0.15.0

What's Changed

• 0.14.0 by @ntfargo in #77
• Option added: Install synonymous mutation in CDS by @Jinyeong-Yang in #83
• Enhancements to Genetic Analysis Functions by @ntfargo in #85
• sync branch by @Goosang-Yu in #87
• GenET v0.15.0 updates by @Goosang-Yu in #91

1. SynonymousPE @Jinyeong-Yang

• Bug fixed 65c9f6c 4c10437 6b7fe12 9bfc8dc
• Additional .stack option 2716e24

2. DeepPrime

• Input format changed. Only single sequence information required. 647c3e1

Before (GenET < 0.15.0)

from genet.predict import DeepPrime

seq_wt   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGAAGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'
seq_ed   = 'ATGACAATAAAAGACAACACCCTTGCCTTGTGGAGTTTTCAAAGCTCCCAGAAACTGAGACGAACTATAACCTGCAAATGTCAACTGAAACCTTAAAGTGAGTATTTAATTGAGCTGAAGT'

pegrna = DeepPrime('SampleName', seq_wt, seq_ed, edit_type='sub', edit_len=1)

After (from GenET >= 0.15.0)

from genet.predict import DeepPrime

seq = 'CCGAGTTGGTTCATCATCATTCAACGGTGGCCGACGGGCTCATCACCACGCTCCATTATC(C/T)AGCCCCAAAGCGCAACAAGCCCACTGTCTATGGTGTGTCCCCCAACTACGACAAGTGGGA'

pegrna = DeepPrime(seq)

3. DeepPrimeGuideRNA

• Input sequences in uppercase or lowercase give different outputs, reported by @francoiskroll (#89)
• Bug fixed ae059ec

4. Torch > 2.0 supported

• Version dependency changed 65dc2d8
• ViennaRNA and torch now installed with GenET 65dc2d8

Full Changelog: 0.14.1...0.15.0