python-workshop

Harvard FAS Informatics materials for the Practical Python on Odyssey

Prerequisites

Workshop participants must have basic Unix proficiency, some operational knowledge of Python, and an Odyssey account.

Python basics will be covered, but not in depth.

Production branch contains the answer

A checkout of the production branch will provide a hisnhers.py script that works.

To try out the functional script follow these steps:

• Checkout the production branch of the project

  $ git clone https://github.com/harvardinformatics/python-workshop.git
  $ cd python-workshop
  $ git checkout production
  

• Setup PYTHONPATH (assuming you're in the pythong-workshop directory)

  $ export PYTHONPATH=`pwd`:$PYTHONPATH
  

• Install the lookkool annotation package; make sure gcc is 4.9 or better

  $ module load gcc/4.9.3-fasrc01
  $ pip install git+https://github.com/harvardinformatics/lookkool.git
  

• Set LD_LIBRARY_PATH to find the liblookkool.so. It should be in site-packages.

  $ export LD_LIBRARY_PATH=/path/to/site-packages:$LD_LIBRARY_PATH
  

• Run hisnhers.py against the example file in the data subir

   $ cd data
   $ ../bin/hisnhers.py example.fq
   Length 0: 40
   Base counts- A: 8   T: 9    C: 10   G: 13   
   Length 1: 40
   Base counts- A: 11  T: 5    C: 16   G: 8    
   Length 2: 40
   Base counts- A: 8   T: 6    C: 9    G: 17   
   Length 3: 40
   Base counts- A: 9   T: 8    C: 12   G: 11   
   Length 4: 40
   Base counts- A: 11  T: 9    C: 10   G: 10   
   Length 5: 40
   Base counts- A: 9   T: 6    C: 15   G: 10   
   Length 6: 40
   Base counts- A: 9   T: 2    C: 12   G: 17   
   Writing to example.fa
   Elapsed assembly time 5 seconds
   Elapsed annotation time 7 seconds
   Elapsed annotation time 14 seconds
  

• Checkout the results in example.fa.annotations

  $ head -20 example.fa.annotations
  {
      "contig2": [
          {
              "start": 2, 
              "seqid": "contig2", 
              "end": 5, 
              "key": "palindrome"
          }, 
          {
              "start": 3, 
              "seqid": "contig2", 
              "end": 5, 
              "key": "start_codon"
          }, 
          {
              "start": 31, 
              "seqid": "contig2", 
              "end": 34, 
              "key": "palindrome"
          },