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#												#	
# 				Fix gtfs and build RSEM reference				#
#												#
#   Download from ucsc tables the BED file for ucsc genes and the corresponding kgXref file	#
#												#
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source ~xz18w/ve
~xz18w/bin/group_bed_v2.py -i mm10_ucsc.bed -o mm10_ucsc_clusters_new.bed
grep "_TR.1" mm10_ucsc_clusters_new.bed | awk -F "	chr" '{print "chr"$2}' > mm10_ucsc_clusters_new_tr1.bed
awk -F "\t" '{print $1,$2,$3,$4,int($5),$6,$7,$8,$9,$10,$11,$12}' mm10_ucsc_clusters_new_tr1.bed | sed "s/ /\t/g" > mm10_ucsc_clusters_new_tr1_mod.bed
bedToGenePred mm10_ucsc_clusters_new_tr1_mod.bed stdout | genePredToGtf file stdin stdout -honorCdsStat | sed "s/stdin/Gene/" > mm10_ucsc_clusters_new_tr1_mod.gtf
perl name_gtf.pl mm10_kgXref mm10_ucsc_clusters_new_tr1_mod.gtf > mm10_ucsc_final.gtf
awk -F "gene_id" '{print $2}' mm10_ucsc_final.gtf | sed "s/\"//g;s/ //g;s/;//g;s/transcript_id/\t/" | sort | uniq > mm10_gene_transcript_ref.rsem
egrep -v "random|chrUn" mm10_ucsc_final.gtf > truechr_mm10_ucsc_final.gtf
awk -F "gene_id" '{print $2}' truechr_mm10_ucsc_final.gtf | sed "s/\"//g;s/ //g;s/;//g;s/transcript_id/\t/" | sort | uniq > truechr_mm10_gene_transcript_ref.rsem
module load RSEM/1.2.11
rsem-prepare-reference --gtf truechr_mm10_ucsc_final.gtf --transcript-to-gene-map truechr_mm10_gene_transcript_ref.rsem --bowtie2 --bowtie2-path /project/umw_garberlab/bin/bowtie2-2.1.0 ../mouse/mm10/mm10.fa ./mm10/mm10_ref_rsem