User: Bastien Hervé
Bastien Hervé • 560
- Reputation:
- 560
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- Location:
- Limoges, CBRS, France
- Last seen:
- 2 hours ago
- Joined:
- 1 year, 2 months ago
- Email:
- b****************@orange.fr
Posts by Bastien Hervé
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... If you just want the lcpm's numbers for genes
write.csv(highly_variable_lcpm, row.names=TRUE, file = "highly_variable_lcpm_genes.csv")
If you have gene names in your `y2` and you want to export them too. You need to join `y2` and `highly_variable_lcpm`.
Then make your gene names column as `ro ...
written 2 days ago by
Bastien Hervé • 560
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... I link you this to insert an image to a Biostars post : https://www.biostars.org/p/309884/
I got that your `highly_variable_lcpm` indexes are your genes.
What do you have in `y2` ? Is it the correlation between `highly_variable_lcpm` index and gene names ?
Could you give the result of `typeof(y2) ...
written 2 days ago by
Bastien Hervé • 560
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... Could you give us the result of `head(y2, 5)` and `head(highly_variable_lcpm, 5)` please ...
written 2 days ago by
Bastien Hervé • 560
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... If you didn't see it yet, you can try this : https://www.biostars.org/p/50882/ ...
written 2 days ago by
Bastien Hervé • 560
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... Nice !
Some explanation from here : https://github.com/kennethreitz/legit/issues/212
kapinga's comment :
> dict.keys() returns a generator in Python 3, but in Python 2, dict.keys() returns a list. ...
written 3 days ago by
Bastien Hervé • 560
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... Yes (Aaaaah Biostars... I can't just answer "yes" because my message is too short, so here some text...) ...
written 3 days ago by
Bastien Hervé • 560
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... Did that solve your issue ? ...
written 3 days ago by
Bastien Hervé • 560
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... Hard without data so I can't test what i'll give you.
Modify :
for genomicKey in self.alignement_dic.keys():
By :
for genomicKey in list(self.alignement_dic): ...
written 3 days ago by
Bastien Hervé • 560
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... Why downgrade your python version ?
Actually that could be great if you could show your code till line 77. Or at least between line 70 and line 80
> File "overlapping_reads.py", `line 77`, in query_positions for genomicKey in self.alignement_dic.keys(): RuntimeError: dictionary changed size duri ...
written 3 days ago by
Bastien Hervé • 560
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... Your `overlapping_reads.py` code would be helpful :) Thanks
And your python version. ...
written 3 days ago by
Bastien Hervé • 560
Latest awards to Bastien Hervé
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For A: fastq parsing inefficiencies with python
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For A: fastq parsing inefficiencies with python
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created 100 posts.
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For A: fastq parsing inefficiencies with python
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For A: fastq parsing inefficiencies with python
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created an answer that has been accepted.
For A: fastq parsing inefficiencies with python
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For A: fastq parsing inefficiencies with python
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