1#!/bin/sh 2# 3# Currently, we run RazerS only on 4 5# We use revision 13816 for building the gold standard. 6RAZERS=${RAZERS:-../../../../../seqan-trunk-build/release/bin/razers3} 7 8for tc in 0 1; do # number of threads, 0 and >0 have different code paths 9 10# ============================================================ 11# Run Adeno Single-End Example 12# ============================================================ 13 14for rl in 36 100; do 15 # Run with defaults for everything. 16 ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-tc${tc}.razers > se-adeno-reads${rl}_1-tc${tc}.stdout 17 18 # No gaps. 19 ${RAZERS} -tc ${tc} --no-gaps adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-ng-tc${tc}.razers > se-adeno-reads${rl}_1-ng-tc${tc}.stdout 20 21 # Compute forward/reverse maches only. 22 ${RAZERS} -tc ${tc} -f adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-f-tc${tc}.razers > se-adeno-reads${rl}_1-f-tc${tc}.stdout 23 ${RAZERS} -tc ${tc} -r adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-r-tc${tc}.razers > se-adeno-reads${rl}_1-r-tc${tc}.stdout 24 25 # Compute with different identity rates. 26 for i in 90 91 92 93 94 95 96 97 98 99 100; do 27 ${RAZERS} -tc ${tc} -i ${i} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-i${i}-tc${tc}.razers > se-adeno-reads${rl}_1-i${i}-tc${tc}.stdout 28 done 29 30 # Run with different output formats. 31 for pair in 0.razers 1.fa 2.eland 3.gff 4.sam 5.afg; do 32 of=$(echo $pair | sed 's/\..*$//g') 33 suffix=$(echo $pair | sed 's/^.\.//g') 34 ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-of${of}-tc${tc}.${suffix} > se-adeno-reads${rl}_1-of${of}-tc${tc}.stdout 35 done 36 37 # Run with different match ordering. 38 for so in 0 1; do 39 ${RAZERS} -tc ${tc} -so ${so} adeno-genome.fa adeno-reads${rl}_1.fa -o se-adeno-reads${rl}_1-so${so}-tc${tc}.razers > se-adeno-reads${rl}_1-so${so}-tc${tc}.stdout 40 done 41done 42 43# ============================================================ 44# Run Adeno Paired-End Example 45# ============================================================ 46 47for rl in 36 100; do 48 # Run with defaults for everything. 49 ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-tc${tc}.razers > pe-adeno-reads${rl}_2-tc${tc}.stdout 50 51 # Allow indels. 52 ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-tc${tc}.razers > pe-adeno-reads${rl}_2-tc${tc}.stdout 53 54 # Compute forward/backward maches only. 55 ${RAZERS} -tc ${tc} -f adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-f-tc${tc}.razers > pe-adeno-reads${rl}_2-f-tc${tc}.stdout 56 ${RAZERS} -tc ${tc} -r adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-r-tc${tc}.razers > pe-adeno-reads${rl}_2-r-tc${tc}.stdout 57 58 # Compute with different identity rates. 59 for i in 90 91 92 93 94 95 96 97 98 99 100; do 60 ${RAZERS} -tc ${tc} -i ${i} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-i${i}-tc${tc}.razers > pe-adeno-reads${rl}_2-i${i}-tc${tc}.stdout 61 done 62 63 # Run with different output formats. 64 for pair in 0.razers 1.fa 2.eland 3.gff 4.sam 5.afg; do 65 of=$(echo $pair | sed 's/\..*$//g') 66 suffix=$(echo $pair | sed 's/^.\.//g') 67 ${RAZERS} -tc ${tc} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-of${of}-tc${tc}.${suffix} > pe-adeno-reads${rl}_2-of${of}-tc${tc}.stdout 68 done 69 70 # Run with different match ordering. 71 for so in 0 1; do 72 ${RAZERS} -tc ${tc} -so ${so} adeno-genome.fa adeno-reads${rl}_1.fa adeno-reads${rl}_2.fa -o pe-adeno-reads${rl}_2-so${so}-tc${tc}.razers > pe-adeno-reads${rl}_2-so${so}-tc${tc}.stdout 73 done 74done 75 76done # for nt 77