Hello,
I am working on inputting my data from stringtie -e-B to then perform differential expression on my samples using Deseq. I am running the command 'python prepDE.py -i sample_list.txt' but keep getting this error :
python ./prepDE.py -i /scratch/exp_radonc/bkirby/scratch/mazur_lab_scratch/mazur_lab/SH-ERK5_RNA480/ballgown/sample_list.txt
File "./prepDE.py", line 32
print "Error: Text file with sample ID and path invalid (%s)" % (line.strip())
^
SyntaxError: invalid syntax
my sample_list file looks like this :
[bkirby@cnode241 ballgown]$ head sample_list.txt
sample1 /SH-11/SH-11.gtf
sample2 /SH-12/SH-12.gtf
sample3 /SH-13/SH-13.gtf
sample4 /SH-14/SH-14.gtf
sample5 /SH-15/SH-15.gtf
sample6 /SH-16/SH-16.gtf
sample7 /SH-17/SH-17.gtf
sample8 /SH-18/SH-18.gtf
sample9 /SH-19/SH-19.gtf
and subsequent directories containing the .gtf files in my working directory like this:
[bkirby@cnode241 ballgown]$ ls
SH-11 SH-12 SH-13 SH-14 SH-15 SH-16 SH-17 SH-18 SH-19 prepDE.py prepDE_multi.py sample_list.txt sample_lst.txt
Here is what each "SH" directory contains inside it:
[bkirby@cnode241 SH-11]$ ls
SH-11.gtf e2t.ctab e_data.ctab i2t.ctab i_data.ctab t_data.ctab
Has anyone come across this issue or know any quick fixes? Am I missing something here with the way I'm setting up the command?
Here is the section of code that is giving me an error:
samples = [] # List of tuples. If sample list, (first column, path). Else, (subdirectory name, path to gtf file in subdirectory)
if (os.path.isfile(opts.input)):
# gtfList = True
try:
fin = open(opts.input, 'r')
for line in fin:
if line[0] != '#':
lineLst = tuple(line.strip().split())
if (len(lineLst) != 2):
print "Error: Text file with sample ID and path invalid (%s)" % (line.strip())
exit(1)
Any help is appreciated!
Thanks so much,
Bryce
Please use the formatting bar (especially the![Formatting bar](http://i66.tinypic.com/33kdnjt.png)
code
option) to present your post better. I've done it for you this time.What is the full path to
/SH-11/SH-11.gtf
?