diff bin/last-bisulfite.sh @ 0:06f8460885ff

migrate from GitHub

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/last-bisulfite.sh	Sun Apr 19 20:51:13 2015 +0900
@@ -0,0 +1,37 @@
+#! /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'