GenET v0.12.0

What's Changed

• Merge from main to dev_goosang by @Goosang-Yu in #43
• Release v0.12.0 by @Goosang-Yu in #46

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: ae4b0ba
The problem was PAM window for available pegRNA setting.

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: ae4b0ba

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: 528cb03

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.

Full Changelog: 0.11.0...0.12.0