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Biopython/enterz.efetch issue with certain accession listed. Seems to effect all compete refseq accessions and some shotgun sequenced Refseq accessions.
List of effected accessions:
NC_008268
NC_012…
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Annotating intermediate nodes
https://stackoverflow.com/questions/30317688/annotating-dendrogram-nodes-in-scipy-matplotlib
We shall import scipy only within the visualization function:
https://st…
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There are cases of GenBank files not having a few standard fields.
1. While converting such files, the converter fills those fields with their default values before outputting the converted/round tr…
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### Setup
Seen with latest code from git while preparing the 1.73 release on Linux, but applies to all platforms.
### Expected behaviour
```
$ python run_tests.py test_PDB_StructureAlignment…
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Hello there, thank you for fastp. I have used it for roughly a year and am very happy with it.
However, there is one thing that bugs me. When fastp is called to merge paired-end files, it also chan…
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Another category, besides data integrity (#4), should be file retrieval. One current request in particular is to add documents by Pubmed ID. The code would go from Pubmed ID to file, download the file…
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https://github.com/peterjc/galaxy_blast/blob/d31e21d684a5dfa55dfb1a9aead744e2e7b87923/tools/blast_rbh/blast_rbh.py#L270
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This time I attempted to install BioCompass requirements using conda, according to the commands below
```
$ scp -r -i ~/Downloads/my-key.pem ~/Desktop/BioCompass/antiSMASH_input/ ubuntu@ec2-54-153-11…
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I tried to make predictions on the following protein files taken from pdb.
https://files.wwpdb.org/pub/pdb/data/structures/divided/structure_factors/rq/r1rq0sf.ent.gz
https://files.wwpdb.org/pub/pd…
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This should probably be handled by a class. We should try to extend the Seq class from biopython so that we can just use the seq variable that's already there to get what we need, will greatly clean u…