GIGGLE

GIGGLE is a genomics search engine that identifies and ranks the significance of shared genomic loci between query features and thousands of genome interval files.

For questions and discussion about GIGGLE please visit/join the mailing list: https://groups.google.com/d/forum/giggle-discuss

For more information about how GIGGLE works, please read the preprint: http://www.biorxiv.org/content/early/2017/06/29/157735

Building

Dependencies

From a fresh install of Ubuntu, the following steps should provide all the required dependencies.

sudo apt install gcc make autoconf zlib1g-dev libbz2-dev libcurl4-openssl-dev libssl-dev ruby

Giggle command line interface

git clone https://github.com/ryanlayer/giggle.git
cd giggle
make
export GIGGLE_ROOT=`pwd`

Run tests

The first set of tests require bedtools to be in your path.

git clone https://github.com/arq5x/bedtools2.git
cd bedtools2
make
cd bin
export PATH=$PATH:`pwd`

Now run the tests

cd $GIGGLE_ROOT/test/func
./giggle_tests.sh
cd ../unit
make
cd ../../..

Web server (optional)

This is based on libmicrohttpd

mkdir -p $HOME/usr/local/
wget http://ftpmirror.gnu.org/libmicrohttpd/libmicrohttpd-0.9.46.tar.gz
tar zxvf libmicrohttpd-0.9.46.tar.gz
cd libmicrohttpd-0.9.46
./configure --prefix=$HOME/usr/local/
make
make install

export LD_LIBRARY_PATH=$HOME/usr/local/lib/

cd ..

sudo apt install libtool

wget https://github.com/json-c/json-c/archive/json-c-0.12.1-20160607.tar.gz
tar xvf json-c-0.12.1-20160607.tar.gz  
cd json-c-json-c-0.12.1-20160607
./configure --prefix=$HOME/usr/local/
make
make install

cd giggle
make
make server

Example analysis

NOTE: Index files and query files MUST be bgzipped (https://github.com/samtools/htslib, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176/).

Roadmap Epigenomics

# details of how to recreate the data at 
# https://github.com/ryanlayer/giggle/blob/master/examples/rme/README.md
wget https://s3.amazonaws.com/layerlab/giggle/roadmap/roadmap_sort.tar.gz
tar -zxvf roadmap_sort.tar.gz

# NOTE, if the following command gives "Too many open files" try:
# ulimit -Sn 16384
$GIGGLE_ROOT/bin/giggle index -s -f \
    -i "roadmap_sort/*gz" \
    -o roadmap_sort_b 

wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1218nnn/GSM1218850/suppl/GSM1218850_MB135DMMD.peak.txt.gz
# take the just the top peaks
zcat GSM1218850_MB135DMMD.peak.txt.gz \
| awk '$8>100' \
| cut -f1,2,3 \
| $GIGGLE_ROOT/lib/htslib/bgzip -c \
> GSM1218850_MB135DMMD.peak.q100.bed.gz

# List files in the index
$GIGGLE_ROOT/bin/giggle search -l \
    -i roadmap_sort_b/ 

# Search
$GIGGLE_ROOT/bin/giggle search -s \
    -i roadmap_sort_b/ \
    -q GSM1218850_MB135DMMD.peak.q100.bed.gz \
> GSM1218850_MB135DMMD.peak.q100.bed.gz.result


# Plot
sudo apt install python python-pip python-tk
pip install matplotlib
$GIGGLE_ROOT/scripts/giggle_heat_map.py \
    -s $GIGGLE_ROOT/examples/rme/states.txt \
    -c $GIGGLE_ROOT/examples/rme/EDACC_NAME.txt \
    -i GSM1218850_MB135DMMD.peak.q100.bed.gz.result \
    -o GSM1218850_MB135DMMD.peak.q100.bed.gz.result.3x11.pdf \
    -n $GIGGLE_ROOT/examples/rme/new_groups.txt \
    --x_size 3 \
    --y_size 11 \
    --stat combo \
    --ablines 15,26,31,43,52,60,72,82,87,89,93,101,103,116,120,122,127 \
    --state_names $GIGGLE_ROOT/examples/rme/short_states.txt \
    --group_names $GIGGLE_ROOT/examples/rme/new_groups_names.txt

Roadmap webserver

giggle/bin/server_enrichment roadmap_sort_b/ /tmp/ giggle/examples/rme/data_def.json 8080 

APIs

Python by Brent Pedersen

from giggle import Giggle
index = Giggle('existing-index-dir') # or Giggle.create('new-index-dir', 'files/*.bed')
print(index.files)

result = index.query('chr1', 9999, 20000)
print(result.n_files)
print(result.n_total_hits) # integer number sum of hits across all files

print(result.n_hits(0)) # integer number of hits for the 0th file...

for hit in result[0]:
    print(hit) # hit is a string

Installation

make sure you have liz, libcurl, libcrypto, libbz2 and liblzma installed in the appropriate place on your system.

git clone --recursive https://github.com/brentp/python-giggle
cd python-giggle
python setup.py test
python setup.py install

Go by Brent Pedersen

import (
    giggle "github.com/brentp/go-giggle"
    "fmt"
) 

func main() {

    index := giggle.Open("/path/to/index")
    res := index.Query("1", 565657, 567999)

    // all files in the index
    index.Files()

    // int showing total count
    res.TotalHits()

    // []uint32 giving number of hits for each file
    res.Hits()

    var lines []string
    # access results by index of file.
    lines = res.Of(0)
    fmt.Println(strings.Join(lines, "\n"))
    lines = res.Of(1)
}