Andreas Prlic

command line execution of protein comparison tools is broken for -file arguments

1

this does not work: bash runCE.sh -file1 /tmp/data/structures/divided/mmCIF/cd/1cdg.cif.gz -file2 file:/tmp/data/structures/divided/mmCIF/ti/1tim.cif.gz -show3d it fails with the following, although the files do exist locally. 16:05:39 [main] WARN org.biojava.nbio.structure.align.util.UserConfiguration - Could not read...

Add support for parsing Sanger sequencing files (ABI, SCF)

2

see this thread on the mailing list http://lists.open-bio.org/pipermail/biojava-l/2016-July/011489.html A test file is here https://github.com/biopython/biopython/blob/master/Tests/Abi/3730.ab1

Add better support for serializing collections of Sequences

2

We don't have an easy way of serializing/deserializing a collection of sequences. This does not work: http://mailman.open-bio.org/pipermail/biojava-l/2015-February/011357.html Alternative workarounds could be: - Tweak Kryo for some nonstandard InstantiatorStrategy - Use...

Open up Symmetry visualization API (quaternary and internal)

4

Currently the CE-symm visualization is tied closely to Jmol. Add a couple of utility classes that make it easier to build up a visualization also with other viewers.

Add ability to create a Profile from a multiple sequence alignment file

4

would be great to be able to create a Profile from some of the popular file formats for representing multiple sequence alignment files. Currently we can read Stockholm files like...

see discussion on the mailing list http://mailman.open-bio.org/pipermail/biojava-l/2015-March/011367.html

Biocommons seems currently blocked by requiring a travis subscription. The CI needs to be either moved away from travis (github actions?) or somebody needs to pay for travis ...

Add support for pulling from seqrepo-rest-service.

6

**Summary** It would be nice to be able to connect hgvs to pull sequence data from an instance of [seqrepo-rest-service](https://github.com/biocommons/seqrepo-rest-service), rather than a local copy of the data (or NCBI)....

hgvs_p shows Ter, although no new stop codon got introduced.

3

Hi, Looks like the following code results in a slightly incorrect hgvs_p string: ``` In [1]: hgvs_c = 'NM_002485.4:c.2256_2258del' In [2]: var_c = parse(hgvs_c) In [3]: c_to_p(var_c) Out[3]: SequenceVariant(ac=NP_002476.2, type=p,...

Add support for literate programming

1

Perhaps this might be a good choice for keeping the tutorial more up-to-date with the latest code base. https://github.com/rusthon/Rusthon/wiki/Literate-Programming