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mortazavilab / swan_vis

A Python library to visualize and analyze long-read transcriptomes
https://freese.gitbook.io/swan/
MIT License
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relation between splicing in/out sites and exons #18

Closed xiaonalu closed 2 years ago

xiaonalu commented 2 years ago

Hi, I was wondering if there is a tabular info of the relation between splicing in/out sites and exons of genes. It will be very helpful when the gene is very long. Thanks

fairliereese commented 2 years ago

Hi,

I'm not entirely sure what you're referring to but you might try the following function get_edge_abundance, which will return a DataFrame detailing what the coordinates of each edge (intron or exon) are. Is this what you're looking for?

xiaonalu commented 2 years ago

Many Thanks. This is what I need, while I still have the no attribute error happen again. Will you suggest I uninstall and reinstall everything? Thanks Best Xiaona

From: Fairlie Reese @.> Sent: Monday, December 13, 2021 16:45 To: mortazavilab/swan_vis @.> Cc: Lu, Xiaona @.>; Author @.> Subject: Re: [mortazavilab/swan_vis] relation between splicing in/out sites and exons (Issue #18)

Hi,

I'm not entirely sure what you're referring to but you might try the following function get_edge_abundancehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmortazavilab%2Fswan_vis%2Fblob%2F5cc178ee664732b87272756337e31bc388e63c99%2Fswan_vis%2Fswangraph.py%23L1869&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W8UtqM5k%2FTEhDhFXKWdJ6%2BcSg3KEc4QEsvC1UzNFua8%3D&reserved=0, which will return a DataFrame detailing what the coordinates of each edge (intron or exon) are. Is this what you're looking for?

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xiaonalu commented 2 years ago

Umm... It shows as below Read in graph from data/swan.p Traceback (most recent call last): File "/Swan/Swan_quantification.py", line 16, in df = sg.get_edge_abundance(kind='tpm', prefix='test') File "/conda_envs/swan/lib/python3.9/site-packages/swan_vis/swangraph.py", line 1853, in get_edge_abundance columns = self.edge_adata.var.index.tolist() AttributeError: 'SwanGraph' object has no attribute 'edge_adata'

Thank you

fairliereese commented 2 years ago

Ah, I suggest you follow the installation instructions to install from GitHub. This function is relatively new and hasn't been added to the pip release yet.

On Tue, Dec 14, 2021, 04:40 xiaonalu @.***> wrote:

Many Thanks. This is what I need, while I still have the no attribute error happen again. Will you suggest I uninstall and reinstall everything? Thanks Best Xiaona

From: Fairlie Reese @.> Sent: Monday, December 13, 2021 16:45 To: mortazavilab/swan_vis @.> Cc: Lu, Xiaona @.>; Author @.> Subject: Re: [mortazavilab/swan_vis] relation between splicing in/out sites and exons (Issue #18)

Hi,

I'm not entirely sure what you're referring to but you might try the following function get_edge_abundance< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmortazavilab%2Fswan_vis%2Fblob%2F5cc178ee664732b87272756337e31bc388e63c99%2Fswan_vis%2Fswangraph.py%23L1869&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W8UtqM5k%2FTEhDhFXKWdJ6%2BcSg3KEc4QEsvC1UzNFua8%3D&reserved=0>, which will return a DataFrame detailing what the coordinates of each edge (intron or exon) are. Is this what you're looking for?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmortazavilab%2Fswan_vis%2Fissues%2F18%23issuecomment-992938698&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=71J%2BXCfLzQWyIQn3pE9IrWm0UNGaixLXq4ghrkf4QqI%3D&reserved=0>, or unsubscribe< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAVMDD7UQBOYIIVSJEXHS5OLUQZSQTANCNFSM5J6J2J5Q&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LVLiIm%2BHGYg5Bz%2F8xzo6qBDU01OiQGuACEFzcZpsiww%3D&reserved=0

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xiaonalu commented 2 years ago

Got it. Thank you very much Best Xiaona

From: Fairlie Reese @.> Sent: Tuesday, December 14, 2021 11:52 To: mortazavilab/swan_vis @.> Cc: Lu, Xiaona @.>; Author @.> Subject: Re: [mortazavilab/swan_vis] relation between splicing in/out sites and exons (Issue #18)

Ah, I suggest you follow the installation instructions to install from GitHub. This function is relatively new and hasn't been added to the pip release yet.

On Tue, Dec 14, 2021, 04:40 xiaonalu @.***> wrote:

Many Thanks. This is what I need, while I still have the no attribute error happen again. Will you suggest I uninstall and reinstall everything? Thanks Best Xiaona

From: Fairlie Reese @.> Sent: Monday, December 13, 2021 16:45 To: mortazavilab/swan_vis @.> Cc: Lu, Xiaona @.>; Author @.> Subject: Re: [mortazavilab/swan_vis] relation between splicing in/out sites and exons (Issue #18)

Hi,

I'm not entirely sure what you're referring to but you might try the following function get_edge_abundance< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmortazavilab%2Fswan_vis%2Fblob%2F5cc178ee664732b87272756337e31bc388e63c99%2Fswan_vis%2Fswangraph.py%23L1869&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=W8UtqM5k%2FTEhDhFXKWdJ6%2BcSg3KEc4QEsvC1UzNFua8%3D&reserved=0>, which will return a DataFrame detailing what the coordinates of each edge (intron or exon) are. Is this what you're looking for?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmortazavilab%2Fswan_vis%2Fissues%2F18%23issuecomment-992938698&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=71J%2BXCfLzQWyIQn3pE9IrWm0UNGaixLXq4ghrkf4QqI%3D&reserved=0>, or unsubscribe< https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAVMDD7UQBOYIIVSJEXHS5OLUQZSQTANCNFSM5J6J2J5Q&data=04%7C01%7Cxiaona.lu%40yale.edu%7C2fbb2109ed3a42bee5d108d9be81eba4%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637750287484316279%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LVLiIm%2BHGYg5Bz%2F8xzo6qBDU01OiQGuACEFzcZpsiww%3D&reserved=0

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