sclamons
sclamons
**Primary change** This fix changes the behavior of Sequence objects created inside for loops over Fasta objects, so that they don't unexpectedly change when used repeatedly. EXAMPLE: 1) Create a...
Adds the ability to use custom barcodes defined in a (user-specified) CSV file using a -f flag. If the flag is on, the first thing porechop.py does is to parse...
For example, can now use a region definition like "chr1:123125:1231500".
I have a simulation of a very simple birth-death process (DNA replicating uncontrolledly) where I'm running the same model through bioscrape with different initial conditions. When I run these, I...
In multiple SSA algorithms, we have species counts stored as doubles. This allows an unwary user (such as myself) to start a simulation with non-integer species counts. If you do...
**Use case**: I have a control circuit. I've already verified (or don't care about) how it behaves dynamically. I want to see what kind of stationary distribution it leads to,...
When a new process is spawned by multiprocessing's map function, Numpy's random number generator is copied exactly into all of the children, including its seed. A description of the problem...
BeautifulSoup, which is used by Bioscrape's model parser, requires a tree parser to work. It can use Python's default HTML parser, but some OSX installations use an old enough core...
Bioscrape uses a lot of cdef'ed functions with a wrapper for python, e.g. the cdef function "simulate_model" (which cannot be called from python) wrapped with a python function "py_simulate_model". This...
A common error I've encountered when using preseq is "ERROR: too many defects in the approximation, consider running in defect mode". I have a few questions about this for which...