gpertea
prepDE.py Error: Text file with sample ID and path invalid ()
Hi,
I was trying to extract count matrix by prep.DE, but I was getting the error.
Error: Text file with sample ID and path invalid ()
This is the command I used,
$ python prepDE.py -i sample_lst_2M.txt -g ./gene_count_matrix_2M.csv -t ./transcript_count_matrix_2M.csv
This is how the sample_lst_2M.txt looks like.
Ctrl1 /home/IrisC/Hisat2/Stringtie/S0311-4h-c_L1/Ctrl1.gtf
Ctrl2 /home/IrisC/Hisat2/Stringtie/S0316-4h-c_L1/Ctrl2.gtf
2M1B1 /home/IrisC/Hisat2/Stringtie/S0311-4h-2_L1/2M1B1.gtf
2M1B2 /home/IrisC/Hisat2/Stringtie/S0316-4h-2_L1/2M1B2.gtf
The directory structure:
$ tree -L 3 /home/IrisC/Hisat2/Stringtie/
Stringtie/
├── DE
│ └── sample_lst_2M.txt
├── S0311-4h-2_L1
│ ├── 2M1B1.gtf
│ ├── e2t.ctab
│ ├── e_data.ctab
│ ├── i2t.ctab
│ ├── i_data.ctab
│ ├── S0311-4h-2_L1_gene_abund.tab
│ └── t_data.ctab
├── S0311-4h-c_L1
│ ├── Ctrl1.gtf
│ ├── e2t.ctab
│ ├── e_data.ctab
│ ├── i2t.ctab
│ ├── i_data.ctab
│ ├── S0311-4h-c_L1_gene_abund.tab
│ └── t_data.ctab
├── S0316-4h-2_L1
│ ├── 2M1B2.gtf
│ ├── e2t.ctab
│ ├── e_data.ctab
│ ├── i2t.ctab
│ ├── i_data.ctab
│ ├── S0316-4h-2_L1_gene_abund.tab
│ └── t_data.ctab
├── S0316-4h-c_L1
│ ├── Ctrl2.gtf
│ ├── e2t.ctab
│ ├── e_data.ctab
│ ├── i2t.ctab
│ ├── i_data.ctab
│ ├── S0316-4h-c_L1_gene_abund.tab
│ └── t_data.ctab
└── Read.md
I have tried executing prepDE.py by the following command but it didn't fix the error.
$ python2.7 prepDE.py -i sample_lst_2M.txt -g ./gene_count_matrix_2M.csv -t ./transcript_count_matrix_2M.csv
Does anyone know how to fix this? Any suggestion would be appreciated.
Thanks, Iris
Hi, I faced a similar issue. I found that there was an empty line at the bottom of the .txt file. Removing that empty line fixed my problem. You can check your txt file.
Hi, I faced a similar issue. I found that there was an empty line at the bottom of the .txt file. Removing that empty line fixed my problem. You can check your txt file.
Yes, I had the same problem. Thanks very much!!!
