Thanks for the scripting tips!

I have a 'counting' issue which I need to quickly resolve. A typical sequence input file (5 - 700 bases) looks like :

AGTAGTCGATCATNATANCTANTACNACTACTAACTATGCTAGNNAATATAAAAAAAAANAAA

I have over 500 files, named *.seq. I would like to create a script which :

a. runs through all the files,

b. counts the length of the 'poly A' tail (defined as the longest stretch containing either A or N)

c. sends the output to a file, eg.

25 1.seq

87 2.seq

13 3.seq

Example valid poly A tails (I desire the full length reported) :

AAAANANANANAAANNAAAAAA
AAAAAAAAAAAAAA
NNNNNNNNNNNNN
AAANNNNNNNNNNNAAAAAAAAA

Thank you so much for your expertise!

In reply to Count Occurrences of a string by MiamiGenome

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