Python

Install

The easiest way to install is via pip:

 python3 -m pip install hic-straw

Straw uses the requests library for support of URLs. Be sure it is installed.

You can always see usage via help(straw)

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[0])):
     print("{0}\t{1}\t{2}".format(result[0][i], result[1][i], result[2][i]))

• Extract reads from a URL: chromosome 14 with KR normalization at 2.5Mb resolution, from the Cell 2014 GM12878 combined replicate map:

  import straw
  result = straw.straw("KR", "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic", "14", "14", "BP", 2500000)

  All the maps listed in the Juicebox menu available at http://hicfiles.tc4ga.com/juicebox.properties

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

  import straw
  straw.printme("KR", "HIC001.hic", "1:1000000:7500000", "1:1000000:7500000", "BP", 25000, 'out.txt')

  To get in an array:

  import straw
  result = straw.straw("KR", "HIC001.hic", "1:1000000:7500000", "1:1000000:7500000", "BP", 25000)

• 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[0])):
     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).