O'Connor-Chung submission#2
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| rm *.hmm | ||
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| cat *.tbl | grep -v "#" | awk '{print $1 = substr($1, length($1)-3, length($1)), $3, $5}' > hmmOut.txt |
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Very efficient and generalizable! nice!
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good job. another approach could be:
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library(stringr)
inFile=scan("motifsort.fasta",sep="\n",what=character())
motif1=file("motif1.fasta",open="w")
motif2=file("motif2.fasta",open="w")
other=file("nomotif.fasta",open="w")
for(i in 1:length(inFile)){
if(str_detect(inFile[i],">")){
seqID=inFile[i]
}else{
if(str_detect(inFile[i],"AKKPRVZE")){
writeLines(seqID,motif1)
writeLines(inFile[i],motif1)
}else if(str_detect(inFile[i],"AAQWWRNYGG")){
writeLines(seqID,motif2)
writeLines(inFile[i],motif2)
}else{
writeLines(seqID,other)
writeLines(inFile[i],other)
}
}
}
close(motif1)
close(motif2)
close(other)
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