X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_scripts%2Fremove_adaptor.sh;fp=bp_scripts%2Fremove_adaptor.sh;h=0000000000000000000000000000000000000000;hb=6420a0576fd75c449289ea86fc429e9d9fb836c4;hp=c5181c8cf6ada1093c712b90af7ba7bf8b62fb28;hpb=503ce0da86ded4e33fd7fb6b517bada4f4318447;p=biopieces.git

diff --git a/bp_scripts/remove_adaptor.sh b/bp_scripts/remove_adaptor.sh
deleted file mode 100755
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