Any tutorial in order to run your script?
Closed this issue · 6 comments
enriiquee commented
Hello. Is there any tutorian to run your script with my own samples? Thank you
ShahriyariLab commented
Hello,
There is a tutorial up on the github (full_tutorial.py) that can be run. The default setting for the tutorial is to download data from CBio portal (line no 50) but if you would like to use your own data you can comment out this line and instead un-comment line no 55, and replace the path to the file with your own data.
This is the line no 55:
55 # rna = td.read_rna_file(data_loc+'coadred_data_RNA_Seq_v2_expression_median.txt')
you can change it to
rna = td.read_rna_file(your_path+'name_of_your_file')
… On Mar 5, 2021, at 6:23 AM, Enrique Perez ***@***.***> wrote:
Hello. Is there any tutorian to run your script with my own samples? Thank you
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enriiquee commented
Thanks!
But I have a bug. When I try to run your example, I got this report:
ileNotFoundError: [Errno 2] No such file or directory: '~/sig_matrix_tutorial/ensembl_version_GSE115978.txt'
Do you know where can I download that file? Thanks again.
ShahriyariLab commented
Hello,
The information on how to download these files is included right at the beginning of the signature matrix section of the tutorial file, in the commented block that runs from lines 61-68 (and is pasted here below). You then need to change the path in line 74 to point to where you have downloaded and saved the data.
However, we apologize that there was a small typo in the URL listed - we've since corrected this!
"""
The following section walks through an example of generating a signature matrix from raw
data files. The data used in this tutorial are single cell profiles from the Gene
Expression Omnibus (GEO) repository. They are available to download on the NCBI website,
as well as from our GitHub page, at:
https://github.com/ShahriyariLab/TumorDecon/tree/master/TumorDecon/data/sig_matrix_tutorial <https://github.com/ShahriyariLab/TumorDecon/tree/master/TumorDecon/data/sig_matrix_tutorial>
"""
################################################################################
######## BEGIN: Building a signature matrix from raw data files ###############
################################################################################
# Define location where data is downloaded:
single_cell_data_loc = "sig_matrix_tutorial/" # CHANGE THIS to where you have downloaded the data
… On Mar 8, 2021, at 6:19 AM, Enrique Perez ***@***.***> wrote:
Thanks!
But I have a bug. When I try to run your example, I got this report:
ileNotFoundError: [Errno 2] No such file or directory: '~/sig_matrix_tutorial/ensembl_version_GSE115978.txt'
Do you know where can I download that file? Thanks again.
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enriiquee commented
Yes!, I checked that link, but there isn't a GSE115978.txt file. This is the file that is giving me an error.
ShahriyariLab commented
Sorry, the problem was about GitHub’s size limit. Here you can find all files: https://drive.google.com/file/d/167R7Sw9ZxLzY0pZCr0IYa6YUd2y3CHjZ/view?usp=sharing <https://drive.google.com/file/d/167R7Sw9ZxLzY0pZCr0IYa6YUd2y3CHjZ/view?usp=sharing>
… On Mar 8, 2021, at 12:53 PM, Enrique Perez ***@***.***> wrote:
Yes!, I checked that link, but there isn't a GSE115978.txt file. This is the file that is giving me an error.
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ShahriyariLab commented
Thank you so much!
On Mar 18, 2022, at 6:50 PM, raronow ***@***.******@***.***>> wrote:
Closed #1<#1>.
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