1#!/bin/sh 2# 3# Expected output generation for rabema. 4 5# We use the current trunk version of 2011-10-13 (r10463) for building the 6# reference. 7RAZERS=../../../../build/Release/apps/razers2/razers2 8RABEMA_PREPARE=../../../../build/Release/apps/rabema/rabema_prepare_sam 9RABEMA_BUILD=../../../../build/Release/apps/rabema/rabema_build_gold_standard 10RABEMA_EVALUATE=../../../../build/Release/apps/rabema/rabema_evaluate 11 12# ============================================================ 13# Map reads for gold standard and with too low error rate. 14# ============================================================ 15 16${RAZERS} -m 10000 -vv -of 4 -ds -i 92 -o gold-adeno-hamming-08.sam adeno-genome.fa reads.fasta 17${RAZERS} -m 10000 -vv -of 4 -ds -i 92 -id -o gold-adeno-edit-08.sam adeno-genome.fa reads.fasta 18 19${RAZERS} -vv -of 4 -ds -i 92 -o razers2-adeno-hamming-08.sam adeno-genome.fa reads.fasta 20${RAZERS} -vv -of 4 -ds -i 92 -id -o razers2-adeno-edit-08.sam adeno-genome.fa reads.fasta 21 22${RAZERS} -vv -of 4 -ds -i 96 -o razers2-adeno-hamming-04.sam adeno-genome.fa reads.fasta 23${RAZERS} -vv -of 4 -ds -i 96 -id -o razers2-adeno-edit-04.sam adeno-genome.fa reads.fasta 24 25# ============================================================ 26# Prepare SAM. 27# ============================================================ 28 29${RABEMA_PREPARE} -i gold-adeno-hamming-08.sam -o gold-adeno-hamming-08.by_qname.sam 30samtools view -Sb gold-adeno-hamming-08.by_qname.sam > gold-adeno-hamming-08.by_qname.bam 31samtools sort gold-adeno-hamming-08.by_qname.bam gold-adeno-hamming-08.by_coordinate 32samtools view gold-adeno-hamming-08.by_coordinate.bam > gold-adeno-hamming-08.by_coordinate.sam 33${RABEMA_PREPARE} -i gold-adeno-edit-08.sam > gold-adeno-edit-08.by_qname.sam 34samtools view -Sb gold-adeno-edit-08.by_qname.sam -o gold-adeno-edit-08.by_qname.bam 35samtools sort gold-adeno-edit-08.by_qname.bam gold-adeno-edit-08.by_coordinate 36samtools view gold-adeno-edit-08.by_coordinate.bam > gold-adeno-edit-08.by_coordinate.sam 37 38# ============================================================ 39# Build Gold Standard 40# ============================================================ 41 42${RABEMA_BUILD} --distance-metric hamming -e 8 -o gold-adeno-hamming-08.gsi --reference adeno-genome.fa --in-bam gold-adeno-hamming-08.by_coordinate.sam > gold-adeno-hamming-08.stdout 43${RABEMA_BUILD} --distance-metric edit -e 8 -o gold-adeno-edit-08.gsi --reference adeno-genome.fa --in-bam gold-adeno-edit-08.by_coordinate.sam > gold-adeno-edit-08.stdout 44 45# ============================================================ 46# Compare Against Gold Standard 47# ============================================================ 48 49${RABEMA_EVALUATE} --distance-metric hamming -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-hamming-08.sam --in-gsi gold-adeno-hamming-08.gsi > razers2-adeno-hamming-08.stdout 50${RABEMA_EVALUATE} --distance-metric hamming -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-hamming-04.sam --in-gsi gold-adeno-hamming-08.gsi > razers2-adeno-hamming-04.stdout 51${RABEMA_EVALUATE} --distance-metric edit -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-edit-08.sam --in-gsi gold-adeno-edit-08.gsi > razers2-adeno-edit-08.stdout 52${RABEMA_EVALUATE} --distance-metric edit -e 8 --reference adeno-genome.fa --in-bam razers2-adeno-edit-04.sam --in-gsi gold-adeno-edit-08.gsi > razers2-adeno-edit-04.stdout 53