Python error in dataProcessing.py

[maxdudek]

Hi,

When I run the script like this:

conda activate TRACE_env
python dataProcessing.py $PEAKS $BAM $GENOME --atac-seq pe --prefix ./$PREFIX

I get the following error:

Traceback (most recent call last):
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 290, in <module>
    main()
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 273, in main
    loessSignal, deriv2nd, deriv1st, bc_loess = signal.get_signal(args.span, args.is_atac, args.shift)
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 193, in get_signal
    maximum = int(self.size[1][self.size[0] == peak[0]])
  File "/home/maxdudek/local/miniconda3/envs/TRACE_env/lib/python3.7/site-packages/pandas/core/series.py", line 131, in wrapper
    raise TypeError("cannot convert the series to " "{0}".format(str(converter)))
TypeError: cannot convert the series to <class 'int'>

As far as I can tell my bam, bed3, and genome files are all in the correct format, and I don't know enough about the code to figure out what's going wrong. Looking up the error tells me to use .astype(int), instead if int(), but then I just get another error later down:

Traceback (most recent call last):
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 280, in <module>
    main()
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 263, in main
    loessSignal, deriv2nd, deriv1st, bc_loess = signal.get_signal(args.span, args.is_atac, args.shift)
  File "/home/maxdudek/local/src/TRACE/scripts/dataProcessing.py", line 186, in get_signal
    ext_r = 5000 if int(peak[2]) + 5000 < maximum else maximum - int(peak[2])
  File "/home/maxdudek/local/miniconda3/envs/TRACE_env/lib/python3.7/site-packages/pandas/core/generic.py", line 1556, in __nonzero__
    self.__class__.__name__
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

I printed out the values of the variables when the error occurs in case it helps. Any insight would be greatly appreciated!

self.size:

                    0          1
0                chr1  248956422
1                chr2  242193529
2                chr3  198295559
3                chr4  190214555
4                chr5  181538259
..                ...        ...
450  chrUn_KI270539v1        993
451  chrUn_KI270385v1        990
452  chrUn_KI270423v1        981
453  chrUn_KI270392v1        971
454  chrUn_KI270394v1        970

[455 rows x 2 columns]

peak:

1	9957	10639

self.size[0] == peak[0]:

0      False
1      False
2      False
3      False
4      False
       ...  
450    False
451    False
452    False
453    False
454    False
Name: 0, Length: 455, dtype: bool

self.size[1][self.size[0] == peak[0]]:

Series([], Name: 1, dtype: int64)

[OuyangNX]

I believe the error was caused by chromosome format in your peak file, you have 1 in the first column instead of chr1, so it was not able to get the right chromosome size.