Python

Examples

• Extract all reads on chromosome X at 1MB resolution with no normalization in local file "HIC001.hic"

  import straw
  
  result = straw.straw('NONE', 'HIC001.hic', 'X', 'X', 'BP', 1000000)
  
  # the values returned are in x / y / counts
  for i in range(len(result)):
     print("{0}\t{1}\t{2}".format(result[0][i], result[1][i], result[2][i]))

• Extract reads between 1MB and 7.5MB on chromosome 1 at 25KB resolution with KR (balanced) normalization:

  import straw
  
  result = straw.straw("KR", "HIC001.hic", "1:1000000:7400000", "1:1000000:7400000", "BP", 25000)
  # the values returned are in results
  for i in range(len(result)):
     print("{0}\t{1}\t{2}".format(result[0][i], result[1][i], result[2][i]))

• Extract all interchromosomal reads between chromosome 5 and chromosome 12 at 500 fragment resolution with VC (vanilla coverage) normalization:

  import straw
  
  result = straw.straw("VC", "HIC001.hic", "5", "12", "FRAG", 500)
  # the values returned are in results
  for i in range(len(result)):
     print("{0}\t{1}\t{2}".format(result[0][i], result[1][i], result[2][i]))

See the script straw.py for an example of how to print the results to a file.

Read header

See the file read_hic_header.py for a Python script that reads the header of a hic file and outputs the information (including resolutions).

OLD: Compiling (Bootstrap version)

These are old instructions and are no longer necessary.

Straw can be called from Python by using Boost http://www.boost.org/

The files Jamroot, straw.py, and main-python.cpp are used to hook the C++ to Python. main-python.cpp is essentially the same as main.cpp

1. Get Boost:
   http://www.boost.org/doc/libs/1_61_0/more/getting_started/unix-variants.html#get-boost
2. Compile bjam:
   http://www.boost.org/doc/libs/1_49_0/more/getting_started/unix-variants.html#prepare-to-use-a-boost-library-binary (just do --with-libraries python)
3. Type "bjam" in the directory with the files (assuming you've put boost and bjam in your path).