Dear Ozagordi,
I have been using Shorah for my viral data to identify true haplotypes. But it gives out these Error in the end. I am not sure why these errors are appearing.
Traceback (most recent call last):
File "/home/software/install/ShoRAH/shorah.py", line 194, in
for s in SeqIO.parse('%s_cor.popl' % in_stem, 'fasta'):
File "/usr/lib64/python2.7/site-packages/Bio/SeqIO/init.py", line 342, in parse
raise TypeError("Need a file handle, not a string (i.e. not a filename)")
Moreover, can you please tell which frequency for haplotype are considered to be significant. Because most of the haplotypes it makes have frequencies below 0.0113..
ozagordi
commented
8 years ago
Dear Ozagordi, I have been using Shorah for my viral data to identify true haplotypes. But it gives out these Error in the end. I am not sure why these errors are appearing.
Traceback (most recent call last): File "/home/software/install/ShoRAH/shorah.py", line 194, in
for s in SeqIO.parse('%s_cor.popl' % in_stem, 'fasta'):
File "/usr/lib64/python2.7/site-packages/Bio/SeqIO/init.py", line 342, in parse
raise TypeError("Need a file handle, not a string (i.e. not a filename)")
Moreover, can you please tell which frequency for haplotype are considered to be significant. Because most of the haplotypes it makes have frequencies below 0.0113..
Makes thanks,