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.

After importing, you can always see usage via help(straw)

import straw
help(straw)

Examples

See an example with Google Colab here: notebook

• 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).