diff --git a/oyster.mk b/oyster.mk index d1126cf..c9d7559 100755 --- a/oyster.mk +++ b/oyster.mk @@ -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 @@ -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 diff --git a/version.txt b/version.txt index 5bc1cc4..23a63f5 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -2.2.7 +2.2.8