pipeline.sh

#!/bin/bash

set -e # abort on error

function usage
{
  echo "usage: pipeline.sh GFA_FILE [-b 00 -e 01 -s bSnSnS -w 4,16,64 -t 12 -h]"
  echo "   ";
  echo "  -s | --sort           : Sort option on odgi";
  echo "  -c | --cells-per-file : Cells per file on component_segmentation";
  echo "  -w | --width          : Bin width for each zoom layer on odgi";
  echo "  -t | --threads        : Threads on odgi";
  echo "  -p | --port           : Pathindex port";
  echo "  -i | --host           : Pathindex host";
  echo "  -h | --help           : This message";
}

function parse_args
{
  # positional args
  args=()

  # named args
  while [ "$1" != "" ]; do
      case "$1" in
          -s | --sort )                 sort_opt="$2";           shift;;
          -c | --cells-per-file )       cpf="$2";                shift;;
          -t | --threads )              threads_opt="$2";        shift;;
          -w | --width )                width_opt="$2";          shift;;
          -p | --port )                 port="$2";               shift;;
          -i | --host )                 host="$2";               shift;;
          -h | --help )                 usage;                   exit;; # quit and show usage
          * )                           args+=("$1")             # if no match, add it to the positional args
      esac
      shift # move to next kv pair
  done

  # restore positional args
  set -- "${args[@]}"

  # set positionals to vars
  gfa_path="${args[0]}"

  # validate required args
  if [[ -z "$gfa_path" ]]; then
      echo "Invalid arguments"
      usage
      exit;
  fi
}

parse_args "$@"

ODGI=odgi
GFA=$gfa_path
FASTA=${GFA%.gfa}.fasta
OG=${GFA%.gfa}.og
SOG=${GFA%.gfa}.sorted.og
XP=${GFA%.gfa}.og.xp
PORT=${port:-3010}
THREADS=${threads_opt:-12}
width_array=(${width_opt//,/ })
if [ ${#width_array[@]} -eq 0 ]; then
  width_array=(1 4 16 64 256 1000 4000 16000)
fi
w="$w"
CPF=${cpf:-100}
SORT=${sort_opt:-bSnSnS}
HOST=${host:-localhost}

echo "### sort-option: ${SORT}"
echo "### width-option: ${width_array[@]}"

## Build the sparse matrix form of the gfa graph
echo "### odgi build"
BLDPREF=${GFA%.gfa}_01_build
/usr/bin/time -v -o ${BLDPREF}.time \
ionice -c2 -n7 \
$ODGI build \
--progress \
--gfa=$GFA \
--out=$OG \
> ${BLDPREF}.log 2>&1

if [ ! -f $OG ]; then
  echo "### odgi build failed"
  exit 255
fi

## Sort paths by 1D sorting
echo "### odgi sort"
SRTPREF=${GFA%.gfa}_02_sort
/usr/bin/time -v -o ${SRTPREF}.time \
ionice -c2 -n7 \
$ODGI sort \
--pipeline="$SORT" \
--sgd-use-paths \
--paths-max \
--progress \
--idx=$OG \
--out=$SOG \
--threads="$THREADS"\
> ${SRTPREF}.log 2>&1

if [ ! -f $SOG ]; then
  echo "### odgi sort failed"
  exit 255
fi

##
echo "### odgi bin"
for w in "${width_array[@]}"; do
	BIN=${GFA%.gfa}.w${w}.json
	BINPREF=${0%.sh}_04_bin_w${w}
	/usr/bin/time -v -o ${BINPREF}.time \
	ionice -c2 -n7 \
	$ODGI bin \
	--json \
	--idx=$SOG \
	--bin-width=${w} \
	--fasta $FASTA \
	1> $BIN \
	2> ${BINPREF}.log

	if [ ! -f $BIN ]; then
  echo "### odgi bin failed"
  exit 255
  fi
done
echo "Done outputting bin and fasta."

## Create path index
echo "### odgi pathindex"
BLDPREF=${GFA%.gfa}_05_pathindex
/usr/bin/time -v -o ${BLDPREF}.time \
ionice -c2 -n7 \
$ODGI pathindex \
--idx=$OG \
--out=$XP \
> ${BLDPREF}.log 2>&1

if [ ! -f $XP ]; then
  echo "### odgi pathindex failed"
  exit 255
fi


## Run component segmentation
echo "### component segmentation"
SEGPREF=${GFA%.gfa}.seg

if [ ! -d "${GFA%.gfa}.seg" ]; then
  mkdir ${GFA%.gfa}.seg
fi
if [ ! -d "component_segmentation" ]; then
  git clone --depth 1 https://github.com/graph-genome/component_segmentation
fi
cd component_segmentation
pip3 install -r requirements.txt
export PYTHONPATH=`pwd`:PYTHONPATH 
/usr/bin/time -v -o ../${SEGPREF}.time \
ionice -c2 -n7 \
python3 segmentation.py -j ../${GFA%.gfa}'*' -f ../${FASTA} --cells-per-file ${CPF} -o ../${SEGPREF} -p ${THREADS} \
> ../${SEGPREF}.log 2>&1
cd ..

for w in "${width_array[@]}"; do
    NOF=$(ls ${GFA%.gfa}.seg/${w}/*.schematic.json | wc -l)
    if [ $NOF -lt 1 ]; then
      echo "### component segmentation failed"
      exit 255
    fi
done

## Run PathIndex Server
echo "### PathIndex Server"

$ODGI server -i $XP -p 3010 -a "0.0.0.0" &

## Run Schematize
echo "### Schematize"
SCHEMATIC=${GFA%.gfa}.seg
if [ ! -d "Schematize" ]; then
  git clone --depth 1 https://github.com/graph-genome/Schematize
  cd Schematize
  npm install
  cd ..
fi
cp -r ${SCHEMATIC} Schematize/public/test_data

BASENAME=`basename ${SCHEMATIC}`
sed -E "s|run1.B1phi1.i1.seqwish|${BASENAME}|g" Schematize/src/ViewportInputsStore.js > Schematize/src/ViewportInputsStore2.js
sed -E "s|193.196.29.24:3010|${HOST}:${PORT}|g" Schematize/src/ViewportInputsStore2.js > Schematize/src/ViewportInputsStore1.js
mv Schematize/src/ViewportInputsStore1.js Schematize/src/ViewportInputsStore.js
cd Schematize
npm run-script build
serve -s build -p 3000