Hi
I'm processing sequencing data trying to collapsing the locations of each
unique sequence and write the results to a file (as storing that in a table
will require 10GB mem at least)
so I wrote a function that, given a sequence id, provide the needed line to
be stored
library(doMC) # load library
registerDoMC(12) # assign the Number of CPU


fileConn<-file(paste(fq_file,"_SeqID.txt",sep=""),open = "at") # open
connection
writeLines(paste("ReadID","Freq","Seq","LOC_UG","Nb_UG_Seq",sep="\t"),
fileConn) # write header
foreach(i=1:length(uniq.Seq)) %dopar% # for eqch unique sequence
{
writeLines(paste(gettable1(uniq.Seq[i]),collapse="   "), fileConn) #write
the the results line
}
close(fileConn)

the code excute well, but the problem is that some lines are wired:
The  header and lot of lines are ok :
ReadID    Freq    Seq    LOC_UG    Nb_UG_Seq
HWI-EA332_0036:5:16:9530:21025#ATGC/1   XXXXXXXXXXXXXXXXXXXX  2
XXXXX_10130:489:+,XXXXX_10130:489:+   2
HWI-EA332_0036:5:117:6674:4940#ATGC/1   XXXXXXXXXXXXXXXXXXXX   1
XXXXX:432:-,XXXXX:432:-   2
HWI-EA332_0036:5:62:15592:7375#ATGC/1   XXXXXXXXXXXXXXXXXXXX   2
XXXXX_22660:253:+,XXXXX_22660:253:+   2
HWI-EA332_0036:5:110:14349:8422#ATGC/1   XXXXXXXXXXXXXXXXXXXX   4
XXXXX_13806:399:+,XXXXX_13806:399:+,XXXXX_27263:481:+,XXXXX_27263:481:+   4
other looks wired
HWI-EA332_0036:5:17:1400ReadID    Freq    Seq    LOC_UG    Nb_UG_Seq
HWI-EA332_0036:5:61:7734:4201ReadID    Freq    Seq    LOC_UG    Nb_UG_Seq
HWI-EA332_0036:5:117:5361:10666#ATGReadID    Freq    Seq    LOC_UG
Nb_UG_Seq
HWI-EA332_0036:5:115:7421:20664#ATGC/1   GATCReadID    Freq    Seq
LOC_UG    Nb_UG_Seq
HWI-EA332_0036:5:175:95:-   2
HWI-EA332_0036:5JCVI_35536:444:+   2
XXXXXXXXX   1  XXXXX_22484:571:-,XXXXX_22484:571:-   2

Is this due to the fact that one process start to write prior the other has
finished ?
Is there a way to solve this problem ?
Any suggestions would be greatly appreciated.
Thanks and have a nice day.


Best,
Ramzi TEMANNI
http://www.linkedin.com/in/ramzitemanni

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