PhyloSkims/annotate
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Make changes to better detect pseudo genes frameshited and annotate them

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correctly

Former-commit-id: d827908d63149941538e686b48f60a132173cb80
Former-commit-id: 2841c75b415c6c8fa35a6a90e23cf82c3c84408b
This commit is contained in:
Eric Coissac
2016-10-06 10:06:37 -03:00
parent 860cd217d4
commit 16b5e2927d
2 changed files with 69 additions and 23 deletions
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33
detectors/cds/bin/do_exonerate.csh
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@ -150,20 +150,25 @@ endif
#
Notify " running exonerate of $GenoName on $ProtName"
exonerate --model protein2genome \
--percent $PASS1_PERCENT \
--showalignment TRUE \
--showvulgar TRUE \
--showtargetgff TRUE \
--geneticcode $PASS1_GENETIC_CODE \
--minintron $PASS1_MIN_INTRON \
--maxintron $PASS1_MAX_INTRON \
--bestn $PASS1_BESTN \
--frameshift $PASS1_FRAMESHIFT \
--proteinsubmat $PASS1_SUBMAT \
--splice3 $SPLICE3MODEL \
--splice5 $SPLICE5MODEL \
$DbFile $GenoFile > $base.exo.raw
exonerate \
--model protein2genome \
--percent $PASS1_PERCENT \
--showalignment TRUE \
--showvulgar TRUE \
--showtargetgff TRUE \
--geneticcode $PASS1_GENETIC_CODE \
--minintron $PASS1_MIN_INTRON \
--maxintron $PASS1_MAX_INTRON \
--bestn $PASS1_BESTN \
--frameshift $PASS1_FRAMESHIFT \
--proteinsubmat $PASS1_SUBMAT \
--splice3 $SPLICE3MODEL \
--splice5 $SPLICE5MODEL \
--refine region \
--refineboundary 5000 \
--singlepass FALSE \
--dpmemory 128 \
$DbFile $GenoFile > $base.exo.raw
CheckAbort 20 "exonerate failure"
#