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#!/bin/bash -x
#To trim these sequences and merge them:
#pushd .. && make clean && make && popd
#6 * 3 * 5 * 4
Z=( 26 )
M=( 0.02 )
N=( 0.87 )
X=( 0.125 )
M2=( 0.02 )
N2=( 0.9 )
Q=( 13)
rm trimmed_*
rm lendist_*
for z in "${Z[@]}"
do
for m in "${M[@]}"
do
for n in "${N[@]}"
do
for x in "${X[@]}"
do
for q in "${Q[@]}"
do
for m2 in "${M2[@]}"
do
for n2 in "${N2[@]}"
do
../../SeqPrep \
-f ./simSeq10k_1.fq \
-r ./simSeq10k_2.fq \
-1 ./simSeq_trimmed_1.fq.gz \
-2 ./simSeq_trimmed_2.fq.gz \
-Z ${z} \
-M ${m} \
-N ${n} \
-X ${x} \
-q ${q} \
-n ${n2} \
-m ${m2}
rm simSeq_trimmed_1.fq
rm simSeq_trimmed_2.fq
gunzip simSeq_trimmed_1.fq.gz
gunzip simSeq_trimmed_2.fq.gz
python3 ./simseq_trimmed_error_check.py simSeq10k_1.fq simSeq10k_2.fq simSeq_trimmed_1.fq simSeq_trimmed_2.fq > trimmed_M${m}_N${n}_X${x}_Z${z}_Q${q}_m${m2}_n${n2}.txt
python3 ../seqlens.py < simSeq_trimmed_1.fq > lendist_M${m}_N${n}_X${x}_Z${z}_Q${q}_m${m2}_n${n2}.txt
done
done
done
done
done
done
done
#cp simSeq10k_1.fq simSeq10k_mcf_1.fq
#cp simSeq10k_1.fq simSeq10k_mcf_2.fq
#ea-utils-read-only/clipper/fastq-clipper simSeq10k_mcf_1.fq
#ea-utils-read-only/clipper/fastq-clipper -o simSeq10k_mcf_1.fq simSeq10k_1.fq AGATCGGAAGAGCGGTTCAG
#ea-utils-read-only/clipper/fastq-clipper -o simSeq10k_mcf_2.fq simSeq10k_2.fq AGATCGGAAGAGCGTCGTGT
#python3 ./simseq_trimmed_error_check.py simSeq10k_1.fq simSeq10k_2.fq simSeq10k_mcf_1.fq simSeq10k_mcf_2.fq >trimmed_M99_N99_X99_Z99_Q99_m99_n99.txt
python3 sens_vs_spec.py
#open result.html
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