
#############################################################
# ParTIES DENOVO
#############################################################
MAC_GENOME=REFERENCE/ptetraurelia_mac_51.fa

pies Run -genome $MAC_GENOME -out_dir ParTIES_DeNovo -config parties_denovo.cfg


#############################################################
# ParTIES ON THE REFERENCE SET
#############################################################

MAC_GENOME=/data/PARAMECIUM/REFERENCES/tetraurelia/ptetraurelia_mac_51.fa
MAC_IES_GENOME=/data/PARAMECIUM/REFERENCES/tetraurelia/ptetraurelia_mac_51_with_ies.fa

IES_ON_MAC=/data/PARAMECIUM/ANALYSIS/tetraurelia/PGM/SAMPLES/ABK_COSP/ParTIES_DeNovo/MICA/MICA.gff3
IES_ON_MAC_IES=/data/PARAMECIUM/ANALYSIS/tetraurelia/PGM/SAMPLES/ABK_COSP/ParTIES_DeNovo/MICA/MICA.ies.gff3

MIRET_CONTROL=/data/PARAMECIUM/ANALYSIS/tetraurelia/MAC/SAMPLES/KLEB/ParTIES/MIRET/MIRET.gff3


parties MIRET -threads 6 -genome $MAC_GENOME -ies $IES_ON_MAC  -germline_genome $MAC_IES_GENOME  -germline_ies $IES_ON_MAC_IES -out_dir MicGSC_BCP_AAIOSF_1_MiSeq/ParTIES -control $MIRET_CONTROL \
   -bam /data/PARAMECIUM/MAPPING/tetraurelia/ptetraurelia_mac_51/DNAseq/micronucleus//MicGSC_BCP_AAIOSF_1_MiSeq.BOWTIE.pt_51.pe.sorted.bam \
   -germline_bam /data/PARAMECIUM/MAPPING/tetraurelia/ptetraurelia_mac_51_with_ies/DNAseq/micronucleus//MicGSC_BCP_AAIOSF_1_MiSeq.BOWTIE.pt_51_with_ies.pe.sorted.bam 
   

parties MILORD -threads 6 -genome $MAC_IES_GENOME -out_dir MicGSC_BCP_AAIOSF_1_MiSeq/ParTIES \
   -bam /data/PARAMECIUM/MAPPING/tetraurelia/ptetraurelia_mac_51_with_ies/DNAseq/micronucleus//MicGSC_BCP_AAIOSF_1_MiSeq.BOWTIE.pt_51_with_ies.pe.sorted.bam  
   

parties Compare -threads 6 -genome $MAC_IES_GENOME -out_dir MicGSC_BCP_AAIOSF_1_MiSeq/ParTIES \
   -reference_set $IES_ON_MAC_IES -current_set MicGSC_BCP_AAIOSF_1_MiSeq/ParTIES/MILORD/MILORD.gff3
