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mv3.sh
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mv3.sh
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#!/bin/bash
g=/filer/misko/mini_chr/git/minichr/
p=/filer/misko/picard/picard-tools-1.56/
s=/home/misko/apps/bin/samtools
j=/usr/bin/java
b=/filer/misko/bedtools-2.17.0/
c=/data/misko/2013.04.12/cs2-4.3/cs2.exe
export LD_LIBRARY_PATH=/home/buske/arch/sge6/lib:/home/buske/arch/sge6/lib::/dupa-filer/misko/gurobi/gurobi550/linux64/lib/:/dupa-filer/misko/gurobi/gurobi550/linux64/lib/
#using hg19
#ref=/filer/hg19/hg19.fa
#or hg18
#ref=/filer/hg18/hg18.fa
if [ $# -ne 1 ]; then
echo $0 folder
exit
fi
wd=$1
function mwalker {
i=$1
sq=$2
m=$3
pushd $wd
#$g/walker/walker_c $wd/nsubtract_centrosubtract_1000bp ${wd}/hmm N 0 ${m} 2 > walker_out_q${i}sq${sq}_m${m}
$g/walker/walker_c_v2 $wd/nsubtract_centrosubtract_1000bp ${wd}/hmm N 0 ${m} 2 > walker_out_q${i}sq${sq}_m${m}
mv problem_file.gz problem_file_q${i}sq${sq}_m${m}.gz
zcat problem_file_q${i}sq${sq}_m${m}.gz | /data/misko/2013.04.12/cs2-4.3/cs2.exe | gzip > solved_q${i}sq${sq}_m${m}.gz
#make the lp problem
pypy /filer/misko/mini_chr/git/minichr/cplex/graph_c_to_lp.py problem_file_q${i}sq${sq}_m${m}.gz el_q${i}sq${sq}_m${m}.gz nsubtract_centrosubtract_1000bp_mqs ${i} ${sq} ${m} Qproblem_file_q${i}sq${sq}_m${m} > lp_prob_q${i}sq${sq}_m${m}.lp
rm Qproblem_file_q${i}sq${sq}_m${m}.gz
gzip Qproblem_file_q${i}sq${sq}_m${m}
#sovle LP
#/dupa-filer/misko/gurobi/gurobi550/linux64/bin/gurobi_cl MIPGap=0.15 Threads=8 ResultFile=result_q${i}sq${sq}_m${m}.sol lp_prob_q${i}sq${sq}_m${m}.lp
#/dupa-filer/misko/gurobi/gurobi550/linux64/bin/gurobi_cl Threads=8 ResultFile=result_q${i}sq${sq}_m${m}.sol lp_prob_q${i}sq${sq}_m${m}.lp
#conver LP to flow
#pypy /filer/misko/mini_chr/git/minichr/cplex/lp_to_flow.py el_q${i}sq${sq}_m${m}.gz result_q${i}sq${sq}_m${m}.sol | gzip > lp_flow_q${i}sq${sq}_m${m}.gz
#flow to graph
#pypy /filer/misko/mini_chr/git/minichr/walker/flow_to_graph_v2.py problem_file_q${i}sq${sq}_m${m}.gz lp_flow_q${i}sq${sq}_m${m}.gz ${m} 0 1000 > g_lp_q${i}sq${sq}_m${m}
#update graph with no flows
#pypy /filer/misko/mini_chr/git/minichr/insert_no_flows.py g_lp_q${i}sq${sq}_m${m} hmm > g_lp_q${i}sq${sq}_m${m}_whmm
zcat Qproblem_file_q${i}sq${sq}_m${m}.gz | $c > Qproblem_file_q${i}sq${sq}_m${m}.solved
rm Qproblem_file_q${i}sq${sq}_m${m}.solved.gz
gzip Qproblem_file_q${i}sq${sq}_m${m}.solved
#flow to graph
pypy /filer/misko/mini_chr/git/minichr/walker/flow_to_graph_v2.py Qproblem_file_q${i}sq${sq}_m${m}.gz Qproblem_file_q${i}sq${sq}_m${m}.solved.gz ${m} 0 1000 > Qg_lp_q${i}sq${sq}_m${m}
#update graph with no flows
pypy /filer/misko/mini_chr/git/minichr/insert_no_flows.py Qg_lp_q${i}sq${sq}_m${m} hmm > Qg_lp_q${i}sq${sq}_m${m}_whmm
#do the IP stuff
zcat Qproblem_file_q${i}sq${sq}_m${m}.solved.gz > Qproblem_file_q${i}sq${sq}_m${m}.solved.tmp
pypy $g/decompose_and_report.py Qproblem_file_q${i}sq${sq}_m${m}.solved.tmp decompositions_q${i}sq${sq}_m${m}.loops decompositions_q${i}sq${sq}_m${m}.loops.full
pypy /filer/misko/mini_chr/git/minichr/cplex/graph_c_to_lp_wsimple.py problem_file_q${i}sq${sq}_m${m}.gz el_q${i}sq${sq}_m${m}.gz nsubtract_centrosubtract_1000bp_mqs ${i} `expr ${sq} / 2` ${m} Qproblem_file_q${i}sq${sq}_m${m}.tmp decompositions_q${i}sq${sq}_m${m}.loops > ip_prob_q${i}sq${sq}_m${m}.lp
#wait for IP solver
#touch ip_prob_q${i}sq${sq}_m${m}.lp.go
#while [ -e ip_prob_q${i}sq${sq}_m${m}.lp.go ] ; do
# sleep $[ ( $RANDOM % 25 ) + 1 ]
#done
/dupa-filer/misko/gurobi/gurobi550/linux64/bin/gurobi_cl MIPGap=0 ResultFile=ip_prob_q${i}sq${sq}_m${m}.lp.sol ip_prob_q${i}sq${sq}_m${m}.lp
cat ip_prob_q${i}sq${sq}_m${m}.lp.sol | grep c | awk '{if ($2>0) {print $0}}' | pypy $g/cplex/contigs_to_flow.py decompositions_q${i}sq${sq}_m${m}.loops | gzip > ip_prob_q${i}sq${sq}_m${m}.lp.flow.gz
pypy $g/walker/flow_to_graph_v2_noerror.py Qproblem_file_q${i}sq${sq}_m${m}.gz ip_prob_q${i}sq${sq}_m${m}.lp.flow.gz ${m} 0 1000 > Qg_ip_q${i}sq${sq}_m${m}
cat ip_prob_q${i}sq${sq}_m${m}.lp.sol | awk '{if ($2>0) {print $0}}' | grep "^c" | while read line; do
z=`echo $line | awk '{print $1}'`_m`echo $line | awk '{print $2}'`
echo $line | pypy /filer/misko/mini_chr/git/minichr/cplex/contigs_to_flow.py decompositions_q${i}sq${sq}_m${m}.loops | gzip > $z.gz
pypy /filer/misko/mini_chr/git/minichr/walker/flow_to_graph_v2_noerror.py Qproblem_file_q${i}sq${sq}_m${m}.gz $z.gz ${m} 0 1000 > g_q${i}sq${sq}_m${m}_${z}
done
rm Qproblem_file_q${i}sq${sq}_m${m}.solved.tmp
popd
}
#run overlaps
#mwalker 4000 1000
#mwalker 1350 300 3 # contigQ somatic_base_Q multiplier
mwalker 1350 290 3 # contigQ somatic_base_Q multiplier