uniprot | command-line and python interface to the uniprot database | REST library

There are several issues with your code.

First, Object.get() does not return the contents of the Amazon S3 object. Instead, as per the Object.get() documentation, it returns:

First of all, you did not define list. Its not printing anything because the variable list is blank. Second of all, you have to change the format of code in line 6. It should be d = u.search(f"id: {line}", frmt = "tab",.

Use pd.read_csv, after encapsulating your output in a StringIO (to present a file-like interface):

Sharing 3 methods to solve the mentioned problem.

Method I: Using aggregate function

Just move the print FILE "$id\t" into the other if block, i.e. only populate the $id when it's specified, print it for every domain.

You might add a check that the $id isn't empty before printing it, but it shouldn't happen if I understand the format correctly.

First, need to change the parser from "lxml" to "xml".
lxml is an alias for lxml.html.soupparser, which is for HTML.

Also note the XML snippet in your question is an invalid XML file with no closing segment or listResidue elements. There is no root XML element, only 2 entity elements which is not valid. BeautifulSoup handles invalid documents but always recommended to start with a valid XML document if possible.

If want to skip an entire residue group and all crossRefDb children in it then need to iterate over all residue and check if any child crossRefDb has has a null in dbresnum in the same line as dbSource="PDB".

Try something like this:

OK, this took me a minute to grok, but I think I have this for you. We discussed the example in chat, so you should probably update your question to reflect my answer since it varies from the original.

This is just iterating over the tables, so it's not a more efficient version, but I wasn't aware if you had anything at this point to start from, so at least this is something.

We're trying to create table2 from table1 and table3:

Starting with these CSV files:

table1.csv

The problem here is in ylim, which, along with scale_y_continuous(limits = ...), has a behavior that catches some users by surprise. As noted in the help at ?ylim,

This is a shortcut for supplying the limits argument to the individual scales. By default, any values outside the limits specified are replaced with NA. Be warned that this will remove data outside the limits and this can produce unintended results. For changing x or y axis limits without dropping data observations, see coord_cartesian().

This has a particularly confusing result during summary operations like what you'd have for geom_boxplot(), since it doesn't error out, it just produces a different result and a warning that you might miss or ignore.

For example, in the chart below, we'd expect a boxplot ranging from 0 to 100, but only get the zero value. That's because using ylim or scale_y_continuous(limits = ...) will both filter out the data outside the range before any summary calculations are performed.

Some values in your data are bigger than your limit in ylim, so they are removed from the plot