ALLHiC_adjuster is a toolset contains several scripts for adjusting ALLHiC result.
matplotlib
cd /path/to/install
git clone https://github.com/sc-zhang/ALLHiC_adjuster.git
pip install -r requirements.txt
chmod +x ALLHiC_adjuster/ALLHiC_adjuster.py
echo 'export PATH=/path/to/install/ALLHiC_adjuster:$PATH' >> ~/.bash_profile
source ~/.bash_profile
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.
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>
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
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