brew install pythonfollowed by
brew link pythondid the trick
make coverage.xml(or whatever it's called) was segfaulting
Makefilewhich looks like it should be used by
gcovrbut isn't actually used ever and from the branch name it sounds like it does something with unreachable branches, which is the commandline argument that seems to "fix" things
Hi guys! (sorry found this room only after asking this by email)
After a long while I am returning to khmer for a new genome, but find myself a bit confused about the best approach to digital normalisation (I want ~100x) with your pipeline v.2.0.
One thing is that filter-abund.py apparently needs the kmer hash table, but normalize-by-median.py appears to lack the --savehash option now.
Would/could you maybe point me to the most recent example of the workflow? That would be very helpful.
And this is the error I receive:
Traceback (most recent call last):
File "/local/cluster/khmer-legacy/sandbox/filter-below-abund.py", line 49, in <module>
File "/local/cluster/khmer-legacy/sandbox/filter-below-abund.py", line 22, in main
ht = khmer.load_counting_hash(counting_ht)
AttributeError: 'module' object has no attribute 'load_counting_hash'
I am concerned that I am getting this error because the filter-below-abund.py script is no longer part of the khmer pipeline.
The newest installed khmer in our linux /local/cluster/bin is version 2.0+103.g8300de0, but the filter-below-abundance.py script did not show up after the installation.
The script I used came from an older installation of khmer in /local/cluster.
(The python version I am using: Python 2.7.14, and the OS Version:
Linux 3.10.0-693.11.6.el7.x86_64 x86_64)
I wanted to know if anyone would know why I am getting this error, if the filter-below-abund.py script should be included in installations of the latest khmer version, and if this script is still functioning.
filter-abund-single.pyscripts from the newer version can satisfy your needs?