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fix bug in reporting, bump to 2.2.8
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Matthew MacManes committed Sep 13, 2019
1 parent 0d7f54d commit 4cb41c2
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10 changes: 5 additions & 5 deletions oyster.mk
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Original file line number Diff line number Diff line change
Expand Up @@ -320,10 +320,10 @@ ${DIR}/assemblies/diamond/${RUNOUT}.orthomerged.diamond.txt ${DIR}/assemblies/di
diamond blastx -p $(CPU) -e 1e-8 --top 0.1 -q ${DIR}/assemblies/${RUNOUT}.trinity.Trinity.fasta -d ${MAKEDIR}/software/diamond/swissprot -o ${DIR}/assemblies/diamond/${RUNOUT}.trinity.diamond.txt

${DIR}/assemblies/diamond/${RUNOUT}.unique.trinity.txt ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp75.txt ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp55.txt ${DIR}/assemblies/diamond/${RUNOUT}.unique.transabyss.txt:${DIR}/assemblies/diamond/${RUNOUT}.orthomerged.diamond.txt ${DIR}/assemblies/diamond/${RUNOUT}.transabyss.diamond.txt ${DIR}/assemblies/diamond/${RUNOUT}.spades55.diamond.txt ${DIR}/assemblies/diamond/${RUNOUT}.spades55.diamond.txt ${DIR}/assemblies/diamond/${RUNOUT}.trinity.diamond.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.trinity.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f2 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.trinity.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.spades75.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f2 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp75.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.spades55.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f2 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp55.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.transabyss.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f2 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.transabyss.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.trinity.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f1 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.trinity.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.spades75.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f1 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp75.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.spades55.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f1 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.sp55.txt
awk '{print $$2}' ${DIR}/assemblies/diamond/${RUNOUT}.transabyss.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f1 | sort | uniq | wc -l > ${DIR}/assemblies/diamond/${RUNOUT}.unique.transabyss.txt

#list1 is unique geneIDs in orthomerged
#list2 is unique geneIDs in other assemblies
Expand Down Expand Up @@ -363,7 +363,7 @@ ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt:${DIR}/assemblies/${RUNOUT}.ORP.inte
touch ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt

${DIR}/assemblies/working/${RUNOUT}.unique.ORP.done:${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt
awk '{print $$2}' ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f2 | sort | uniq | wc -l > ${DIR}/assemblies/working/${RUNOUT}.unique.ORP.txt
awk '{print $$2}' ${DIR}/assemblies/${RUNOUT}.ORP.diamond.txt | awk -F "|" '{print $$3}' | cut -d _ -f1 | sort | uniq | wc -l > ${DIR}/assemblies/working/${RUNOUT}.unique.ORP.txt
touch ${DIR}/assemblies/working/${RUNOUT}.unique.ORP.done

${DIR}/quants/${RUNOUT}.ortho.idx:${DIR}/assemblies/${RUNOUT}.ORP.intermediate.fasta
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2 changes: 1 addition & 1 deletion version.txt
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@@ -1 +1 @@
2.2.7
2.2.8

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