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Signal strength from ABI trace files?

Stephen R. Lasky srlasky at cellworks.mbt.washington.edu
Thu Aug 12 04:01:36 EST 1999


Nirav Merchant wrote:
> 
> Please download the tar file ..it includes the source code and should compile
> on any *NIX platform ..it includes the binary for linux ...
> ftp://public.arl.arizona.edu/pub/sware/abibasecalls.tar
> It can be tailored to ouput anything from the abi trace file ..this version
> outputs the signal strength. [ I have one which outputs data for excel to
> create a trace]
> 
> Typical output:
>  ./abibasecalls 12_1az_tmp_17303.CRO
> G:76 A:68 T:63 C:88
> 
> The program was based on the skeletal code provided by Peter Kline.
> 

I compiled this prgm on my linux box and it works nicely, however it
only does one file at a time (in my hands anyway).  If you want to look
at a lot of files at the same time, you can apply this shell script to
automate the output of the c progrm.  Just compile the abibasecalls
prgm, cut and paste the script using any wp (like vi?) into a file named
batchSigStrength.sh (for instance), change the permissions so you can
execute it, change the paths to reflect your paths, and try running it:



---------------cut below this line--------------------------

#!/bin/sh

###########################################################
#       Script to extract abi base signals from abi files  
#	using a c program suggested by Nirav Merchant.
#	That program takes the abi chromat file
#	and extracts the base signal numbers from it.
#	Problem is that it only does one file at a time.
#	The purpose of this script is to write all the 
#	scores from a directory of chromat files into a single file so it 
#	can be picked up by a spreadsheet and analyzed.
#	first try 990811 srlasky
############################################################
# First copy the script and compiled C program into a dir that you
# have write and execute permissions for (try your home dir)
# change the lines in the script noted below to reflect that address
# change the mod so you can execute both files (chmod 755).
# Then goto  the directory above the dirs that have your chromats
# and run the script /path/to/batchBaseQual.sh
# The script will look for any abi chromat file and run the
# abibasecaller program on it and append the values to 
# the sigStrength.txt file. (remember this is an append, so
# if you run it twice you'll get the same output twice.
# If I was really ambitious, I would parse out all the N:'s
# and bad file remarks, but that would take more time.
#############################################################

# this grep statement is included  to make sure any mac resource
# fork files are not included in the find
	for MATCH in `find . -name "*" | grep -v '.rsrc'`;
		do
# obviously you want to change to the full path to the abibasecalls 
# prgm on your machine
		/path/to/abibasecalls $MATCH >> /path/to/sigStrength`date
'+%y%m%d'`.txt
		done
	echo "done acquiring base strengths"

# Now mail the results to the important people
# this assumes you have mail running on your unix box

mail username at your.domain < "/path/to/sigStrength`date '+%y%m%d'`.txt"


	echo "done mailing"
		
# this should have worked (it did on my box when I filled in the paths)
# if it didn't work, let me know what the stderr output was.
# The easiest way to deal with this data may be to take it into a wp
# do a global search and replace for the G:, A:, T:, C:, and Invalid ABI
file,
# (replace with nothing), replace the spaces with tabs or commas and
import it into
# a spreadsheet.  


----------------------------cut above this line-----------------------
-- 
Stephen R. Lasky, Ph.D.			#
University of Washington		#
Department of Molecular Biotechnology	#
srlasky at u.washington.edu		#
#########################################




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