PRADA

Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. The BAM files generated by the pipeline are readily compatible with different tools for mutation calling and to obtain read counts for further downstream analysis.

Contents [hide] PRADA Modules Documentation Installation

Modules

PRADA currently supports 6 modules to process and identify abnormalities from RNAseq data:

preprocess	: Generates aligned and recalibrated BAM files.
fusion	: Identifies candidate gene fusions.
guess-ft	: Supervised search for fusion transcripts.
guess-if	: Supervised search for intragenic rearrangements.
homology	: Calculates homology between given two genes.
frame	: Predicts functional consequence of fusion transcript

Documentation

Detail description of installation steps and the usage of each module with examples is available in the documentation.

Installation

shenzy@shenzy-ubuntu:~/Desktop/zhanglei/pgenes/pseudopipe/bin$ ./pseudopipe.sh /home/shenzy/Desktop/zhanglei/pgenes/ppipe_output/prodigal/tcs4/ /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.fasta.masked /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.%s.fasta /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/pep/tcs4_prodigal.pep /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/mysql/contig.%s_exlocs 0
outDir=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_output/prodigal/tcs4
rmkDir=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.fasta.masked
Making directories
Copying sequences
inputDNA=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.fasta.masked
Fomatting the DNAs
formatDB start…….
Preparing the blast jobs
Finished blast
Processing blast output
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
Finished Pseudopipe on strand M
Working on P strand
Finished Pseudopipe on strand P
Generating final results
Finished generating pgene full alignment
Finished running Pseudopipe

 

 

 

 

 

./pseudopipe.sh /home/shenzy/Desktop/zhanglei/pgenes/ppipe_output/caenorhabditis_elegans_62_220a /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs 0

 

http://www.pseudogene.org/DOWNLOADS/pipeline_codes/readme.txt

http://www.pseudogene.org/DOWNLOADS/pipeline_codes/

 

shenzy@shenzy-ubuntu:~/Desktop/zhanglei/pgenes/pseudopipe/bin$ ./pseudopipe.sh /home/shenzy/Desktop/zhanglei/pgenes/ppipe_output/caenorhabditis_elegans_62_220a /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs 0
outDir=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_output/caenorhabditis_elegans_62_220a
rmkDir=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa
Making directories
Copying sequences
inputDNA=/home/shenzy/Desktop/zhanglei/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa
Fomatting the DNAs
Preparing the blast jobs
Finished blast
Processing blast output
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
Finished Pseudopipe on strand M
Working on P strand
Finished Pseudopipe on strand P
Generating final results
Finished generating pgene full alignment
Finished running Pseudopipe

 

./pseudopipe.sh

#/bin/sh
if [ $# -lt 5 ]
then
echo “Usage: ppipe [output dir] [masked dna dir] [input dna dir] [input pep dir] [exon mask dir] [PBS?]”
exit 1
fi

. `dirname $0`/../bin/env.sh

outDir=`if [ ! -d $1 ]; then mkdir -p $1; fi;cd $1;pwd`
rmkDir=`if [ -d $2 ]; then echo \`cd $2;pwd\`; else echo $2; fi`
pepDir=`if [ -d $4 ]; then echo \`cd $4;pwd\`; else echo $4; fi`
dnaTmp=`if [ -d $3 ]; then echo \`cd $3;pwd\`/%s.fa; else echo $3; fi`
emkTmp=`if [ -d $5 ]; then echo \`cd $5;pwd\`/%s_exLocs; else echo $5; fi`

echo “outDir=”$outDir
echo “rmkDir=”$rmkDir
inputDNA=$outDir/dna/dna_all.fa
inputPEP=$outDir/pep/pep_all.fa

jobsExec=$sqDummy; if [ “$6″ = “1” ]; then jobsExec=$sqDedicated; fi
echo Making directories
cd $outDir
if [ ! -d dna ]; then mkdir dna; fi
if [ ! -d pep ]; then mkdir pep; fi
if [ ! -d blast ]
then
mkdir blast
cd blast
mkdir stamps
mkdir output
mkdir status
mkdir processed
cd ..
fi
if [ ! -d pgenes ]
then
mkdir pgenes
cd pgenes
mkdir minus plus
cd minus
mkdir log stamp
cd ../plus
mkdir log stamp
cd ../../
fi

echo Copying sequences
if [ ! -f $inputDNA ]
then
if [ -f $rmkDir ]
then
inputDNA=$rmkDir
else
cat $rmkDir/*.fa > $inputDNA
fi
fi

echo “inputDNA=”$inputDNA

if [ ! -f $inputPEP ]
then
if [ -f $pepDir ]
then
inputPEP=$pepDir
else
cat $pepDir/*.fa > $inputPEP
fi
fi

echo Fomatting the DNAs
cd dna
if [ ! -f formatdb.log ]
then
if [ -f $rmkDir -a -f $rmkDir.nin ]
then
for i in $rmkDir.*
do
ext=`echo $i | sed ‘s/.*\.\(.*\)/\1/’`
if [ ! -e $inputDNA.$ext ]
then
ln -s $i $inputDNA.$ext
fi
done
touch formatdb.log
else
echo “formatDB start…….”
$formatDB -i $inputDNA -o T -p F
fi
fi
cd ..

echo Preparing the blast jobs
cd blast

if [ ! -f jobs ]
then
pepNum=`grep ‘>’ $inputPEP | wc | sed ‘s/\s*\([0-9]*\).*/\1/’`
$pythonExec $fastaSplitter $inputPEP $((($pepNum+359)/360)) ‘split%04d’
for f in `ls split*`
do
echo “\”( cd $(pwd); touch stamps/${f}.Start ; ( $blastExec -p tblastn -m 8 -z 3.1e9 -e .1 -d $inputDNA -i $f -o output/${f}.Out ; touch stamps/${f}.Stamp ) >status/${f}.Status 2>&1 )\””
done > jobs

$pythonExec $jobsExec jobs

echo Finished blast
else
echo Skipping blast
fi

echo Processing blast output
cd processed
if [ ! -f ./processed.stamp ]
then
echo “\”(cd $(pwd); $pythonExec $blastHandler $inputPEP ‘split\d{4}.Out\Z’ ../output; touch processed.stamp)\”” > jobs

$pythonExec $jobsExec jobs

echo Finished processing blast output
else
echo Skipping the processing of blast output
fi

echo Running Pseudopipe on both strands
cd ../../pgenes

for t in ‘M’ ‘P’
do
echo ‘Working on ‘$t’ strand’

if [ $t = ‘M’ ]
then
cd minus
else
cd plus
fi

echo “export BlastoutSortedTemplate=${outDir}/blast/processed/%s_${t}_blastHits.sorted;export ChromosomeFastaTemplate=${dnaTmp};export ExonMaskTemplate=${emkTmp};export ExonMaskFields=’2 3′;export FastaProgram=${fastaExec};export ProteinQueryFile=${inputPEP}” > setenvPipelineVars

ms=$(cd ../../blast/processed ; for f in *_${t}_*sorted; do echo ${f/_${t}_blastHits.sorted/}; done)

for c in $ms
do
echo “\”(cd $(pwd); . setenvPipelineVars; touch stamp/$c.Start ; $pythonExec $pseudopipe $c > log/$c.log 2>&1; touch stamp/$c.Stop)\””
done > jobs

$pythonExec $jobsExec jobs

echo Finished Pseudopipe on strand $t

cd ..
done

echo Generating final results
outFilePrefix=$outDir/pgenes/`basename $outDir`_pgenes
$genPgeneResult $outDir $outFilePrefix.txt
$genFullAln $outDir $outFilePrefix.align.gz

echo Finished running Pseudopipe

 

NOTE:

sh1 source not found

sh source not work,    we need to use “.” to replace “source” in the sh script !

 

sh: 1: .: setenvPipelineVars: not found
Finished Pseudopipe on strand M
Working on P strand
sh: 1: .: setenvPipelineVars: not found

we must give it an absolute path for the file of  setenvPipelineVars

echo “\”(cd $(pwd); .  /home/shenzy/lib/pgenes/ppipe_output/tcs/pgenes/minus/setenvPipelineVars; touch stamp/$c.Start ; $pythonExec $pseudopipe $c > log/$c.log 2>&1; touch stamp/$c.Stop)\””