#!/bin/bash
rm pip.sh
echo "#!/bin/bash" >> pip.sh
echo "PATH=/data/results/tools/samtools/samtools-0.1.19:/data/results/tools/align/bowtie2-2.2.8:/data/results/tools/align/tophat-2.1.1.Linux_x86_64:$PATH; export PATH" >> pip.sh
awk 'BEGIN{printf("echo %cUsing tophat2 installation at%c\n",34,34);exit}' >> pip.sh
echo "which tophat2" >> pip.sh
echo "tophat --version" >> pip.sh
awk 'BEGIN{printf("echo %cUsing bowtie installation at%c\n",34,34);exit}' >> pip.sh
echo "which bowtie2" >> pip.sh
echo "bowtie2 --version" >> pip.sh

#tophat2 -p 4 --keep-fasta-order --GTF /mnt/raid/data/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2011-08-30-22-53-30/Genes/genes.gtf  /mnt/raid/data/reference/mmu/bowtie2/mm9 adaptorTrim.fastq &> tophat-ion3a-mm9-run.log
#tophat2 -p 5 --library-type fr-secondstrand --read-realign-edit-dist 1 --keep-fasta-order --GTF /mnt/raid/data/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2011-08-30-22-53-30/Genes/genes.gtf  /mnt/raid/data/reference/mmu/bowtie2/mm9 adaptorTrim.fastq &> tophat-ion3a-mm9-run.log
#tophat2 -p 5  --keep-fasta-order --GTF /mnt/raid/data/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Archives/archive-2011-08-30-22-53-30/Genes/genes.gtf  /mnt/raid/data/reference/mmu/bowtie2/mm9 adaptorTrim.fastq &> tophat-ion3a-mm9-run.log

x=1

for i in *q.gz
do
echo $i
#echo "/home/reczko/tools/align/adapter/cutadapt-1.2.1/bin/cutadapt -m 16 -g GGCCAAGGCG  -o adaptorTrim.$i $i &> $i.cutadaptlog.txt" >>pip.sh



 if [ $x == 1 ]; then 	
echo $i | awk '{i=substr($1,length($1)-8,3);x=sprintf("/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3   --no-novel-juncs --output-dir tophat_%s --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts --GTF /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome  %s &> %s.tophat-mm9.log",i,$1,i);print x;}' >> pip.sh
     else
echo $i | awk '{i=substr($1,length($1)-8,3);x=sprintf("/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_%s --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome %s &> %s.tophat-mm9.log",i,$1,i);print x;}' >> pip.sh

 fi
echo $i | awk '{i=substr($1,length($1)-8,3);x=sprintf("cd tophat_%s;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.bam; samtools view sort.bam   | awk -f /data/results/tools/formats/sam-remove-read-multimaps-to-same-location2.awk | samtools view -bt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai  - > sort_uniq.bam; rm sort.bam; cd ..;",i);print x;}' >> pip.sh
 let x+=1;

done

chmod u+x pip.sh