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Pull requests list

Use modes in SequenceWriter
#4850 by mdehoon was merged Sep 23, 2024 Loading…
3 tasks done
2
Speed up QualityIO's quality mapping and improved error messages
#4849 by flaar94 was merged Dec 31, 2024 Loading…
3 tasks done
40
Replace deprecated @abstractproperty decorators
#4848 by flaar94 was merged Sep 19, 2024 Loading…
3 tasks done
Add a context manager to SeqIO.parse and avoid side effects
#4845 by mdehoon was merged Sep 20, 2024 Loading…
3 tasks done
5
Bio.SeqIO QualityIO q_mapping
#4844 by mdehoon was merged Sep 18, 2024 Loading…
3 tasks done
Remove copy from the Array class in BIo.Align.substitution_matrices
#4843 by mdehoon was merged Sep 18, 2024 Loading…
3 tasks done
Allow parsers in Bio.SeqIO to handle both text and binary modes
#4842 by mdehoon was merged Sep 18, 2024 Loading…
3 tasks done
2
Add type annotations to methods in Bio.PDB.Atom
#4841 by michaelfm1211 was merged Sep 29, 2024 Loading…
3 tasks done
10
Add type annotations for Bio.PDB.Atom methods
#4840 by michaelfm1211 was closed Sep 17, 2024 Loading…
3 tasks done
1
Bio.SeqIO QualityIO subclass
#4838 by mdehoon was merged Sep 17, 2024 Loading…
3 tasks done
11
Faster initialization of SeqRecords via lazy letter annotation initialization and _from_validated method
#4837 by flaar94 was merged Sep 23, 2024 Loading…
3 tasks done
1
30
Faster Fasta
#4835 by mdehoon was merged Sep 17, 2024 Loading…
3 tasks done
5
avoid having a double context manager
#4834 by mdehoon was merged Sep 17, 2024 Loading…
3 tasks done
2
In Bio.SeqIO Uniprot, use SequenceIterator
#4833 by mdehoon was merged Sep 17, 2024 Loading…
3 tasks done
8
Bio.SeqIO SwissProtIO use SequenceIterator
#4832 by mdehoon was merged Sep 11, 2024 Loading…
3 tasks done
use SequenceIterator in Bio.SeqIO.QualityIO
#4831 by mdehoon was merged Sep 11, 2024 Loading…
3 tasks done
use SequenceIterator in Bio.SeqIO.Phd
#4830 by mdehoon was merged Sep 10, 2024 Loading…
3 tasks done
Bio.SeqIO PdbIO use sequenceiterator
#4829 by mdehoon was merged Sep 10, 2024 Loading…
3 tasks done
Bio.SeqIO.GfaIO, use SequenceIterator
#4828 by mdehoon was merged Sep 10, 2024 Loading…
3 tasks done
Document mode and fmt in SequenceIterator
#4827 by peterjc was merged Sep 10, 2024 Loading…
3 tasks done
1
Bio.Align read, ensure that file handles are closed
#4826 by mdehoon was merged Sep 9, 2024 Loading…
3 tasks done
Bio.SeqIO.AceIO, use SequenceIterator
#4824 by mdehoon was merged Sep 9, 2024 Loading…
3 tasks done
4
remove the parse from the SequenceIterator in Bio.SeqIO.Interfaces
#4823 by mdehoon was merged Sep 8, 2024 Loading…
3 tasks done
Avoid going through yield in Bio.SeqIO.FastaIO
#4822 by mdehoon was merged Sep 7, 2024 Loading…
3 tasks done
codonalign test numpy
#4820 by mdehoon was merged Sep 2, 2024 Loading…
3 tasks done
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