glennhickey / cactus2hal

Convert progressive cactus database into a hal file

Welcome

I am a freelance software consultant, specializing in comparative genomics research. I work primarily on open source projects using C++ and Python, such as Cactus and vg. I have a PhD in Computer Science from McGill University.

My consulting company, Arenaria, has been in business since 2015. If you are interested in working together feel free to contact me (my first name dot my last name @arenaria.ca).

cactus2hal's Issues

Keep cactus config xml in hal

It would be cool if we kept the config xml that cactus used in a field in the overall metadata. Also somewhat nice would be to keep the outgroups used in a metadata field in each ancestor.

Not a priority, just making notes for later.

Does not handle newlines in FASTA sequences

FASTA files are allowed to have newlines in their sequence data, which should be ignored. FastaReader only takes the first line of any given FASTA sequence, ignoring the others.

experimentWrapper

I do believe in
/scratch/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py

the cactus.progressive.experimentWrapper should be changed to cactus.shared.experimentWrapper to make it work with recent versions of Progressive Cactus

Broken on OS X Mavericks

See.. dentearl/mafTools#2 (and the hal issue I just made)

On the dev branch I added:

ifeq (${SYS},Darwin) #This is to deal with the Mavericks replacing gcc with clang fully and changing libraries
cppflags += -stdlib=libstdc++
cflags += -stdlib=libstdc++
endif

right after line 44 of the include.mk file and it fixed it. Please add, or give me write permission. I'm not clever enough to make a pull request.