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jameshadfield / phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny
http://phandango.net
MIT License
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Roary gene_Presence_Absence.csv file is not being displayed #138

Closed LilCros closed 2 years ago

LilCros commented 2 years ago

Hello, I did perform Roary Pan Genome analysis on my data using the GALAXY platform. However the Gene_Presence_Absence.csv file is not being displayed despite the tree and the metadata files are. Could you please advice? I am not sure if there could be something wrong with the csv file. Best, Lil

jameshadfield commented 2 years ago

Hi @LilCros - Could you try using these datasets: https://github.com/jameshadfield/phandangoExampleData/tree/master/roary_S.Weltevreden to work out if it's a problem with Phandango (in your browser) or your particular files?

LilCros commented 2 years ago

Hi Jason, I will try with these datasets and let you know. Thank you, Francy

Francy Liliana Crosby PhD Research Assistant Professor University of Florida College of Veterinary Medicine Academic Buildg, Second floor, room V2-200 Office phone # 352-294-4182 Laboratory Phone # 352-294-4134 Email: @.***

From: james hadfield @.> Sent: Sunday, August 1, 2021 4:44 PM To: jameshadfield/phandango @.> Cc: Crosby,Francy L @.>; Mention @.> Subject: Re: [jameshadfield/phandango] Roary gene_Presence_Absence.csv file is not being displayed (#138)

[External Email]

Hi @LilCroshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LilCros&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=pkaIlsuDFxErRemetQ4Zbw&m=j3j8BXg92d9_OSFXWEYmgIqE3rIJt3bBrfhKtJLcK7c&s=V0OUPdph-G_g0KtHVb8XWXikgo3CiOyz3ry4FF-BK70&e= - Could you try using these datasets: https://github.com/jameshadfield/phandangoExampleData/tree/master/roary_S.Weltevredenhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jameshadfield_phandangoExampleData_tree_master_roary-5FS.Weltevreden&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=pkaIlsuDFxErRemetQ4Zbw&m=j3j8BXg92d9_OSFXWEYmgIqE3rIJt3bBrfhKtJLcK7c&s=i1wE_NLqEeXUH3cOfy0x2CXpF-bB-5FinBPsyflmvLE&e= to work out if it's a problem with Phandango (in your browser) or your particular files?

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LilCros commented 2 years ago

Hello James, I downloaded the files you kindly sent me and everything is working fine. Do you think is something wrong with my files. Please see https://github.com/LilCros/Ap-Roary Thank you, Francy

From: james hadfield @.> Sent: Sunday, August 1, 2021 4:44 PM To: jameshadfield/phandango @.> Cc: Crosby,Francy L @.>; Mention @.> Subject: Re: [jameshadfield/phandango] Roary gene_Presence_Absence.csv file is not being displayed (#138)

[External Email]

Hi @LilCroshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LilCros&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=pkaIlsuDFxErRemetQ4Zbw&m=j3j8BXg92d9_OSFXWEYmgIqE3rIJt3bBrfhKtJLcK7c&s=V0OUPdph-G_g0KtHVb8XWXikgo3CiOyz3ry4FF-BK70&e= - Could you try using these datasets: https://github.com/jameshadfield/phandangoExampleData/tree/master/roary_S.Weltevredenhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jameshadfield_phandangoExampleData_tree_master_roary-5FS.Weltevreden&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=pkaIlsuDFxErRemetQ4Zbw&m=j3j8BXg92d9_OSFXWEYmgIqE3rIJt3bBrfhKtJLcK7c&s=i1wE_NLqEeXUH3cOfy0x2CXpF-bB-5FinBPsyflmvLE&e= to work out if it's a problem with Phandango (in your browser) or your particular files?

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jameshadfield commented 2 years ago

Thanks - in your ROARY CSV, the first line contains strings such as"ApBov1_FRA:gff", "ApCRT35_MN:gff" etc. They shouldn't have the trailing :gff. If you do a simple find & replace to remove :gff from the file (only appears in the first line) then it works:

image

(It's been a long time since I looked at these files, so I don't know what is causing this, or what this may mean.)

LilCros commented 2 years ago

Excellent! I would do the changes form the file. Again, thank you for your time, Lil

Francy Liliana Crosby Ph.D Research Assistant Professor Department of Infectious Diseases and Immunology University of Florida|College of Veterinary Medicine (352) 294 4182 (Office) (352 294 4134 (Laboratory)

From: james hadfield @.> Sent: Monday, August 2, 2021 4:15 PM To: jameshadfield/phandango @.> Cc: Crosby,Francy L @.>; Mention @.> Subject: Re: [jameshadfield/phandango] Roary gene_Presence_Absence.csv file is not being displayed (#138)

[External Email]

Thanks - in your ROARY CSV, the first line contains strings such as"ApBov1_FRA:gff", "ApCRT35_MN:gff" etc. They shouldn't have the trailing :gff. If you do a simple find & replace to remove :gff from the file (only appears in the first line) then it works:

[image]https://urldefense.proofpoint.com/v2/url?u=https-3A__user-2Dimages.githubusercontent.com_8350992_127918204-2D6e1c36fd-2D16c3-2D401a-2D8d66-2D7b3734759501.png&d=DwMCaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=pkaIlsuDFxErRemetQ4Zbw&m=MiceGnkZZ4v7d1tSfXpIXHarC-IFey8rr4ANNJUgKec&s=l1sCG9RJfOYJ6wtctQ1bZ4zDIFpm-J_ThLQvZb3bqMQ&e=

(It's been a long time since I looked at these files, so I don't know what is causing this, or what this may mean.)

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