fixed pipes for adaptor removal

[biopieces.git] / bp_scripts / remove_adaptor_illumina.sh

diff --git a/bp_scripts/remove_adaptor_illumina.sh b/bp_scripts/remove_adaptor_illumina.sh
new file mode 100755 (executable)
index 0000000..c5181c8
--- /dev/null
+++ b/bp_scripts/remove_adaptor_illumina.sh
@@ -0,0 +1,16 @@
+#!/bin/sh
+
+# Remove adaptor from sequences and produce a number of plots.
+
+# Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq
+
+#adaptor='AGATCGGAAGACACACGTCT'  # Solexa adaptor
+adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
+pid=$$
+
+#find_adaptor -a $adaptor |
+parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
+plot_histogram -t post -o remove_adaptor_histogram.$pid.ps -k ADAPTOR_POS -s num |
+plot_lendist -t post -o remove_adaptor_lendist.$pid.ps -k ADAPTOR_LEN |
+analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o remove_adaptor_analyze_vals.$pid.txt |
+clip_adaptor