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fixed the manifest.in and setup.py to include .pyx, .cpp, and .h files. We need those blank files for the model maker to have access too, the previous setup file was excluding them from packaged versions on Pypi
* Updated Optimization to use the correct ssa_solution * DiffusionCalc added cy3 * Added TODO for realistic excitation of the intensity vector/probes * Linted trna solver
when calculating which reaction happened changed wn.topLeftCorner to wn.head() to be safer in versions of eigen. Additionally added one buffer spot to the end of forward ratematrix to make sure no ribosomes enter unreserved memory.
genbank polling but was joining the path incorrectly, resulting in the gb files not saving properly once pulled from genbank.
* File parser now accepts multi-sequence fastas and will place them into protein objects with different "source seqs" from the fasta. * ballistic model now can be passed only a ntseq and ki,ke for the calculation, will ignore intensity if there is no fluorescent tag passed * seqmanip now has "get_largest_poi" to instantly get the largest protein object out of a sequence file if you know it should be the largest ORF in a given fasta.
* added a frap end time as a user input * removed the frapresult matrix and calculation, FRAP is simulated within the C++ now * changed the pyx file to allow for cases where user does not provide a probe, ie no fluorsecent probe. The C++ will still run the simulation with intensity set to zero if the user wants a tasep with no fluorescence * removed old model maker from the rsnapsim as its now defunct * defaulted poi probevec and probeloc to np.int32 * colors are now set by the probe provided / protein given to the simulation, not outside the simulation * updated warnings for the user with the simulation
C++ SSA simulation has the following changes: * Fixed bug with harringtonine where the tau leaping would allow a binding after harringtonine because t was set before the inhibition check * Added photobleaching flag and calculation * FRAP bleaching sped up partially, wont set probe_matrix to zero if already zero.
* added kmer frequency and GC content to seqmanip * added gc content to poi objects * added a method to wash input sequences with various options for the user: random sub based on IPUAC nt, upper/lower, custom substitution dictionary
* added TAI to seqmanip methods * added arbitrary weight by codon to metric function * fixed geomean to be in log space so it calculates when multiple values are from 0 < 1.
MW was accidently considering all aavec[0] positions, not setting to 0 when no ribosomes were actively translating.
* added normalization options to inta * added ribosome analyses class for spacing of probes in x and y over time
* added codon uniform flat / rate flat metrics to sequence manips * fixed setup.py so snapgenereader / dnafeaturesviewer are requirements
* fixed the center indexing of cross correlation calculation for jagged arrays * wrote the cross correlation tests * change acov calculation to do it along axis instead of with a for loop
* Added better docstrings and errors to the propensity vector module * Added two new functions that convert codon pairs or triplets to stepping rates
poi.detect_tag(aa_seq, name) will add a new tag to the poi.tag_epitopes
Loading .dna files is now mostly done barring any major changes to .dna file structure, our parser is untied from BioPython and should be more stable.
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