Posted in Research

Biopython Biopython Statistics & Issues

 September 25, 2021

Issue Title State Comments Created Date Updated Date Closed Date Add .islower() and .isupper() methods to Seq?


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0 2021-09-25 2021-09-18 – Apparently random fluctuations in coverage via CodeCov?


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1 2021-09-23 2021-09-18 – BgzfWriter accepts read-only fileobj


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1 2021-09-23 2021-09-18 – BgzfReader argument `mode` not tested if a fileobj is specified


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20 2021-09-23 2021-09-18 2021-09-23 Stockholm not funny


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3 2021-09-22 2021-09-18 – Failure to parse origin-spanning features


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1 2021-09-22 2021-09-18 – making the example for Bio.PDB.SASA work


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4 2021-09-18 2021-09-18 – Add support for a codon optimization algorithm


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2 2021-09-18 2021-09-18 2021-09-20 ValueError: Unknown prefix ‘ali’ with uri ‘http://www.niso.org/schemas/ali/1.0/’


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5 2021-09-16 2021-09-18 2021-09-17 Can’t write peptide genbank files with extra long headers


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3 2021-09-15 2021-09-18 – Speeding up flake8 and/or black


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0 2021-09-09 2021-09-18 – Error when opening CEL file


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7 2021-09-09 2021-09-18 – [Question] need documentation on submat module and matrix details


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5 2021-09-08 2021-09-18 2021-09-17 substitution_matrices.load() returns README.txt


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1 2021-08-30 2021-09-18 2021-09-04 Access to UniProtKB API via Biopython


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1 2021-08-25 2021-09-18 – lcc.lcc_mult returns extra zero value


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4 2021-08-17 2021-09-18 2021-09-08 how set biopython for python2.7


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11 2021-08-14 2021-09-18 2021-08-15 Bio.KEGG.Compound get ID from name


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0 2021-08-11 2021-09-18 – distutils will be deprecated in the upcoming Python release (3.10)


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3 2021-08-05 2021-09-18 – Moving CI to Github Actions – Roadmap


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1 2021-08-05 2021-09-18 – Fastq to fasta conversion


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1 2021-08-04 2021-09-18 – SeqIO.parse on ENA database returns ValueError: Could not determine molecule_type for seq_type linear XXX


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1 2021-08-03 2021-09-18 – Allow using Entrez.read to parse local archives of pubmed


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21 2021-08-02 2021-09-18 2021-08-03 github actions macOS pypy broken


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4 2021-07-30 2021-09-18 2021-08-01 Installation error


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2 2021-07-23 2021-09-18 2021-07-23 Entrez.efetch reaises a urllib.error.URLError


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4 2021-07-22 2021-09-18 2021-07-23 Provide a function call to check if `Seq` object has undefined sequence data


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31 2021-07-15 2021-09-18 – feature.extract(record) fails:


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1 2021-07-14 2021-09-18 2021-07-14 Consistently validate the input in the user exposed API


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2 2021-07-07 2021-09-18 – Sequence multiplication tests failing (Linux pypy3)


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4 2021-07-07 2021-09-18 2021-07-30 Error while trying to set custom matrix


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6 2021-07-07 2021-09-18 2021-07-08 Maximum Parsimony trees works only with dna type alignments??


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1 2021-07-06 2021-09-18 – Order of coordinates of a multi-part feature that maps to the reverse strand maybe ‘wrong’ in GenBank file generated from SnapGene file?


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16 2021-07-05 2021-09-18 2021-09-07 Replacing LaTeX based Tutorial (pdflatex and hevea)?


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12 2016-08-03 2021-09-24 –

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