From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 10 May 2011 16:49:36 +0000 (+0000)
Subject: fixed pipes for adaptor removal
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6420a0576fd75c449289ea86fc429e9d9fb836c4;hp=503ce0da86ded4e33fd7fb6b517bada4f4318447;p=biopieces.git

fixed pipes for adaptor removal

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1398 74ccb610-7750-0410-82ae-013aeee3265d
---

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=$$
-
-#find_adaptor -a $adaptor |
-parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
-plot_histogram -t post -o remove_adaptor_histogram.$pid.ps -k ADAPTOR_POS -s num |
-plot_lendist -t post -o remove_adaptor_lendist.$pid.ps -k ADAPTOR_LEN |
-analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o remove_adaptor_analyze_vals.$pid.txt |
-clip_adaptor
diff --git a/bp_scripts/remove_adaptor_454.sh b/bp_scripts/remove_adaptor_454.sh
new file mode 100755
index 0000000..34013b1
--- /dev/null
+++ b/bp_scripts/remove_adaptor_454.sh
@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Remove adaptor from sequences and produce a number of plots.
+
+# Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq
+
+adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
+pid=$$
+
+#find_adaptor -a $adaptor |
+plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN |
+parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
+plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
+plot_lendist -t post -o 02_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
+plot_lendist -t post -o 03_remove_adaptor_lendist_seq_after.$pid.ps -k SEQ_LEN |
+analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 04_remove_adaptor_analyze_vals.$pid.txt |
+clip_adaptor
diff --git a/bp_scripts/remove_adaptor_illumina.sh b/bp_scripts/remove_adaptor_illumina.sh
new file mode 100755
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