Straw

Straw enables programmatic access to .hic files. .hic files store the contact matrices from Hi-C experiments and the normalization and expected vectors, along with meta-data in the header.

The main function, straw, takes in the normalization, the filename or URL, chromosome1 (and optional range), chromosome2 (and optional range), whether the bins desired are fragment or base pair delimited, and bin size.

It then reads the header, follows the various pointers to the desired matrix and normalization vector, and stores as [x, y, count]

Usage: straw <NONE/VC/VC_SQRT/KR> <hicFile(s)> <chr1>[:x1:x2] <chr2>[:y1:y2] <BP/FRAG> <binsize>

See https://github.com/theaidenlab/straw/wiki/Python for more documentation

Install

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

Examples

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

  from straw 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 all reads from chromosome 4 at 500KB resolution with VC (coverage) normalization from the combined MAPQ 30 map from Rao and Huntley et al. 2014

  from straw import straw
  result = straw.straw('VC', 'https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_30.hic', '4', '4', 'BP', 500000)
  # 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 between 1MB and 7.5MB on chromosome 1 at 25KB resolution with KR (balanced) normalization and write to a file:

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

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

  from straw 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).