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pyStraw: rapidly stream data from .hic files - python only flavor [DEPRECATED]

Straw is library which allows rapid streaming of contact data from .hic files. This repository contains source code for the pure Python flavor Straw, which is kept only for legacy purposes. The latest straw code can be found at https://github.com/aidenlab/straw/

For questions, please use the Google Group.

If you use this tool in your work, please cite

Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. "Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom." Cell Systems 3(1), 2016.

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

Usage: strawObj = straw <hicFile(s)> matrixObj = strawObj.getNormalizedMatrix <chr1> <chr2> <NONE/VC/VC_SQRT/KR> <BP/FRAG> <binsize> data = matrixObj.getDataFromBinRegion <x1,x2,y1,y2>

• Extract reads on chromosome 5 at 5Kb resolution with KR normalization

  import straw
  strawObj = straw(filename)
  matrixObj = strawObj.getNormalizedMatrix('5', '5', 'KR', 'BP', 5000)
  result = matrixObj.getDataFromBinRegion(0,500,0,500)
  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/metadata

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).