Lecture 6

[yoavram]

Phylogenetic trees? See http://etetoolkit.org/

[yoavram]

ETE isn't supported. Posted a question let's see if it fares better than the one in SoF.

[yoavram]

The bottom of the lecture has lectureX instead of lecture6.

[soungalo]

Uploaded a (almost) complete version. You are welcome to review if you want. I'm still considering showing some phylogenetics, but I don't want to overload.

[yoavram]

Great job, looks terrific. I have a host of petty remakrs:

• [x] "the notebook is still a draft"
• [x] qoutes are better put in "blockqoutes" meaning in lines starting with ">". Then you don't need " or italics
• [x] maybe make "bioinformatics" bold
• [x] link to explanations on FASTA, GenBank, ....? I'm not sure. (They already know FASTA, and the link to the list of file formats also leads to explanations about each format)
• [x] Installation instructions - the minimum is to provide a link, but I think you can also say "open cmd, run c:\pyzo2014a\scripts\conda install biopython. Worked for me.
• [x] "Biopythons"->"BioPython's"
• [x] you mention you talked about the csv reader, didn't you remove it? (they had to use it in HW4, so they should be familiar with it)
• [x] "one of the most basic objects in bioinformatics are sequences"
• [x] "enables"->"has"
• [x] from Bio.Seq import Seq - you are actually improting a class, not a module
• [x] "with the required" ?
• [x] you my_DNA_seq with an explicit string but compare it to the variable seq (I am showing them that seq is of type str, while my_dna_seq is of type seq)
• [x] "in another sequence object" -> "in a new sequence object"?
• [x] why did you make the exercise header blue? (its like this in all my lectures. Easier to spot them that way)
• [x] you do from IPython.display import HTML twice (I prefer this since if someone missed the first one, it'll still work and I don't get complaints during the class)
• [x] a sentence on what is GenBank? Entrez? is it the same thing?
• [ ] lec6_files/Orchids.fasta -> can you read it from the web? or do urlretrieve to local filesystem before reading it? see bottom of lecture7 where I do this with a zip file.
• [x] "available here" -> missing closing )
• [ ] "handle" - > "file object, like open". No need for a new name to the same concept.
• [ ] object names (SeqRecord etc.) and any code really should be inside `
• [x] missing a title after the 2nd exercise.
• [x] "SeqIO,parse()"->"SeqIO.parse()", right?
• [x] "We can easily change the function to create files in a different format." -> better yet, have the output format (maybe also the input format) an argument of the function, perhaps with a default value.
• [ ] try to always write "biopython" the same. capital B, italics (single underline)?
• [x] in "Fin" remove the PDF link as we didn't really make PDFs...