scripts for iteratively running the old unitigger

consensus.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+id=`printf "%03d" $SGE_TASK_ID`
+
+/bluearc/home/schatz/gurtowsk/sources/wgs.svn/Linux-amd64/bin/utgcns -g cns.gkpStore -t mod.tigstore.03 1 $id -V 

correct.sh

@@ -9,10 +9,10 @@ source ~/.bashrc
 ##SET THE FOLLOWING PARAMETERS
 
 #path to correct script in pbtools repo
-CORRECT_SCRIPT=/bluearc/home/schatz/gurtowsk/workspace/ectools/pb_correct.py
+CORRECT_SCRIPT=/path/to/ectools/pb_correct.py
 
 #pre filter delta file
-PRE_DELTA_FILTER_SCRIPT=/bluearc/home/schatz/gurtowsk/workspace/ectools/pre_delta_filter.py
+PRE_DELTA_FILTER_SCRIPT=/path/to/ectools/pre_delta_filter.py
 
 #smallest alignment allowed, filter out alignments smaller than this
 MIN_ALIGNMENT_LEN=200
@@ -25,7 +25,7 @@ WIGGLE_PCT=0.05
 CONTAINED_PCT_ID=0.80
 
 #path to high identity unitigs
-UNITIG_FILE=/seq/schatz/a.thaliana/xiwang/james_workspace/nucmer-round-sim/misim.utg.g10frg.fa
+UNITIG_FILE=/path/to/unitigs.fa
 
 #Trim out regions with lower identity than
 CLR_PCT_ID=0.96
@@ -40,15 +40,15 @@ FILE=p${suffix}
 
 ORIGINAL_DIR=`pwd`
 
-Move to sge temp storage
+#Move to sge temp storage
 if [[ $TMPDIR ]]
 then
     cd $TMPDIR
 fi
 
 cp ${ORIGINAL_DIR}/${FILE} .
 
-nucmer --maxmatch -l 11 -b 2000 -g 1000 -p ${FILE} ${FILE} ${UNITIG_FILE}
+nucmer --maxmatch -l 11 -b 10000 -g 1000 -p ${FILE} ${FILE} ${UNITIG_FILE}
 
 cp ${FILE}.delta ${ORIGINAL_DIR}
 

tigiterate.sh

@@ -0,0 +1,33 @@
+#!/bin/bash
+
+#symlink unitigs.layout
+#symlink ovlStore
+#cp gkpStore to gkpStore.modified
+
+GENOME_SIZE=12000000
+FRAGS_PER_PARTITION=10
+ERROR_RATE=0.02
+
+for i in {01..09}
+do
+    cat unitigs.layout | awk '{if($1=="FRG"){$1=$2=$3=$4=""; print $0}else if($1=="unitig"){print}}' |sed "s/^\s*//" | uniq  > unitigs.layout.${i}.clean
+
+    cat unitigs.layout.${i}.clean | awk '{print $1}' | sed "s/unitig/>/g" | tr '\n' ' ' | tr '>' '\n' | awk 'NF < 3' | tr ' ' '\n' | awk 'NF >0' | awk '{ print "frg iid "$1" isdeleted t" }' > bad.${i}
+
+    #python ~/workspace/ectools/filter.py <(/bluearc/data/schatz/mschatz/devel/bin/tig_length.pl unitigs.layout | awk '$2 < 100000' | awk '{ print $1}') <(less unitigs.layout.${i}.clean  | sed "s/unitig />/g" | awk '{print $1}' | tr '\n' ' ' | tr '>' '\n' | awk 'NF > 0') | awk '{ for(i=2;i<=NF;i++){print $i}}' | awk '{print "frg iid "$1" isdeleted t" }' > bad.${i}
+
+    /bluearc/home/schatz/gurtowsk/sources/wgs.svn/Linux-amd64/bin/gatekeeper --edit bad.${i} gkpStore.modified &> mod.log.${i}
+
+    /bluearc/home/schatz/gurtowsk/sources/wgs.svn.utgdevel/Linux-amd64/bin/unitigger  -I ovlStore  -F gkpStore.modified -T mod.tigstore.${i}  -B $FRAGS_PER_PARTITION  -e $ERROR_RATE  -k  -d 1 -x 5 -z 10 -j 5 -U 1  -o utg.${i}  &> log.${i}
+
+    /bluearc/home/schatz/gurtowsk/sources/wgs.svn/Linux-amd64/bin/tigStore -g gkpStore.modified -t mod.tigstore.${i} 1 -d layout -U  > unitigs.layout.${i}
+
+    /bluearc/data/schatz/mschatz/devel/bin/tig_length.pl unitigs.layout.${i} | sort -n -r -k2,2 > unitigs.layout.${i}.lens
+
+    stats -f 2 -n50 $GENOME_SIZE unitigs.layout.${i}.lens  | tee unitigs.layout.${i}.stats
+
+    unlink unitigs.layout
+
+    ln -s unitigs.layout.${i} unitigs.layout
+
+done