In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
Hi,
running version 2.4 with python 3(.11).
HLA calling gets stuck during/after the 2nd iteration of non-class determination with the output below.
Thanks for any help :)
The digital haplotype is written into [filename]-ClassI-nonclass.digitalhaplotype3
Took 0.5041732788085938 seconds
Traceback (most recent call last):
File "seq2HLA.py", line 791, in
main()
File "seq2HLA.py", line 786, in main
pipe.run()
File "seq2HLA.py", line 152, in run
self.call_HLA(
File "seq2HLA.py", line 304, in call_HLA
if fourDigit_solutions1[locus] > 1:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: '>' not supported between instances of 'str' and 'int'
Hi, running version 2.4 with python 3(.11). HLA calling gets stuck during/after the 2nd iteration of non-class determination with the output below.
Thanks for any help :)