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 #
#########################################
