Mercurial > repos > yutaka-saito > bsfcall
view bin/last-bisulfite.sh @ 0:06f8460885ff
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author | yutaka-saito |
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date | Sun, 19 Apr 2015 20:51:13 +0900 |
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#! /bin/sh # Align bisulfite-converted DNA reads to a genome. # This assumes that the reads are all from the converted strand # (i.e. they have C->T conversions, not G->A conversions). [ $# -gt 1 ] || { cat <<EOF Typical usage: lastdb -uBISF my_f mygenome.fa lastdb -uBISR my_r mygenome.fa $(basename $0) my_f my_r reads.fastq > results.maf EOF exit 2 } my_f=$1 my_r=$2 shift 2 # Try to get the LAST programs into the PATH, if they aren't already: PATH=$PATH:$(dirname $0)/../src tmp=${TMPDIR-/tmp}/$$ trap 'rm -f $tmp.*' EXIT # Convert C to t, and all other letters to uppercase: perl -pe 'y/Cca-z/ttA-Z/ if $. % 4 == 2' "$@" > "$tmp".q lastal -pBISF -s1 -Q1 -e120 "$my_f" "$tmp".q > "$tmp".f lastal -pBISR -s0 -Q1 -e120 "$my_r" "$tmp".q > "$tmp".r last-merge-batches "$tmp".f "$tmp".r | last-split -m0.1 | perl -F'(\s+)' -ane '$F[12] =~ y/ta/CG/ if /^s/ and $s++ % 2; print @F'