Ilia Minkin
Ilia Minkin
Hi, spoa is a fantastic tool, but the memory usage is a bit high. Is there any way to adjust the parameters to make it smaller?
### Setup I am reporting a problem with Biopython version, Python version, and operating system as follows: 3.8.10 (default, Mar 15 2022, 12:22:08) [GCC 9.4.0] CPython Linux-5.13.0-48-generic-x86_64-with-glibc2.29 1.79 ### Expected...
Hi, Suppose that I have N long genomes (e.g. primates) and want to compute mappings between all pairs of the genomes. What is the best way to do so using...
Hi, Just a question: is it possible to find out how much time it took for each of the alignment stage: pairwise alignment, filtering and HMM-alignment?
Tried: ./bin/runProgressiveCactus.sh ./work3/seqfile3 ./temp3 ./work3/work3.hal Got: iminkin@iminkin-VirtualBox:~/Program/progressiveCactus$ ./bin/runProgressiveCactus.sh ./work3/seqfile3 ./temp3 ./work3/work3.hal Beginning Alignment --- --- *\* ALERT ** --- --- The only jobs that I have detected running for at...
Ubuntu 12.04.3 LTS, 64 bit, Python 2.7.3 just installed from scratch. The folder with sonLib is at "/home/iminkin/Program", the variable $PYTHONPATH is set to "/home/iminkin/Program:" Running make all went ok,...
Hi, I would like to report (what seems to be) a bug with with MafIO.get_spliced function. Here is the output of running system information script suggested in the issue template:...
1) Add error checking after the first pass 2) Add try/catch around checking constructing the parser (checking if file exists)