming across this error while running the python script to Filter the Uncorrectable illumina paired end reads FilterUncorrectabledPEfastq.py) published by Adam H Freedman in github, harvardinformatics page.

Traceback (most recent call last):
     File "FilterUncorrectabledPEfastq.py", line 51, in <module>
         head1,seq1,placeholder1,qual1=[i.strip() for i in entry]
AttributeError: 'NoneType' object has no attribute 'strip'

Any input for rectifying this error?

the script is:

 import sys        
 import gzip
 from itertools import izip,izip_longest
 import argparse
 from os.path import basename

def get_input_streams(r1file,r2file):
if r1file[-2:]=='gz':
    r1handle=gzip.open(r1file,'rb')
    r2handle=gzip.open(r2file,'rb')
else:
    r1handle=open(r1file,'r')
    r2handle=open(r2file,'r')

return r1handle,r2handle


 def grouper(iterable, n, fillvalue=None):
"Collect data into fixed-length chunks or blocks"
# grouper('ABCDEFG', 3, 'x') --> ABC DEF Gxx
args = [iter(iterable)] * n
return izip_longest(fillvalue=fillvalue, *args)  


if __name__=="__main__": 
parser = argparse.ArgumentParser(description="options for filtering and logging rCorrector fastq outputs")
parser.add_argument('-1','--left_reads',dest='leftreads',type=str,help='R1 fastq file')
parser.add_argument('-2','--right_reads',dest='rightreads',type=str,help='R2 fastq file')
parser.add_argument('-o','--out_prefix',dest='outprefix',type=str,help="prefix for filtered fastq output")
opts = parser.parse_args()

r1out=open(opts.outprefix+'_'+basename(opts.leftreads).replace('.gz',''),'w')
r2out=open(opts.outprefix+'_'+basename(opts.rightreads).replace('.gz','') ,'w')

r1_cor_count=0
r2_cor_count=0
pair_cor_count=0
unfix_count=0   

r1_stream,r2_stream=get_input_streams(opts.leftreads,opts.rightreads)

with r1_stream as f1, r2_stream as f2:
    R1=grouper(f1,4)
    R2=grouper(f2,4)
    counter=0
    for entry in R1:
        counter+=1
        if counter%100000==0:
            print "%s reads processed" % counter

        head1,seq1,placeholder1,qual1=[i.strip() for i in entry]
        head2,seq2,placeholder2,qual2=[j.strip() for j in R2.next()]

        if 'unfixable' in head1 or 'unfixable' in head2:
            unfix_count+=1
        else:
            if 'cor' in head1:
                r1_cor_count+=1
            if 'cor' in head2:
                r2_cor_count+=1
            if 'cor' in head1 or 'cor' in head2:
                pair_cor_count+=1

            head1=head1.split('l:')[0][:-1] # keeps all before the low kmer count statistic and removes the trailing whitespace character
            head2=head2.split('l:')[0][:-1] 
            #head1=head1.replace(' cor','')
            #head2=head2.replace(' cor','')
            r1out.write('%s\n' % '\n'.join([head1,seq1,placeholder1,qual1]))
            r2out.write('%s\n' % '\n'.join([head2,seq2,placeholder2,qual2]))

unfix_log=open('rmunfixable.log','w')
unfix_log.write('total PE reads:%s\nremoved PE reads:%s\nretained PE reads:%s\nR1 corrected:%s\nR2 corrected:%s\npairs corrected:%s\n' % (counter,unfix_count,counter-unfix_count,r1_cor_count,r2_cor_count,pair_cor_count))

r1out.close()
r2out.close()
rna-seq • 13k views
ADD COMMENTlink modified 3.3 years ago by WouterDeCoster44k • written 3.3 years ago by stafnymd10
2
gravatar for aays
3.3 years ago by
aays140
Canada
aays140 wrote:

In line 51:

head1,seq1,placeholder1,qual1=[i.strip() for i in entry]

a list comprehension is being used to iterate through the contents of entry and use the strip method on each element. I'm guessing that each element of entry is expected to be a string, given that that's usually what a method called strip would be used on. In this instance, however, it's turning out to be a NoneType object, which tells me that either entry is a blank list or contains at least one instance of a None in it, thus raising the error.

Since entry itself is a placeholder variable for each element in R1, which is created using the grouper() function defined at the top of the script, the real issue may lie somewhere in said function. Try testing grouper() on its own in the console and see if it does what it's supposed to do in grabbing chunks of a fixed length.

That being said, if grouper() indeed does what it's supposed to, see line 40 here:

r1_stream,r2_stream=get_input_streams(opts.leftreads,opts.rightreads)

The other likely cause is that get_input_streams() (also defined at the top) is reading data in incorrectly, which is leading to grouper() parsing the wrong kind of object or even none at all. I can't really replicate the issue without having your data, of course, but try running that in the console as well - ie loading in a file and investigating whether it's in the format it's supposed to be in.

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by aays140

In addition to this, debugging is straightforward by adding in a few print() functions to test your variables and see how they look like at which state, e.g. print(entry)

ADD REPLYlink written 3.3 years ago by WouterDeCoster44k
1

Thank you @aays @WouterDeCoster

ADD REPLYlink written 3.2 years ago by stafnymd10
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