Diffmode demo problems

[tele-med]

Hi all, I'm trying to run the demo code found here: https://xpore.readthedocs.io/en/latest/quickstart.html I'm able to create the dataprep folders correctly for both WT and KO datasets (I have the "--- SUCCESSFULLY FINISHED ---" string in data.log). Anyway, when I run the next command of the tutorial xpore diffmod --config Hek293T_config.yml I get this error:

C:\Users\Sasha\demo>xpore diffmod --config Hek293T_config.yml Using the signal of unmodified RNA from C:\Users\Sasha\AppData\Local\Programs\Python\Python310\lib\site-packages\xpore-2.1-py3.10.egg\xpore\diffmod\model_kmer.csv 2 ids to be testing ... Traceback (most recent call last): File "C:\Users\Sasha\AppData\Local\Programs\Python\Python310\Scripts\xpore-script.py", line 33, in sys.exit(load_entry_point('xpore==2.1', 'console_scripts', 'xpore')()) File "C:\Users\Sasha\AppData\Local\Programs\Python\Python310\lib\site-packages\xpore-2.1-py3.10.egg\xpore\scripts\xpore.py", line 67, in main options.func(options) File "C:\Users\Sasha\AppData\Local\Programs\Python\Python310\lib\site-packages\xpore-2.1-py3.10.egg\xpore\scripts\diffmod.py", line 169, in diffmod data_dict[(condition_name,run_name)] = ujson.loads(json_str) # A data dict for each gene. ujson.JSONDecodeError: Trailing data

How can I solve this problem? Thanks a lot in advance SF

[yuukiiwa]

Hi @tele-med,

This may be a problem for Windows, where the new line character is \r\n instead of \n. What you can do is to replace all the \n of your data.json file with \r\n. Here is an example script of how you can do it:

original_json=open('data.json','r')
new_json=open('new_data.json','w')
for ln in original_json:
    new_json.write(ln.strip()+'\r\n')
new_json.close()

Then you would want to rename your new_data.json to data.json to run xpore diffmod.

Thanks!

Best wishes, Yuk Kei

[Ibisanmi1]

Good day, i'm encountering same error. PS C:\Users\DELL\Desktop\python\RNAmodifications\demo\data\HEK293T-METTL3-KO-rep1\dataprep> original_json=open('data.json','r')

new_json=open('new_data.json','w') for ln in original_json: new_json.write(ln.strip()+'\r\n') new_json.close() At line:3 char:4

• for ln in original_json:
• ~ Missing opening '(' after keyword 'for'. At line:4 char:29
• new_json.write(ln.strip()+'\r\n')
• ~ An expression was expected after '('. At line:5 char:16
• new_json.close()
• ~ An expression was expected after '('.
• CategoryInfo : ParserError: (:) [], ParentContainsErrorRecordException
• FullyQualifiedErrorId : MissingOpenParenthesisAfterKeyword

[yuukiiwa]

Hi @Ibisanmi1,

Please save the following as a python script change_dataprep_json.py:

original_json=open('data.json','r')
new_json=open('new_data.json','w')
for ln in original_json:
    new_json.write(ln.strip()+'\r\n')
new_json.close()

Then you call the script from command line:

python change_dataprep_json.py

Thanks!

Best wishes, Yuk Kei