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guillemylla / Crickets_Genome_Annotation

Gennome annotation scripts for the crickets Gryllus bimaculatus and Laupala kohalensis.
GNU General Public License v3.0
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Python script not found #2

Open Ryuto-sanno opened 2 years ago

Ryuto-sanno commented 2 years ago

Hello,

I am having issues running your analysis steps. When running Analysis (~/CpGoe/1_Count_CpGoe.ipynb), you used part of a python script (~/dn_ds/Dn_Ds_CodeML.ipynb) to extract the longest CDS per gene, so I looked for it. However, I could not find that python script.

Perhaps it is because the version of the directory is newer.

Where can I find the original python script?

Thank you. Guillem Ylla

guillemylla commented 2 years ago

Hi Ryuto-sanno,

This step was simply to get the longest isoform per gene. I had all the genes in a SQL database, and then I could retrieve the longest transcript or peptide per gene. You can find the code here: https://github.com/guillemylla/Gryllus_genome_annotation/blob/master/GBI_Genome_v3/Protein_coding_genes/2-GbiV3_Functional_Annotation.md

Ryuto-sanno commented 2 years ago

Thanks for your reply!

I almost understood your analysis step. But, I cannot check the URL shared by you....