Introduction

ALLHiC_adjuster is a toolset contains several scripts for adjusting ALLHiC result.

Dependencies

Software

jcvi

ALLHiC

Python Modules

matplotlib

Usage

Step 1. Locate each contig block with jcvi anchors

usage: ALLHiC_adjuster.py locator [-h] -q QUERY -r REFERENCE -c ANCHORS -a AGP [-s RESOLUTION] -o OUTPIC

options:
  -h, --help            show this help message and exit
  -q QUERY, --query QUERY
                        Query bed file
  -r REFERENCE, --reference REFERENCE
                        Reference bed file
  -c ANCHORS, --anchors ANCHORS
                        Query.Reference.anchors file, generated by jcvi
  -a AGP, --agp AGP     AGP file of query genome
  -s RESOLUTION, --resolution RESOLUTION
                        Resolution means 1/resolution of chromosome length, default=20
  -o OUTPIC, --outpic OUTPIC
                        Output picture

Example:

ALLHiC_adjuster.py locator -q query.bed -r reference.bed -c query.reference.anchors -a query.agp -s 100

The picture will figure out each block, and show start contig and end contig of each block, and a .block.txt file with same name with picture will save contig list in each block.

Step 2. Adjust

usage: ALLHiC_adjuster.py adjuster [-h] {merge,reverse,split} ...

options:
  -h, --help            show this help message and exit

Adjuster commands:
  {merge,reverse,split}
    merge               Merge tour files
    reverse             Reverse tour file
    split               Split tour file or txt file

This three sub commands of adjuster sub command can be use with tour files, for detail, you can use commands below for more help

ALLHiC_adjuster.py adjuster merge -h
ALLHiC_adjuster.py adjuster reverse -h
ALLHiC_adjuster.py adjuster split -h

Example:

# merge tours
ALLHiC_adjuster.py adjuster merge -i <groupX.tour,groupY.tour> -o <groupM.tour>

# reverse tours
ALLHiC_adjuster.py adjuster reverse -i <groupX.tour>

# split tour
ALLHiC_adjuster.py adjuster split -i <groupX.tour> -c <contig1,contig2>

Step 3. Build

Make sure the folder for building only contain necessary .tour files then run:

ALLHiC_build <draft.asm.fasta>

draft.asm.fasta is contig-level assmbly

Otherwise

Extract sequences

usage: ALLHiC_adjuster.py extractor [-h] {tour,list} ...

options:
  -h, --help   show this help message and exit

extractor commands:
  {tour,list}
    tour       Extract sequences with tour
    list       Extract sequences with list

Convert files

usage: ALLHiC_adjuster.py convertor [-h] {agp2tour,tour2txt,tours2cluster,txt2cluster,anchors2circos,ragoo2agp,ragoo2tour} ...

options:
  -h, --help            show this help message and exit

convertor commands:
  {agp2tour,tour2txt,tours2cluster,txt2cluster,anchors2circos,ragoo2agp,ragoo2tour}
    agp2tour            Convert AGP file to tour files
    tour2txt            Convert tour to txt file
    tours2cluster       Convert tour files to cluster file
    txt2cluster         Convert txt files to cluster file
    anchors2circos      Convert anchors to circos link file
    ragoo2agp           Convert RaGOO ordering files to AGP file
    ragoo2tour          Convert single RaGOO ordering file to tour file

For more information, use command below:

ALLHiC_adjuster.py subcommand1 -h
ALLHiC_adjuster.py subcommand1 subcommand2 -h