Stringtie prepDE.py Error line 32

Question

[bryce.kirby]

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

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[cpak1981]

What is the full path to /SH-11/SH-11.gtf?

Answer 1

[cpad0112]

did you check your python version? I guess prep_de is in python2.7. Try python2.7 and add "." (eg. ./SH-12/SH-12.gtf instead of /SH-12/SH-12.gtf) before gtf path if you are in current directory or add correct path to gtf file.

This worked for me (execution copy/pasted):

$ python2.7 ./prepDE.py -i sample.txt 
0 sample2
1 sample3
2 sample4
3 sample5
4 sample6
5 sample7
6 sample8
7 sample9

with python 3.6:

$ python ./prepDE.py -i sample.txt 
  File "./prepDE.py", line 32
    print "Error: Text file with sample ID and path invalid (%s)" % (line.strip())
                                                                ^
SyntaxError: invalid syntax

input:

$ ls
    prepDE.py  sample.txt  SH-12  SH-13  SH-14  SH-15  SH-16  SH-17  SH-18  SH-19

sample list:

$ cat sample.txt 
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

directory structure post execution:

$ tree .
.
├── gene_count_matrix.csv
├── prepDE.py
├── sample.txt
├── SH-12
│   └── SH-12.gtf
├── SH-13
│   └── SH-13.gtf
├── SH-14
│   └── SH-14.gtf
├── SH-15
│   └── SH-15.gtf
├── SH-16
│   └── SH-16.gtf
├── SH-17
│   └── SH-17.gtf
├── SH-18
│   └── SH-18.gtf
├── SH-19
│   └── SH-19.gtf
└── transcript_count_matrix.csv

8 directories, 12 files

[bryce.kirby]

Thank you so much!!! Changing the version of python worked! I really appreciate it, this had me stuck for a whole day.