[BiO BB] Poly A tail length - script help please
Tristan Fiedler
tfiedler at rsmas.miami.edu
Tue Sep 9 17:00:55 EDT 2003
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
of 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 :
AAAANANANANAAANNAAAAAA
AAAAAAAAAAAAAA
NNNNNNNNNNNNN
AAANNNNNNNNNNNAAAAAAAAA
Thank you so much for your expertise!
Tristan
--
Tristan J. Fiedler, Ph.D.
Postdoctoral Research Fellow
NIEHS Marine & Freshwater Biomedical Sciences Center
Rosenstiel School of Marine & Atmospheric Sciences
University of Miami
tfiedler at rsmas.miami.edu
t.fiedler at umiami.edu (alias)
305-361-4626
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