fixed pipes for adaptor removal

[biopieces.git] / bp_scripts / remove_adaptor.sh

diff --git a/bp_scripts/remove_adaptor.sh b/bp_scripts/remove_adaptor.sh
deleted file mode 100755 (executable)
index c5181c8..0000000
--- a/bp_scripts/remove_adaptor.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/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