2 years, 2 months ago
How do I Export from Softmax Pro to JMP 7?
Softmax Pro from Molecular Devices exports excel files and text files. These can be a hassle to manually import into JMP then stack the data with appropriate labels for 96-well and 384-well microtiter plates. I need a script set up to do these(assuming consistant format coming for Softmax) or a good resource for building my own. I have intermediate skills with Softmax and beginner skills with JMP.
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M$1 Answer
Interesting problem.
JMP 7 supports the import of excel 2007 files using an ODBC driver. This should get the columns etc worked out for you better than just using File/Open
1. have you tried this - you need the ODBC driver. Here is a helpful link:
http://www.jmp.com/support/notes/19/716.html
You can export from Softmax Pro in text from FIle/Export and choosing text. I assume you are using plate format. If you need time format then go to Edit/Preferences and change data export from plate to time. Time is useful for kinetic data
2. If this is not sufficient - and it might not be - then i suggest the following solution. Its going to take you a bit of work but it will be worth it for the amazing amount of customization you will be able to do now and in the future.
- download Python programming language (2.6.5) http://www.python.org/download/
- create a python file to read the text file. E.g. cut and paste the following into a new .py file.
# make sure you save this as a .py file
# E.g. openSPfile.py
import os # allows us to use functions from eth os package
#open the file and read it
def read_SP_file(filename):
if os.path.exists(filename):
inf = open(filename, 'r')
# lets make a nicely named output filename
filedata = os.path.splitext(os.path.abspath(filename))
outfilename = filedata0+"_processed"+ filedata1
outf = open(outfilename, 'w')
# ready to read the data and write out too.
# read all th elines in one go
line_list = inf.readlines()
for line in line_list:
# OK now each line from the file is in line
# so do what you need to do to it here
# lets just print it so you can see what it is
data = line.split(" ")
print data
newline = ''
for d in data:
print d
newline = newline = d + ","
newline = newline + "\n" # an end of line character
# now write out that line
outf.write(newline)
else:
print "File: %s cannot be found" % os.path.abspath(filename)
# This tells python to execute the above functionwhen the file is executed.
# Hit F5 if in IDLE to run it.
if __name__ == '__main__':
#read_SP_file(sys.argv1))
read_SP_file("C:your full filename")
That file will read the file defined in the last statement and then write it back out again separated by commas.
When you have python installed this file will be displayed in IDLE a simple development program that looks like a version of notepad. The program can be run from in there using F5 or choosing Run from the menu.
Add code in the middle section to edit the incoming data and add headings or whatever you need to make it suitable for excel to read.
The text has had its indenting removed. So here is a screenshot of the program. Indent it the same as in this picture.
JMP 7 supports the import of excel 2007 files using an ODBC driver. This should get the columns etc worked out for you better than just using File/Open
1. have you tried this - you need the ODBC driver. Here is a helpful link:
http://www.jmp.com/support/notes/19/716.html
You can export from Softmax Pro in text from FIle/Export and choosing text. I assume you are using plate format. If you need time format then go to Edit/Preferences and change data export from plate to time. Time is useful for kinetic data
2. If this is not sufficient - and it might not be - then i suggest the following solution. Its going to take you a bit of work but it will be worth it for the amazing amount of customization you will be able to do now and in the future.
- download Python programming language (2.6.5) http://www.python.org/download/
- create a python file to read the text file. E.g. cut and paste the following into a new .py file.
# make sure you save this as a .py file
# E.g. openSPfile.py
import os # allows us to use functions from eth os package
#open the file and read it
def read_SP_file(filename):
if os.path.exists(filename):
inf = open(filename, 'r')
# lets make a nicely named output filename
filedata = os.path.splitext(os.path.abspath(filename))
outfilename = filedata0+"_processed"+ filedata1
outf = open(outfilename, 'w')
# ready to read the data and write out too.
# read all th elines in one go
line_list = inf.readlines()
for line in line_list:
# OK now each line from the file is in line
# so do what you need to do to it here
# lets just print it so you can see what it is
data = line.split(" ")
print data
newline = ''
for d in data:
print d
newline = newline = d + ","
newline = newline + "\n" # an end of line character
# now write out that line
outf.write(newline)
else:
print "File: %s cannot be found" % os.path.abspath(filename)
# This tells python to execute the above functionwhen the file is executed.
# Hit F5 if in IDLE to run it.
if __name__ == '__main__':
#read_SP_file(sys.argv1))
read_SP_file("C:your full filename")
That file will read the file defined in the last statement and then write it back out again separated by commas.
When you have python installed this file will be displayed in IDLE a simple development program that looks like a version of notepad. The program can be run from in there using F5 or choosing Run from the menu.
Add code in the middle section to edit the incoming data and add headings or whatever you need to make it suitable for excel to read.
The text has had its indenting removed. So here is a screenshot of the program. Indent it the same as in this picture.
images:
You can leave an optional "tip" with Mahalo's virtual currency, Mahalo Dollars. If you are asking a difficult question that might require some research, or if you'd like a wide variety of feedback, a higher tip often leads to more answers to your question.
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