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make_reads_454.sh
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#!/bin/tcsh
foreach ac (`awk '{print $2}' $argv[1]`)
set size = `grep $ac $argv[1] | awk '{print $3}'`
set chr = `grep $ac $argv[1] | awk '{print $1}'`
set cov = 10
set ins = 0
set length = 500
set set = ""
foreach cov ( 2 4 6 8 10)
if ( $cov < 10 ) then
set sets = "1"
else
set sets = "-A -B -C -D -E -F -G -H"
endif
foreach set ( $sets )
#foreach ins (0 500 2000 8000 20000 40000)
foreach ins (0)
if ( $cov < 10 ) then
set set = ""
endif
if ($ins == 0) then
echo "Fragments ($ins)..."
set reads = `dc -e "$size $cov * $length 2 * / p"`
set header = $ac-454-R$length-I$ins-C${cov}$set
set cycles = `dc -e "$length 0.4 x* p" | sed 's/\..*//'`
echo $ac \(${size}bp\) x $cov = $reads ${length}bp reads \($cycles cycles\) '->' $header.fasta
~/bin/metasim/MetaSim cmd -r $reads --454 --454-cycles $cycles ~/references/rice/chr${chr}.fasta >> metasim.log
sed 's/>r\(.*\)\.1 |.*/>$chr_fragment_\1/' chr{$chr}-454.fna > x
~/bin/scripts/clean_fasta.pl x > $header.fasta
else
echo "Paired ($ins)..."
set stddev = `dc -e "$ins 5 / p"`
set reads = `dc -e "$size $cov * $length 50 - 2 * / p"`
set header = $ac-454-R$length-I$ins-C${cov}$set
set cycles = `dc -e "$length 0.4 x* p" | sed 's/\..*//'`
set pair_len = `dc -e "$length 50 - 2 / p 0 k"`
echo $ac \(${size}bp\) x $cov = $reads ${length}bp reads, $pair_len pairs \($cycles cycles\) '->' $header.fasta
~/bin/metasim/MetaSim cmd -r $reads --454 --454-cycles $cycles --454-mate-probability 100 --454-paired-read-length $pair_len --454-remove-linker --clones-mean $ins --clones-param2 $stddev ~/references/rice/chr${chr}.fasta >> metasim.log
sed 's/>\(r.*1\)\ |SOURCES=.*/>\1/' chr{$chr}-454.fna > $header.fasta
~/bin/scripts/clean_fasta.pl $header.fasta > x
mv x $header.fasta
endif
rm chr{$chr}-454.fna
end
end
end
#foreach library (A B C D E F G H I J)
#echo $library
#~/bin/metasim/MetaSim cmd -r $reads -m -g ~/bin/metasim/examples/ErrorModelSolexaPerfect100bp.mconf -2 ~/bin/metasim/examples/ErrorModelSolexaPerfect100bp.mconf --empirical-pe-probability 100 --clones-mean 500 --clones-param2 50 ~/references/rice/chr${chr}.fasta
#cp chr12-Empirical.fna rice-Illumina-500bp-5x.fna
#rm x
#mv rice-Illumina-500bp-5x.fna rice-chr12-Illumina-500bp-2x.$library.fna
#end
#2.5kb
#8kb
#~/bin/metasim/MetaSim cmd -r $reads --454 --454-cycles 200 --454-mate-probability 100 --454-paired-read-length 200 --454-remove-linker --clones-mean 8000 --clones-param2 800 ~/references/rice/chr${chr}.fasta
#cat chr*-454.fna > rice-454-8kb-5x.fna
#20kb
#foreach library (A B C D E F G H I J)
#echo $library
#~/bin/metasim/MetaSim cmd -r $reads -m -g ~/bin/metasim/examples/ErrorModelSolexaPerfect100bp.mconf -2 ~/bin/metasim/examples/ErrorModelSolexaPerfect100bp.mconf --empirical-pe-probability 100 --clones-mean 20000 --clones-param2 2000 ~/references/rice/chr${chr}.fasta
#cp chr12-Empirical.fna rice-Illumina-20kb-2x.fna
#sed 's/>r\(.*\)\.1 |.*/>2x20kb'"${library}"'_\1_1 library=2x20kb'"${library}"' dir=F template=2x20kb'"${library}"'_\1/' rice-Illumina-20kb-2x.fna > x
#sed 's/>r\(.*\)\.2 |.*/>2x20kb'"${library}"'_\1_2 library=2x20kb'"${library}"' dir=R template=2x20kb'"${library}"'_\1/' x > rice-chr12-Illumina-20kb-2x.$library.fna
#rm x
#end
#~/bin/metasim/MetaSim cmd -r $reads --454 --454-cycles 200 --454-mate-probability 100 --454-paired-read-length 200 --454-remove-linker --clones-mean 20000 --clones-param2 1000 ~/references/rice/chr${chr}.fasta
#cp chr12-Empirical.fna rice-Illumina-20kb-5x.fna
#sed 's/>r\(.*\)\.1 |.*/>5x20kb1_\1_1 library=5x20kb1 dir=F template=5x20kb1_\1/' rice-Illumina-20kb-5x.fna > x
#sed 's/>r\(.*\)\.2 |.*/>5x20kb1_\1_2 library=5x20kb1 dir=R template=5x20kb1_\1/' x > rice-Illumina-20kb-5x.fna
#rm x
#40kb
#~/bin/metasim/MetaSim cmd -r $reads --454 --454-cycles 200 --454-mate-probability 100 --454-paired-read-length 200 --454-remove-linker --clones-mean 40000 --clones-param2 2500 ~/references/rice/chr${chr}.fasta
#rm chr*
#sed 's/>\(.*\)_1/>\1_1 template=\1 dir=F library=5x2/' rice-454-5x-Fragments.2.fna > x
#mv x rice-454-5x-Fragments.2.fna
#sed 's/>r\(.*\) |.*/>5x2_\1/' rice-454-8kb-5x.1.fna | sed 's/\./_/' > x
#mv x rice-454-8kb-5x.1.fna
#sed 's/>\(.*\)_1/>\1_1 template=\1 dir=F library=5x2/' rice-454-5x-Fragments.2.fna > x
#mv x rice-454-8kb-5x.1.fna
#sed 's/>r\(.*\) |.*/>5x2_\1/' rice-454-20kb-5x.1.fna | sed 's/\./_/' > x
#mv x rice-454-20kb-5x.1.fna