#!/bin/bash
# run_evgomcltab.sh : should be part of run_evgomcl

date=20171114
idprefix=DAPHa_G

#myspp for brief table
myspecies=dpx17evg

speciesmap=bemtab=Whitefly,dapmaevg14=Daphnia_magna,dpx17evg=Daphnia_pulex,dapgal16tsa=Daphnia_galeata,dapsim17evg=Daphnia_similoides,drosmel16nc=Fruitfly,tribcas16nc=Beetle,guppync1=Guppy,zebrafish3=Zebrafish,human=Human

export clade=DaphniaInsectFish

# export xml=1
# otopts="-steps=genegroup"
otopts=""

# some dapmag names bad, skip? are dpx17 names ok? zebrafish?   no names for dapgal,dapsim
## * need to use (spp)=  id =~ m/^([a-zA-Z]+)/) here, see arp_condef3
#try2: most human
# goodname='guppy|tribcas|bemtab|drosmel|dpx17evg|human'
# poorname='dapmaevg|zebrafish'
#try 3; leave dpx17evg,zebrafish unclassed
# goodname='guppy:2,tribcas:2,bemtab:1,drosmel:2,human:1'
# poorname='dapmaevg'
# try4: fix names: bemtab,dapmaevg14,dpx17evg,drosmel16nc,guppync1,human,tribcas16nc,zebrafish3
goodname='bemtab,guppync,drosmel,human,tribcas'
poorname='dapmaevg'
otopts="-steps=condef,genegroup,subgroup"

## mcl : used? fix path
export MCL=/bio/bio-grid/mb/mcl9
export evigene=/bio/bio-grid/mb/evigene
# export MCL=$HOME/bio/mcl9
# export evigene=$HOME/bio/evigene

env myspecies=$myspecies xml=0 date=$date clade=$clade speciesmap="$speciesmap" \
 goodname="$goodname" poorname="$poorname" \
 $evigene/scripts/omcl/orthomcl_tabulate.pl $otopts -debug -idprefix=$idprefix -omclpath ./ -namepath ../names

#..............
# ** NEED goodnames/badnames otherwise bad default used, mostly human
#.. deflt name src
# 1676 bemtab
# 3478 dapmaevg14
# 4041 dpx17evg
#  474 drosmel16nc
# 1821 guppync1
# 12699 human
# 5095 na
#  777 tribcas16nc
# 1392 zebrafish3
# 
# #sysrun: /home/ux455375/bio/evigene/scripts/omcl/../omcl/arp_condef3.pl -noput -nodigit -nolike -gtag=DAPHa -idprefix=DAPHa_G -good='mayzebr|human|kfish2|platyfish' -poor='stickleback|medaka|tetraodon' ../names/drosmel16nc.names ../names/dpx7finamd.names ../names/daphmag.names ../names/zebrafish2.names ../names/bemtab16nc.names ../names/guppy14ncbi.names ../names/tribcas16nc.names ../names/human.names daph10omcla_omclgn.tab > daph10omcla_omclgn.consensus_def.txt
# #sysrun: env xml=0 speciesmap=bemtab=Whitefly,dapmaevg14=Daphnia_magna,dpx17evg=Daphnia_pulex,dapgal16tsa=Daphnia_galeata,dapsim17evg=Daphnia_similoides,drosmel16nc=Fruitfly,tribcas16nc=Beetle,guppync1=Guppy,zebrafish3=Zebrafish,human=Human date=20171114 clade=DaphniaInsectFish gtag=DAPHa idprefix=DAPHa_G /home/ux455375/bio/evigene/scripts/omcl/../omcl/genegroupbpo.pl
#....
#______________________
# daph10omcl.spplist
#   13901 bemtab
#   34529 dapgal16tsa
#   28116 dapmaevg14
#   38523 dapsim17evg
#   28496 dpx17evg
#   13916 drosmel16nc
#   22914 guppync1
#   39357 human
#   12861 tribcas16nc
#   26247 zebrafish3
#........
# arp8daph.spplist
#   13901 bemtab
#   29127 dapmaevg14
#   33040 dpx17evg
#   13916 drosmel16nc
#   22914 guppync1
#   12861 tribcas16nc
#   26247 zebrafish3
#..........