Deeptools ValueError: invalid literal for int() with base 10 error

Question

[das2000sidd]

Hi

I am using deeptools for some heatmap plotting and I am running into an error that have never run into before while using deeptools.

The error says: if int(cols[1]) >= int(cols[2]): ValueError: invalid literal for int() with base 10: '3.2e+07'

As I understand, while checking if the third column is larger than the second one in the bed file, a string value was interpreted when an integer was expected. Note that my bed file is a tab delimited text file with no quotes.

Can someone suggest what might be causing the issue here?

Thank you and appreciate the help.

[rpolicastro]

Looking at the error you may have scientific notation for some of the values. How was the bed generated?

[das2000sidd]

I first used biomart database to pull out the coordinates and then I saved the chromosome, start, stop, ensemble id and strand in a tab delimited file and used that file.

[rpolicastro]

Before you save the file, disable scientific notation in R options(scipen=999). You likely have values written as literal scientific notation strings in some of the columns.

[Devon Ryan]

Can you post the command you used and the entire error message? Do you have a position in your BED file of literally 3.2e+07?

[das2000sidd]

Thank you for your reply. Below is the message:

Traceback (most recent call last):
  File "/hpc/software/deeptools/3.1.1/bin/computeMatrix", line 14, in <module>
    main(args)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptools/computeMatrix.py", line 421, in main
    hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptools/heatmapper.py", line 264, in computeMatrix
    verbose=verbose)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptools/mapReduce.py", line 85, in mapReduce
    bed_interval_tree = GTF(bedFile, defaultGroup=defaultGroup, transcriptID=transcriptID, exonID=exonID, transcript_id_designator=transcript_id_designator, keepExons=keepExons)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptoolsintervals/parse.py", line 595, in __init__
    self.parseBED(fp, line, 3, labelColumn)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptoolsintervals/parse.py", line 362, in parseBED
    self.parseBEDcore(line, ncols)
  File "/software/deeptools/3.1.1/lib/python3.6/site-packages/deeptoolsintervals/parse.py", line 228, in parseBEDcore
    if int(cols[1]) >= int(cols[2]):
ValueError: invalid literal for int() with base 10: '3.2e+07'
/software/anaconda3.6/lib/python3.6/site-packages/plotly/tools.py:103: UserWarning:

I have the following lines in my bed with 32 in it.

chr5    31926812    32000000    ENSMUSG00000029136  -
chr5    32000057    32387335    ENSMUSG00000052139  +

[Devon Ryan]

Can you grep e on your BED file?

[das2000sidd]

Okay thanks for this tip. Here is what I get:

chr5    31926812    3.2e+07 ENSMUSG00000029136  -
chr5    31926812    3.2e+07 ENSMUSG00000029136  -

So my guess is when I am exporting the file from R, then the problem is arising?

[Devon Ryan]

Yup, exactly

Answer 1

[delonbest]

The error message invalid literal for int() with base 10 would seem to indicate that you are passing a string that's not an integer to the int() function . In other words it's either empty, or has a character in it other than a digit. You can solve this error by using Python isdigit() method to check whether the value is number or not. The returns True if all the characters are digits, otherwise False . The other way to overcome this issue is to wrap your code inside a Python try...except block to handle this error.

Sometimes the difference between Python2.x and Python3.x that leads to this ValueError: invalid literal for int() with base 10 . With Python2.x , int(str(3/2)) gives you "1". With Python3.x , the same gives you ("1.5"): ValueError: invalid literal for int() with base 10: "1.5".