[Bioperl-l] Scripting help to identify adaptors count in reads

Giorgio C casaburi at ceinge.unina.it
Fri Nov 11 07:21:29 EST 2011


Thanks everybody for answering me so soon !!! Probably another way may be:

perl -ne '$count{s/N+//g}++ if /^[^>]/;END{for $i (keys %count){print
"$count{$i} have $i ADAPTOR\n";}}' myFile.fasta > result.txt 


and/or with 'nawk':

nawk -F'[N]+' '/^[^>]/{a[NF-1]++}END{for(i in a) print a[i] " have " i "
ADAPTOR"}' myFile.fasta > result.txt 

They give the same result. If you will have this problem try these, work
good !!!

Still Thanks to all,

Giorgio



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