primates_orthologs_one2one.sh

#!/bin/bash

# ibsub -m 32Gb primates_orthologs_one2one.sh 

for i in 124 150 153 197 199 200 201 203 204 205 206 207 209 210 216 217 219 221 302 361 465 472 474 476
do
	for j in 124 150 153 197 199 200 201 203 204 205 206 207 209 210 216 217 219 221 302 361 465 472 474 476
	do
		if (($i < $j))
		then
			cp1 ensembl_compara_107 -e " SELECT gm1.stable_id AS gene1_stable_id, sm1.stable_id AS protein1_stable_id, gm2.stable_id AS gene2_stable_id, sm2.stable_id AS protein2_stable_id, h.description AS homology_type, s1.sequence AS prot_seq1, s2.sequence AS prot_seq2, hm1.perc_id AS perc_id1, hm2.perc_id AS perc_id2
			FROM homology_member hm1 JOIN 
         			homology_member hm2 
         			ON hm1.homology_id = hm2.homology_id
         			JOIN homology h 
         			ON hm1.homology_id = h.homology_id 
         			JOIN gene_member gm1 
         			ON hm1.gene_member_id = gm1.gene_member_id 
         			JOIN gene_member gm2 
         			ON hm2.gene_member_id = gm2.gene_member_id 
         			JOIN seq_member sm1 
         			ON hm1.seq_member_id = sm1.seq_member_id 
         			JOIN seq_member sm2 
         			ON hm2.seq_member_id = sm2.seq_member_id 
         			JOIN sequence s1 
         			ON sm1.sequence_id = s1.sequence_id 
         			JOIN sequence s2 
         			ON sm2.sequence_id = s2.sequence_id     
			WHERE h.description='ortholog_one2one' 
        			AND gm1.genome_db_id=$i 
        			AND gm2.genome_db_id=$j
			ORDER BY hm1.homology_id; " >> /homes/ivana/primates_orthologs_one2one.txt
		fi
	done
done


# awk ' /^gene1_stable_id/ && FNR > 1 {next} {print $0} ' primates_orthologs_one2one.txt > primates_orthologs_one2one_w_perc_id.txt