From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 24 May 2011 13:40:44 +0000 (+0000)
Subject: working on clean_reads scripts
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6a2ed80f4b5c98fc7d39ea21e6a71514233623f6;p=biopieces.git

working on clean_reads scripts

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1425 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_scripts/clean_reads_454.sh b/bp_scripts/clean_reads_454.sh
index 70e05e9..3fb7d93 100755
--- a/bp_scripts/clean_reads_454.sh
+++ b/bp_scripts/clean_reads_454.sh
@@ -14,8 +14,7 @@ plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN
 find_adaptor -a $adaptor -p |
 plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$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.$pid.txt |
+analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 03_remove_adaptor_analyze_vals.$pid.txt |
 clip_adaptor |
 plot_scores -t post -o 04_trim_seq_scores_pretrim.$pid.ps |
 plot_lendist -k SEQ_LEN -t post -o 05_trim_seq_lendist_pretrim.$pid.ps |
diff --git a/bp_scripts/clean_reads_illumina.sh b/bp_scripts/clean_reads_illumina.sh
index 6929378..d4ec62a 100755
--- a/bp_scripts/clean_reads_illumina.sh
+++ b/bp_scripts/clean_reads_illumina.sh
@@ -10,18 +10,16 @@ adaptor='AGATCGGAAGACACACGTCT'  # Solexa adaptor
 pid=$$
 
 progress_meter |
-plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN |
 find_adaptor -a $adaptor -p |
-plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$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.$pid.txt |
+plot_histogram -t post -o 00_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
+plot_lendist -t post -o 01_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
+analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 02_remove_adaptor_analyze_vals.$pid.txt |
 clip_adaptor |
-plot_scores -t post -o 04_trim_seq_scores_pretrim.$pid.ps |
-plot_lendist -k SEQ_LEN -t post -o 05_trim_seq_lendist_pretrim.$pid.ps |
+plot_scores -t post -o 03_trim_seq_scores_pretrim.$pid.ps |
+plot_lendist -k SEQ_LEN -t post -o 04_trim_seq_lendist_pretrim.$pid.ps |
 trim_seq |
 grab -e "SEQ_LEN>=30" |
 mean_scores -l |
 grab -e "SCORES_LOCAL_MEAN>=15" |
-plot_scores -t post -o 06_trim_seq_scores_posttrim.$pid.ps |
-plot_lendist -k SEQ_LEN -t post -o 07_trim_seq_lendist_posttrim.$pid.ps
+plot_scores -t post -o 05_trim_seq_scores_posttrim.$pid.ps |
+plot_lendist -k SEQ_LEN -t post -o 06_trim_seq_lendist_posttrim.$pid.ps