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intersect_genes.sh
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intersect_genes.sh
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#!/bin/bash
# Copyright 2015 Angela Yen
# This file is part of ChromDiff.
# ChromDiff is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# ChromDiff is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with ChromDiff. If not, see <http://www.gnu.org/licenses/>.
for model in "core"
do
statecallsdir="statecalls/${model}/"
for int1 in {1..129}
do
## make celltype name of the form Exxx as necessary
if [ $int1 -lt 100 ]; then
if [ $int1 -lt 10 ];
then celltype1="E00${int1}";
else
celltype1="E0${int1}";
fi
else
celltype1="E${int1}"
fi
echo "Processing $celltype1... "
if [ $model == "core" ]; then
statecallfile="${statecallsdir}${celltype1}_15_coreMarks_mnemonics.bed.gz"
fi
if [ -s $statecallfile ]
then
# if [ ! -s "majority/${model}/${celltype1}_majstate.txt" ]; then
bodiesintfile="intersect/${model}/${celltype1}_genes.txt"
## overlap gene bodies with state calls (filter out chrY)
zcat $statecallfile | awk -f filter_chrY.awk | intersectBed -wa -wb -a genes/gencode_genes.bed -b stdin | sort -k5,5 > $bodiesintfile ; awk -f pick_majority.awk $bodiesintfile > majority/${model}/${celltype1}_majstate.txt
# fi
fi
done
done