From bd907ed8c20728409bcc9fe67c1c244cd5c97536 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 17 May 2019 18:41:45 +0200
Subject: [PATCH] ...
---
mix.R | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/mix.R b/mix.R
index 8649b49..3d53e96 100644
--- a/mix.R
+++ b/mix.R
@@ -30,12 +30,17 @@ rmbmix.gen_comp_list<-function(src_fn,dest_fn) {
## Names
nms<-if ("PREFERRED_NAME" %in% names(df)) df$PREFERRED_NAME else df$Name
if (is.null(nms)) stop("Unable to read compound names from the input compound list.")
+
## SMILES
haha<-df$SMILES
- if (is.null(haha)) stop("Unable to read SMILES from the input compound list.")
sz<-length(haha)
- outdf<-data.frame(Name=nms,SMILES=haha,ID=1:sz,RT=rep("",sz),CAS=rep("",sz))
- write.csv(outdf,file=dest_fn,row.names=F)
+
+ ## CAS
+ casvals<-rep(NA,sz) #if ("CASRN" %in% names(df)) df$CASRN else rep(NA,sz)
+ if (is.null(haha)) stop("Unable to read SMILES from the input compound list.")
+
+ outdf<-data.frame(ID=1:sz,Name=nms,SMILES=haha,CAS=casvals,RT=rep(NA,sz))
+ write.csv(outdf,file=dest_fn,row.names=F,na="")
length(nms)
}
@@ -71,5 +76,5 @@ rmbmix.single<-function(fn_data,sett_alist,fn_cmpd_list,wd,mode,readMethod="mzR"
w <-msmsRead(w,filetable=fn_table,readMethod="mzR",mode=mode)
if (!dir.exists(archdir)) dir.create(archdir)
fn_arch<-file.path(archdir,paste(fn_data,".archive",sep=''))
- msmsWorkflow(w, mode=mode, steps=c(2:8),archivename=fn_arch)
+ msmsWorkflow(w, mode=mode, steps=2,archivename=fn_arch)
}
--
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