User: Bastien Hervé

gravatar for Bastien Hervé
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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

<prev • 123 results • page 1 of 13 • next >
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Comment: C: how to give name of genes instead of unique ID created by "lcpm" ?
... 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 Hervé560
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Comment: C: how to give name of genes instead of unique ID created by "lcpm" ?
... 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 Hervé560
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Comment: C: how to give name of genes instead of unique ID created by "lcpm" ?
... Could you give us the result of `head(y2, 5)` and `head(highly_variable_lcpm, 5)` please ...
written 2 days ago by Bastien Hervé560
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Comment: C: Where can you find whole genome SNP map data?
... If you didn't see it yet, you can try this : https://www.biostars.org/p/50882/ ...
written 2 days ago by Bastien Hervé560
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Comment: C: RuntimeError: dictionary changed size during iteration
... 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 Hervé560
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Comment: C: RuntimeError: dictionary changed size during iteration
... 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 Hervé560
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Comment: C: RuntimeError: dictionary changed size during iteration
... Did that solve your issue ? ...
written 3 days ago by Bastien Hervé560
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Comment: C: RuntimeError: dictionary changed size during iteration
... 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 Hervé560
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Answer: C: RuntimeError: dictionary changed size during iteration
... 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 Hervé560
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Comment: C: RuntimeError: dictionary changed size during iteration
... Your `overlapping_reads.py` code would be helpful :) Thanks And your python version. ...
written 3 days ago by Bastien Hervé560

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