changeset 1:b21296a98eb2 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ncPRO-PROFILING.sh	Thu Jan 28 07:43:21 2016 -0500
@@ -0,0 +1,196 @@
+#!/bin/bash
+
+# Copyleft ↄ⃝ 2012 Institut Curie
+# Author(s): Jocelyn Brayet, Laurene Syx, Chongjian Chen, Nicolas Servant(Institut Curie) 2012 - 2015
+# Contact: [e-mail]
+# This software is distributed without any guarantee under the terms of the GNU General
+# Public License, either Version 2, June 1991 or Version 3, June 2007.
+
+while getopts "i:g:t:e:l:o:p:r:n:" optionName; do
+case "$optionName" in
+
+i) INPUT="$OPTARG";;
+g) GENOME="$OPTARG";;
+t) DATATYPE="$OPTARG";;
+e) EXT="$OPTARG";;
+l) LOG_FILE="$OPTARG";;
+o) OUT_AB="$OPTARG";;
+p) OUT_DIS="$OPTARG";;
+r) ROOT_DIR="$OPTARG";;
+n) PROJECTNAME="$OPTARG";;
+
+esac
+done
+
+##### ncPRO-seq annotation - Galaxy #####
+
+GENOME_2=`echo $GENOME | cut -d"_" -f2`
+
+databasePath=$ROOT_DIR/database/files
+
+mkdir -p $databasePath/ncproseqAnnotation
+mkdir -p $databasePath/ncproseqAnnotation/annotation
+annotationPath=$databasePath/ncproseqAnnotation/annotation
+[ ! -d $annotationPath/$GENOME_2 ] && wget http://ncpro.curie.fr/ncproseq/install_dir/annotation/$GENOME.tar.gz -P $annotationPath && cd $annotationPath && tar -zxf $GENOME.tar.gz && rm -rf $GENOME.tar.gz
+
+#########
+
+OUTPUT_PATH_DIR=`dirname $OUT_AB`
+OUTPUT_PATH_NAME=`basename $OUT_AB .dat`
+
+OUTPUT_PATH="${OUTPUT_PATH_DIR}/${OUTPUT_PATH_NAME}_files"
+
+mkdir -p $OUTPUT_PATH
+
+VERSION=`echo $OUTPUT_PATH | cut -d"/" -f3`
+VERSION=`echo $VERSION | cut -d"_" -f2`
+
+#DEBUG_MODE
+
+DEBUG_MODE="on"
+DEBUG="/dev/null"
+
+if [[ $DEBUG_MODE == "on" ]];then
+
+	DEBUG="$OUTPUT_PATH/ncPRO-ANNOTATION.debug"
+
+fi
+
+#Deploy ncPRO directories structure
+
+/usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-deploy -o $OUTPUT_PATH > $DEBUG
+
+#me
+chmod 777 -R $OUTPUT_PATH
+#Go to working directory
+
+cd $OUTPUT_PATH
+
+#Create symbolic link to input and annotations
+
+ln -s $INPUT ${OUTPUT_PATH}/rawdata/input.bam
+
+rm annotation
+
+ln -s $annotationPath annotation
+
+#Edit config-ncrna.txt
+
+CONFIG_FILE=config-ncrna.txt
+
+sed -i "s:^BOWTIE_GENOME_REFERENCE =.*$:BOWTIE_GENOME_REFERENCE = $GENOME_2:g" $CONFIG_FILE
+sed -i "s:^ORGANISM.*$:ORGANISM = $GENOME_2:g" $CONFIG_FILE
+
+sed -i "s:^N_CPU.*$:N_CPU = 4:g" $CONFIG_FILE  #****** Make sure this value matches universe.ini files
+sed -i "s:^PROJECT_NAME =.*$:PROJECT_NAME = $PROJECTNAME:g" $CONFIG_FILE
+
+
+#sed -i "s/LOGFILE = pipeline.log/LOGFILE = $LOG_FILE/g" $CONFIG_FILE
+
+if [[ -f "$annotationPath/$GENOME_2/cluster_pirna.gff" ]]
+then
+    ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/cluster_pirna.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
+else
+    if [[ -f "$annotationPath/$GENOME_2/pirna.gff" ]]
+    then
+        ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/pirna.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
+    else
+    ANNO_CATALOG="$annotationPath/$GENOME_2/precursor_miRNA.gff $annotationPath/$GENOME_2/rfam.gff $annotationPath/$GENOME_2/rmsk.gff $annotationPath/$GENOME_2/coding_gene.gff"
+    fi
+fi
+
+sed -i "s:^ANNO_CATALOG.*$:ANNO_CATALOG = $ANNO_CATALOG:g" $CONFIG_FILE
+
+####### Remove information in config-ncrna.txt file ###############
+
+sed -i "s:^MATURE_MIRNA =.*$:MATURE_MIRNA =:g" $CONFIG_FILE
+sed -i "s:^PRECURSOR_MIRNA =.*$:PRECURSOR_MIRNA =:g" $CONFIG_FILE
+sed -i "s:^TRNA_UCSC =.*$:TRNA_UCSC =:g" $CONFIG_FILE
+sed -i "s:^NCRNA_RFAM =.*$:NCRNA_RFAM =:g" $CONFIG_FILE
+sed -i "s:^NCRNA_RFAM_EX =.*$:NCRNA_RFAM_EX =:g" $CONFIG_FILE
+sed -i "s:^NCRNA_RMSK =.*$:NCRNA_RMSK =:g" $CONFIG_FILE 
+sed -i "s:^NCRNA_RMSK_EX =.*$:NCRNA_RMSK_EX =:g" $CONFIG_FILE 
+sed -i "s:^OTHER_NCRNA_GFF =.*$:OTHER_NCRNA_GFF =:g" $CONFIG_FILE 
+
+#######################################
+
+if [[ $DATATYPE == "matmir" ]];then
+
+	sed -i "s/MATURE_MIRNA =/MATURE_MIRNA = $EXT/g" $CONFIG_FILE
+
+elif [[ $DATATYPE == "premir" ]];then
+
+	sed -i "s/PRECURSOR_MIRNA =/PRECURSOR_MIRNA = $EXT/g" $CONFIG_FILE
+
+elif [[ $DATATYPE == "trna" ]];then
+
+	sed -i "s/TRNA_UCSC =/TRNA_UCSC = $EXT/g" $CONFIG_FILE
+
+elif [[ $DATATYPE == "rfam" ]];then
+
+	sed -i "s/NCRNA_RFAM_EX =/NCRNA_RFAM_EX = $EXT/g" $CONFIG_FILE
+
+elif [[ $DATATYPE == "rmsk" ]];then
+
+	sed -i "s/NCRNA_RMSK_EX =/NCRNA_RMSK_EX = $EXT/g" $CONFIG_FILE 
+
+elif [[ $DATATYPE == "other" ]];then
+	
+	# get the gff3 file
+	IFS=',' read -ra gff <<< "$EXT"
+	echo "${gff[0]}" | sed 's/\//\\\//g' > gff
+	gff_file=$(head -n 1 gff)
+	sed -i "s/OTHER_NCRNA_GFF =/OTHER_NCRNA_GFF = $gff_file/g" $CONFIG_FILE
+
+fi
+
+echo "building the command line" >> $DEBUG
+
+#Build command line
+## ****************************************************************** NEW : check if reads are grouped and change command line accordingly********
+
+RG=`samtools view $INPUT | awk --posix 'BEGIN {RG=1} { if ($1 !~ /^[0-9]{1,}_[0-9]{1,}$/) {RG=0 ; exit} } END { print RG}'`
+
+if [[ $RG  = 0 ]]; then # if not grouped
+	
+	# add -s processBam to do the grouping
+	COMMAND_LINE="-c $CONFIG_FILE -s processBam -s generateNcgff -s ncrnaProcess"
+
+else
+
+	# eliminate [-s processBam] because reads are already grouped + move input.bam
+	ln -s $INPUT ${OUTPUT_PATH}/bowtie_results/input.bam 
+	COMMAND_LINE="-c $CONFIG_FILE -s generateNcgff -s ncrnaProcess"
+fi
+
+echo "cmd : $COMMAND_LINE" >> $DEBUG
+# **************** END NEW *******************************************************************************************************************************
+
+#Launch ncPRO analysis
+echo $COMMAND_LINE >> $DEBUG
+/usr/curie_ngs/ncproseq_v1.6.5/bin/ncPRO-seq $COMMAND_LINE >> $DEBUG 2>&1
+
+#Galaxy output handling
+
+mv ${OUTPUT_PATH}/pipeline.log $LOG_FILE
+
+
+# PROFILE
+
+if [ -f ${OUTPUT_PATH}/pic/input_*_${EXT}_abundant.png ] ; then
+	convert -resize 60% ${OUTPUT_PATH}/pic/input_*_${EXT}_abundant.png $OUT_AB
+else
+	echo -e "Distribution of positional read coverage and the read length distribution are unavailable in this annotation family. Check the coverage profile table :\n" > $OUT_AB
+	cat ${OUTPUT_PATH}/doc/${DATATYPE}_${EXT}_all_samples_scaled_basecov_abundant_all_RPM.data >> $OUT_AB
+fi
+
+if [ -f ${OUTPUT_PATH}/pic/input_*_${EXT}_distinct.png ]; then
+	convert -resize 60% ${OUTPUT_PATH}/pic/input_*_${EXT}_distinct.png $OUT_DIS
+else
+	echo "Distribution of positional read coverage and the read length distribution are unavailable in this annotation family. Check the coverage profile table :\n" > $OUT_DIS
+	cat ${OUTPUT_PATH}/doc/${DATATYPE}_${EXT}_all_samples_scaled_basecov_distinct_all_RPM.data >> $OUT_DIS
+
+fi
+
+rm -rf $OUTPUT_PATH
+