Seqff.r script is giving error while running

Question

[smrutimayipanda]

Hi,

I am getting error while running this code:

if( datatype =="sam" )
{
#dat <- read.table(pipe(paste("cut -f3,4",file("S_57_IonXpress_001.sam"),sep=" ")), header=FALSE,colClasses= c("character","integer"))
dat <- read.table(file("stdin"), header=FALSE,colClasses= c("character","integer"))
colnames(dat)=c("refChr","begin")


dat=dat[dat$refChr!="*" & dat$refChr!="chrM" ,]
binindex = ifelse((dat$begin%%50000)==0,floor(dat$begin/50000)-1,floor(dat$begin/50000))

fastbincount = table(paste(dat$refChr,binindex, sep="_"))
newtemp=as.data.frame(matrix(NA, ncol=2, nrow=length(fastbincount)))
newtemp[,1]=paste(names(fastbincount))
newtemp[,2]=as.numeric(paste(fastbincount))
colnames(newtemp)=c("binName","counts")

}
if( datatype =="counts" )
{
newtemp <- read.table(file.name, header=FALSE,colClasses= c("character","integer"))
colnames(newtemp)=c("binName","counts")
}

bininfo = merge(bininfo, newtemp, by="binName",all.x=T)
bininfo=bininfo[order(bininfo$binorder),]

error is:

Error in if (datatype == "sam") { : missing value where TRUE/FALSE needed. 
Error in if (datatype == "counts") { : 
  missing value where TRUE/FALSE needed.
Error in as.data.frame(y) : object 'newtemp' not found

Please tell me how would I rectify this error? I couldn't understand actually. Thanks in advance

[zx8754]

Errors are clear: datatype is NA. newtemp object doesn't exist.

[4galaxy77]

Please format your code by highlighting it and pressing the Code Sample button. Also that is a lot of code - I don't think anyone wants to step through all that, especially without a reproducible example. Could you try and locate the specific line the error occurs? Thanks.

[smrutimayipanda]

I am getting error in this particular code. Please have a look and help me, if you get the answer.

[smrutimayipanda]

Is there anyone who can help me in this?

[cpad0112]

without example data it is difficult to troubleshoot the code, however working code for loading sam file is here. See if this works for you:

$ cat test.sam 
@HD VN:1.0  SO:unsorted
@SQ SN:test_ref LN:17637
SRR1524970.144283   16  test_ref    1706    255 25M *   00  TGCTGATGAAGCAGAACAACTTTAA   ]YG[^baaaa^W`ab]]````aaba   AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:25 YT:Z:UU
SRR1524970.316478   16  test_ref    1706    255 24M *   00  TGCTGATGAAGCAGAACAACTTTA    `\X_`aaaaaY]``b_aa_aaaaa    AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:24 YT:Z:UU

R code:

> datatype="sam"
> if( datatype =="sam" ){
+     dat=read.table("test.sam",comment.char = "@", header=FALSE)[,c(3,4)]
+     colnames(dat)=c("refChr","begin")
+     
+     
+     dat=dat[dat$refChr!="*" & dat$refChr!="chrM" ,]
+     binindex = ifelse((dat$begin%%50000)==0,floor(dat$begin/50000)-1,floor(dat$begin/50000))
+     
+     fastbincount = table(paste(dat$refChr,binindex, sep="_"))
+     newtemp=as.data.frame(matrix(NA, ncol=2, nrow=length(fastbincount)))
+     newtemp[,1]=paste(names(fastbincount))
+     newtemp[,2]=as.numeric(paste(fastbincount))
+     colnames(newtemp)=c("binName","counts")
+ }
> if( datatype =="counts" ){
+     newtemp <- read.table(file.name, header=FALSE,colClasses= c("character","integer"))
+     colnames(newtemp)=c("binName","counts")
+ }

output:

> newtemp

     binName counts
1 test_ref_0      2

suggestion is to combine two ifs with if else code.

[smrutimayipanda]

Thank you for this code. However, I am pasting the example data:

@RG     ID:10200106485  LB:10200106485  PL:ILLUMINA     PM:HISEQ        SM:10200106485
@PG     ID:bwa  PN:bwa  VN:0.7.17-r1188 CL:bwa mem -Y -M -R @RG\tID:10200106485\tLB:10200106485\tPL:ILLUMINA\tPM:HISEQ\tSM:10200106485 hg19.fa 50_IonXpress_010.fastq
2QC4F:07189:04737       0       chr2    243152517       0       53M     *       0       0       CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA   770762680//)/70793990:;388/88/55*55/58/88388*5/)/6)//   NM:i:0  MD:Z:53 AS:i:53 XS:i:53 RG:Z:10200106485
2QC4F:06025:06043       0       chr2    243152493       0       49M     *       0       0       CCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC       ;;4;;7;:5;;6;:4;:49928;4::28839:3::/55*55/58/5-)-       NM:i:0  MD:Z:49 AS:i:49 XS:i:49 RG:Z:10200106485
2QC4F:02378:12056       0       chr1    10355   0       34M     *       0       0       CCTAACCCTAACCCTAACCCTAACCCTAACCCTA      <7<<7<<4<;4:928:3::1:</57+7:4891//      NM:i:0  MD:Z:34 AS:i:34 XS:i:34 RG:Z:10200106485

[cpad0112]

Pasted data is not in correct example data format (sam).

[smrutimayipanda]

It didnt work for me. It is showing another error.