Paula Berry

q_pos and r_pos indexing

2

The outputs from alignment.dump() indicate a 1-indexed position number for the start and end of the matching region of the query and reference sequence. However, the output from alignment.r_pos and...

commands for splitfasta.pl do not work on conda installs

2

## Expected Behavior For the command `splitfasta.pl ManyProteins.fasta` to produce individual fastas like in the user guide. ## Current Behavior output from `splitfasta.pl .fasta` is `splitfasta.pl: command not found` ##...

Excluding contacts from flanking residues

1

Hi ProDy team - I keep finding myself having to loop through the tuples returned by findNeighbors to look up the atomic indices and find the residue number in my...

Displaying 3Dmol output using local .pdb files on html pages

3

**Description** When c&p-ing the code on the page [How to Embed a 3Dmol Viewer](http://3dmol.csb.pitt.edu/doc/tutorial-embeddable.html) in an html document, the example works perfectly. However, when replacing `data-pdb='2POR'` with `data-href='/link/to/pdbfiles/myprotein.pdb'`, the 3Dmol...

lack of explicit separator in read_csv in /mutate/protocol.py

3

Because there is not an explicit separator in the function that imports the mutation data table in /mutate/protocol.py, pandas expects a comma separator, but the /mutate/calculations.py function that deals with...

Compiling summaries/metadata into an outline

7

I'm not sure if this is already implemented and I'm just having a hard time figuring out options, but if not, I'd love the ability to compile and export the...

Control of output file location/names

1

I would like to be able to specify where/with what prefixes output files should go - right now my workflow involves copying an entire BeadChip sequencing directory from separate sequencing...