Chase W. Nelson 倪誠志

SeqIO.write() documentation suggestion

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### Setup Biopython version=1.79 Python version=3.8.8 OS=macOS Monterey v12.2 ### Suggestion I discovered through trial and error that SeqIO.write() appends a record (rather than overwrites the output file) if provided...

In chapter 3 p. 42, because the two protein .fasta files have no newlines at the end, I think the command `$ cat tb1-protein.fasta tga1-protein.fasta` will result in output that...

Truly amazing book—thank you for this great service. I think, in chapter 2 p. 29, the examples should read: ``` $ ls seqs/zmays[AB]_R1.fastq $ ls seqs/zmays[A-B]_R1.fastq ``` _i.e._, there should...

Order of Peak1 vs. Peak2 after --samples

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Thanks for this great tool. We are finding that the value of IDR changes based on the order of peak1 and peak2 in the --samples argument. For example, "--samples peak1...

How to loop multiple trees in a single newick file

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Apologies if this has been asked and answered: if I have a newick file with multiple trees (one per line), is there a straightforward way to import and loop through...

Feature idea: calcNucleotideDiversity()

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This Issue follows from the [SLiM Google Discussion on "Burn-in nucleotide diversity"](https://groups.google.com/g/slim-discuss/c/6GQdeeVIh1M/m/xFIQT0uHAQAJ). The idea is for a function, say `calcNucleotideDiversity()`, that calculates nucleotide diversity (_π_) as the mean number of...

HyPhy MEME Positive Selection at 0 Branches?

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I'm hoping to understand how to interpret a result in which HyPhy MEME detects positive selection at a codon, but with 0 branches under selection. An example is present in...