refact: Try handling bars in IDs

dalmolingroup · Sep 29, 2024 · 5efc0b4 · 5efc0b4
1 parent 37f73aa
commit 5efc0b4
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Showing 2 changed files with 6 additions and 0 deletions.
diff --git a/bin/gen_tx2gene.r b/bin/gen_tx2gene.r
@@ -26,6 +26,9 @@ txdf <- AnnotationDbi::select(
 tab <- table(txdf$GENEID)
 txdf$ntx <- tab[match(txdf$GENEID, names(tab))]
 
+txdf$TXNAME <- gsub("\\.*", "",  txdf$TXNAME)
+txdf$GENEID <- gsub("\\.*", "",  txdf$GENEID)
+
 tx2gene <- data.frame(
     tx = txdf$TXNAME,
     gene = txdf$GENEID

diff --git a/bin/tximport.r b/bin/tximport.r
@@ -20,6 +20,7 @@ txi_gene <- tximport(
     type = "kallisto",
     tx2gene = tx2gene,
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )
 
@@ -28,6 +29,7 @@ txi_tx <- tximport(
     type = "kallisto",
     txOut = TRUE,
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )
 
@@ -37,6 +39,7 @@ txi_tx_scaled <- tximport(
     txOut = TRUE,
     countsFromAbundance = "scaledTPM",
     ignoreTxVersion = TRUE,
+    ignoreAfterBar = TRUE,
     dropInfReps=TRUE
 )