PERL Beginners - HELP....counting sequences and outputting to Excel

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HELP....counting sequences and outputting to Excel

Captairave

2006-10-11, 10:47 am

Im very new to this and have been thrown in at the deep end....basically I have data in this format (FASTA)...

>seq001
ATTTTCCCCCCGGTTTT
>seq002
TTTGGATTACCTA
>seq003
TTTGAAACCCTTGGTT

I have managed to set up a program that counts the total number of bases (A,T,C,G) and outputs to a CSV file, placing the total for each base in a different cell. What I need to do now is count the bases for each individual sequence and output the result to excel. So basically I will have sequence number/name, number of A's in the sequence, number of T's in the sequence etc....then perl will need to do this for the next sequence and so on. Notice that each sequence line always starts with a >

Thanks for any help you can give!!

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