1. database module is under development!
- GenET database module is easy to use NCBI handler.
- It can download various metadatas and genome files (.gb, .gff,. ....)
- New function for parsing genbank file is under dev. (and will be comming soon..?)
2. Bug fixed: DeepPrime pegRNA design
There were some cases DeepPrime pipeline can not recognize PAM on the reverse strand when nick position is placed exactly at the center (reported by mathinic).
An example in deepprime format:
wt-seq:
CCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGATCcAGGTCCTAcGGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAGACG
mut-seq:
CCCAGGTGCTGACGTAGGTAGTGCTTGAGACCGCCAGAAGCTCGGAAAAGCGATCcAGGTtacCCTAcGGAAGGGATTCCATGAGGTGCGCGAAGGCCCTACTTCCGCTTTCACCTTGGAG
This bug is now fixed: ae4b0bad6e86672bb5a1ce0bdc29fb95c59094c9
The problem was PAM window for available pegRNA setting.
python
def check_PAM_window(dict_sWinSize, sStrand, nIndexStart, nIndexEnd, sAltType, nAltLen, nAltIndex):
nUp, nDown = dict_sWinSize[sAltType][nAltLen]
if sStrand == '+':
nPAMCheck_min = nAltIndex - nUp + 1
nPAMCheck_max = nAltIndex + nDown + 1
else:
nPAMCheck_min = nAltIndex - nDown + 1 <- original code
nPAMCheck_min = nAltIndex - nDown <- Fixed like this
nPAMCheck_max = nAltIndex + nUp + 1
if END:
if nIndexStart < nPAMCheck_min or nIndexEnd > nPAMCheck_max:
return 0
else:
return 1
def END: check_PAM_window
3. Bug fixed: DeepPrime output (spacer) and load model error
This issue was reported by mathinic 45
The output of genet.predict.pe_score, the column named 'Spacer' was not actually spacer
This bug is now fixed: ae4b0bad6e86672bb5a1ce0bdc29fb95c59094c9
python
def pe_score():
DeepPrime pipeline function.
...
df['Spacer'] = [wt74[4:24] for wt74 in df_all['WT74_On']]
....
Also, some files renamed in genet-models repo.
And it causes error when DeepPrime load it's input parameter file (mean.csv, std.csv).
This bug is now fixed: 528cb03e4842c429467e9c9c70d2f1bfcc49256c
4. Documentation updated!
URL: https://goosang-yu.github.io/genet/
New docs home page still under construction.
For more details and examples for genet, docs will be update again.
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**Full Changelog**: https://github.com/Goosang-Yu/genet/compare/0.11.0...0.12.0