outrigger 0.2.9

Bleeding edge code from Github (here)

For advanced users, if you have git and Anaconda Python installed, you can:

1. Clone this repository

2. Change into that directory

3. Create an environment with the necessary packages from Anaconda

4. Activate the environment

5. Install remaining packages from PyPI (`graphlite <https://github.com/eugene-eeo/graphlite>`__ is only available on PyPI, not as a conda package)

6. Install this package

These steps are shown in code below.

git clone git@github.com:YeoLab/outrigger
cd outrigger
conda create --name outrigger --yes --file conda_requirements.txt --channel bioconda
source activate outrigger
pip install -r requirements.txt
pip install .

Quick start summary

Here is a summary the commands in the order you would use them for outrigger!

cd ~/projects/tasic2016/analysis/tasic2016_v1
outrigger index --sj-out-tab *SJ.out.tab \
    --gtf /projects/ps-yeolab/genomes/mm10/gencode/m10/gencode.vM10.annotation.gtf
outrigger validate --genome mm10 \
    --fasta /projects/ps-yeolab/genomes/mm10/GRCm38.primary_assembly.genome.fa
outrigger psi

This will create a folder called outrigger_output, which at the end should look like this:

$ tree outrigger_output
outrigger_output
├── index
│   ├── gtf
│   │   ├── gencode.vM10.annotation.gtf
│   │   ├── gencode.vM10.annotation.gtf.db
│   │   └── novel_exons.gtf
│   ├── junction_exon_direction_triples.csv
│   ├── mxe
│   │   ├── events.csv
│   │   ├── exon1.bed
│   │   ├── exon2.bed
│   │   ├── exon3.bed
│   │   ├── exon4.bed
│   │   ├── splice_sites.csv
│   │   └── validated
│   │       └── events.csv
│   └── se
│       ├── events.csv
│       ├── exon1.bed
│       ├── exon2.bed
│       ├── exon3.bed
│       ├── splice_sites.csv
│       └── validated
│           └── events.csv
├── junctions
│   ├── metadata.csv
│   └── reads.csv
└── psi
    ├── mxe
    │   └── psi.csv
    ├── outrigger_psi.csv
    └── se
        └── psi.csv

10 directories, 22 files

How to run with the Python debugger

How to run the code with the Python debugger. To run the command line functions such that when they break, you jump into the pdb (Python debugger), here is the code:

python -m pdb outrigger/commandline.py index \
--sj-out-tab outrigger/test_data/tasic2016/unprocessed/sj_out_tab/* \
    --gtf outrigger/test_data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.snap25.myl6.gtf

Notice that you replace outrigger with python -m pdb outrigger/commandline.py, which is relative to this github directory.

How to run the tests

If you want to run the tests without calculating what percentage of lines are covered in the test suite, run

make test

If you want to run the tests and see which lines are covered by tests and get an overall percentage of test coverage, run

make coverage

If you want to run an example with ENSEMBL GTF files, do:

make arabdopsis

By default, Travis-CI does all three:

script:
- make coverage
- make lint
- make arabdopsis

v0.2.9 New features

• Add bam alignment files as input option

Miscellaneous

• Parallelized Psi calculation, the exact number of processors can be specified with --n-jobs, and by default, --n-jobs is -1, which means use as many processors as are available.

v0.2.7 New features

• Added outrigger validate command to check for canonical splice sites by default: GT/AG (U1, major spliceosome) and AT/AC (U12, minor spliceosome). Both of these are user-adjustable as they are only the standard for mammalian genomes.

v0.2.7 API changes

• Added --resume and --force options to outrigger index to prevent the overwriting of interrupted indexing operations, or to force overwriting. By default, outrigger complains and cowardly exits.

v0.2.7 Bug fixes

• Support ENSEMBL gtf files which specify chromsome names with a number, e.g. 4 instead of chr4. Thank you to lcscs12345 for pointing this out!

v0.2.7 Miscellaneous

• Added version info with outrigger --version

• Sped up gffutils queries and event finding by running ANALYZE on SQLite databases.

v0.2.6 Bug fixes

• Wasn’t concatenating exons properly after parallelizing

v0.2.6 Miscellaneous

• Clarified .gtf file example for directory output

v0.2.4 New features

• Actually parallelized exon finding for novel exons. Before had written the code and tested the non-parallelized version but now using actually parallelized version!

v0.2.4 Bug fixes

• Don’t need to turn on --debug command for outrigger to even run

Bug fixes

• Subfolders get copied when installing

• Add test for checking that outrigger -h command works

New features

• Parallelized exon finding for novel exons

• Added outrigger validate command to check that your new exons have proper splice sites (e.g. GT/AG and AT/AC)

• Added more test data for other event types (even though we don’t detect them yet)