From aedc5807d4d41948f7f4d68c94412851a479b339 Mon Sep 17 00:00:00 2001
From: nchernia <nchernia@gmail.com>
Date: Tue, 17 Jan 2017 17:13:08 +0100
Subject: [PATCH] adding relaunch prep to CPU scripts

---
 CPU/common/relaunch_prep.sh   | 51 +++++++++++++++++++++++++++++++++++
 UGER/scripts/relaunch_prep.sh |  2 +-
 2 files changed, 52 insertions(+), 1 deletion(-)
 create mode 100755 CPU/common/relaunch_prep.sh

diff --git a/CPU/common/relaunch_prep.sh b/CPU/common/relaunch_prep.sh
new file mode 100755
index 0000000..5e22a8e
--- /dev/null
+++ b/CPU/common/relaunch_prep.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+##########
+#The MIT License (MIT)
+#
+# Copyright (c) 2015 Aiden Lab
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+#  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+#  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+#  THE SOFTWARE.
+##########
+# Helper script for finding what files successfully aligned and preparing the 
+# directory for rerunning juicer.sh
+# Juicer version 1.5
+ls -l splits > ls_splits
+
+awk '($9 ~/_R1/ && $9 ~/fastq$/) || ($9 ~/_R1/ && $9 ~/gz$/) {split($9, a, "_R1");  print a[1]a[2], $9}($9 ~/_R2/ && $9 ~/fastq$/) || ($9 ~/_R2/ && $9 ~/gz$/){split($9,a,"_R2");print a[1]a[2], $9}' ls_splits > fastq.txt
+awk '{name="splits/"$1"_norm.txt.res.txt"; if ((getline line < name) > 0){ split(line, a); if (length(a)<6 || a[2] != a[3]+a[4]+a[5]+a[6] || a[2] == 0){print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"} close(name);}else {print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"}}' fastq.txt > mv_me.sh
+mkdir not_done
+chmod 755 mv_me.sh
+./mv_me.sh
+if [ "$(ls -A not_done)" ]
+    then
+        if [ -d done_splits ]
+        then
+            mv splits/* done_splits/.
+            rmdir splits
+        else
+            mv splits done_splits
+        fi
+        mv not_done splits
+        cat uger.out >> done_uger.out
+        rm uger.out
+else
+    rmdir not_done
+    echo "Fastqs are aligned, run juicer.sh with -S merge flag";
+fi
+rm fastq.txt ls_splits mv_me.sh
diff --git a/UGER/scripts/relaunch_prep.sh b/UGER/scripts/relaunch_prep.sh
index d0c4834..5e22a8e 100755
--- a/UGER/scripts/relaunch_prep.sh
+++ b/UGER/scripts/relaunch_prep.sh
@@ -31,7 +31,7 @@ awk '($9 ~/_R1/ && $9 ~/fastq$/) || ($9 ~/_R1/ && $9 ~/gz$/) {split($9, a, "_R1"
 awk '{name="splits/"$1"_norm.txt.res.txt"; if ((getline line < name) > 0){ split(line, a); if (length(a)<6 || a[2] != a[3]+a[4]+a[5]+a[6] || a[2] == 0){print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"} close(name);}else {print "mv splits/"$2, "not_done; rm -f splits/"$1"*; rm -f splits/"$2"*;"}}' fastq.txt > mv_me.sh
 mkdir not_done
 chmod 755 mv_me.sh
-#./mv_me.sh
+./mv_me.sh
 if [ "$(ls -A not_done)" ]
     then
         if [ -d done_splits ]