jbloomlab / codontilingprimers Goto Github PK

@adingens The new changes to the script look good. I streamlined an updated the README file to more clearly describe how the program now works. Can you check that this README is correct, and if so close this issue?

My laboratory is based at the University of Colorado and investigates various aspects of arbovirus infection and immunity. Based in part on some of your work, we are developing a chikungunya virus deep mutational scanning project, and we have encountered some issues generating the primer sequences for codon mutagenesis. I’m hoping you might be able to help us. I have outlined the issues below. We are not sure why these errors occur. We are running Python 3.7.3 and we are not aware of issues with the system, but honestly, we are not highly experienced with the use of Python scripts-still learning. Any insight would be greatly appreciated!

Best, Tem

We went to your GitHub site, downloaded the folder, and unzipped the files (see below):

test@breck-super1:/Tools$ unzip CodonTilingPrimers-master.zip
Archive: CodonTilingPrimers-master.zip
24dd336
creating: CodonTilingPrimers-master/
extracting: CodonTilingPrimers-master/.gitignore
inflating: CodonTilingPrimers-master/EN72-HA.txt
inflating: CodonTilingPrimers-master/EN72-HA_primers.txt
inflating: CodonTilingPrimers-master/HughSchematic.pdf
inflating: CodonTilingPrimers-master/JesseLabNotes.pdf
inflating: CodonTilingPrimers-master/LICENSE
inflating: CodonTilingPrimers-master/README.rst
inflating: CodonTilingPrimers-master/create_primers.py

We attempted to access the help file:

test@breck-super1:/Tools/CodonTilingPrimers-master$ python create_primers.py -h
File "create_primers.py", line 234
print "Read a sequence of length %d from %s:\n%s" % (len(sequence), sequencefile, sequence)
^
SyntaxError: invalid syntax

We also tried to run the example:

test@breck-super1:/Tools/CodonTilingPrimers-master$ python create_primers.py EN72-HA.txt EN72 1 En72-HA_primers.txt
File "create_primers.py", line 234
print "Read a sequence of length %d from %s:\n%s" % (len(sequence), sequencefile, sequence)
^
SyntaxError: invalid syntax