taxon_collapser.py

[coreyholt]

Hi there,

Where in the pipeline would I use taxon_collapser.py? And is this different from the chimera options in taxa and gene selection?

Cheers!
Corey

[atice]

Hi Corey, Typically, taxon_collapser.py is used after apply_to_db.py. The way it differs from the chimera option you mentioned is that taxon_collapser.py will create a permanent entry in your database with its own unique ID that represents the most complete proteome for all taxa collapsed to make it. While the chimera option will not create a permanent database entry. The chimera produced through this option will exist only in your matrix and single gene alignments for the phylogenomic dataset you created when you invoked the chimera flag. Often times in our lab students will generate several single cell transcriptomes from the same population of an "uncultivable" microbe. After we are sure the cells all represent the same species we use taxon_collapser.py to create a permanent most-complete proteome of that organism for use in subsequent studies. Does this clarify? Let me know if you have any further questions and thank you for your interest in PhyloFisher. Alex Alexander K. Tice, Ph.D. Department of Biological Sciences Mississippi State University 027 Harned Hall Lab Telephone: 662-325-4008

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________________________________ From: coreyholt ***@***.***> Sent: Wednesday, October 5, 2022 1:25 PM To: TheBrownLab/PhyloFisher ***@***.***> Cc: Subscribed ***@***.***> Subject: [TheBrownLab/PhyloFisher] taxon_collapser.py (Discussion #47) Hi there, Where in the pipeline would I use taxon_collapser.py? And is this different from the chimera options in taxa and gene selection? Cheers! Corey — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/1itKGeoHVg_7KUzpA0qWO0o7CcBPZ5hUt6nUEz5GpGXbaD7T0xwgxusN1Q_lkTwRAKIt5Qc8bNEH-PfdFy-si5Ko_HkWhenir8JXN7vqUg390Vbi0PCXYn3xHqNZ0JFxIfqiA0Yr5U2a1iQSZYMcvOy3XXyp0Lj6oa4K4mFXyF-HHqL6WgQ1rOLri-SsuMA6t6MjpwpKbc3F48O5gw6oROPWQqzzfTyZrgtsk3vXKaz8tpvhS_2pZKaniG_J0KI78e_wEY_ZZK2A1_ioz2ODOVo5Ke_UCwbCOX85QoJQl6QkSd7dFcwM_DHh8ciLXXs9r/https%3A%2F%2Fgithub.com%2FTheBrownLab%2FPhyloFisher%2Fdiscussions%2F47>, or unsubscribe<https://secure-web.cisco.com/1wLPFWHmO109OZSyRoYU6EMl_F6noLYk1cj6ynhi9PA8Bej5wKbXANhXY_IhMEEZvf93CR78V7T75-JEyuQMNQBTIPN-17-fOB_9D0ENGCDA-Mnn26yTveF4-DES6OhCWoh9NtI003PHHbczboqLIyfCDe1ovFZv3p6jz3JDeiXblv42VwEpxZuGCwxmYnoEG2e82-txKQ2ED7UreYRWpxH2UJrNvq_piV7gDmrQCBqiTTynwAA1x3nNqJMImXvzY-xkLBaPV7Ya8U3sgGIZjpgSAo1KWextk-wByw58IjGHtcAAY2FpSG5ssiCIK5cJr/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADA4OK2FBLNGP5SNASYMCMTWBXBZJANCNFSM6AAAAAAQ5ZYJZE>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[coreyholt]

Got it. Thank you, Alex!

[atice]

Hey Corey, You should see the file select_taxa.tsv that was created after you ran the script. If it is there then you should be able to continue down the pipeline with no problem. The error message you received was because the script was unable to produce a plot due to some weird panda's issue that shows up when the number of taxa you selected is not divisible by 5. Robert went ahead and added a try-except state where in the future the script will print a friendly message that it could not produce the plot if it can't until this issue is resolved. Hope this helps. Let us know. Alex and Robert Alexander K. Tice, Ph.D. Department of Biological Sciences Mississippi State University 027 Harned Hall Lab Telephone: 662-325-4008

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________________________________ From: coreyholt ***@***.***> Sent: Friday, October 14, 2022 6:26 PM To: TheBrownLab/PhyloFisher ***@***.***> Cc: Tice, Alex ***@***.***>; Comment ***@***.***> Subject: Re: [TheBrownLab/PhyloFisher] taxon_collapser.py (Discussion #47) Hi Alex, I ran taxon_collapser after apply_to_db but now there seems to be a discrepancy when running select_taxa. Traceback (most recent call last): File "/opt/Anaconda3/envs/fisher/bin/select_taxa.py", line 183, in tools.make_plot(taxa_comp, f'taxa_comp', y_count=gene_count, genes=False) File "/opt/Anaconda3/envs/fisher/lib/python3.7/site-packages/phylofisher/tools.py", line 170, in make_plot ax2.set_xticklabels(range(0, gene_num, 5)) File "/opt/Anaconda3/envs/fisher/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 73, in wrapper return get_method(self)(*args, **kwargs) File "/opt/Anaconda3/envs/fisher/lib/python3.7/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper return func(*args, **kwargs) File "/opt/Anaconda3/envs/fisher/lib/python3.7/site-packages/matplotlib/axis.py", line 1779, in _set_ticklabels return self.set_ticklabels(labels, minor=minor, **kwargs) File "/opt/Anaconda3/envs/fisher/lib/python3.7/site-packages/matplotlib/axis.py", line 1701, in set_ticklabels "The number of FixedLocator locations" ValueError: The number of FixedLocator locations (67), usually from a call to set_ticks, does not match the number of ticklabels (66). Any ideas? Cheers! — Reply to this email directly, view it on GitHub<https://secure-web.cisco.com/1rfx-Q3meCMO_Jk3n5EChCdthxEZwmlNdqUI8Z0hWjPCRvX6oOuEgvxjccI4E024HSSQ3KW1aLqV8-sFr_VtanAqWkKQqguCcQyK9GSOIRw8Iy451JHP_BcDGXyz9WvGsMDobYTLgqlgcFE5WiLvPAuJDF3WTcRc9llIoZZJb5uV_STzKmF9VY0WWy6K4c2zu7EwiWcL_5JDTDAGARgWY2MjvoJgTv8mZNHWY79LobT-Hh5Lo-h8EoIU-1DUuZEXYhbbhjUsL4fhGbUgJN2vy1pGxTZtYsbsXcbIjWUJ-iJsu0smfqOIYP0FDrJKBhbM2/https%3A%2F%2Fgithub.com%2FTheBrownLab%2FPhyloFisher%2Fdiscussions%2F47%23discussioncomment-3882721>, or unsubscribe<https://secure-web.cisco.com/1QFaO2vZotpB5VjZS1CF-PUn2yki6jz9hybE6ip3yo4-PUE9JDZr8NSFSa2MpE6PHqtgB98lvPdA-ZnVk7eOwkiojuQ1j58XF5R8N-mRQkkPrZNLu2PllHBkV26cPv6GdRA_stDykQoQJSsorQ45k3NqooUNMuNnP9UGIlERB0VohqXZan_2fmch75bJtb9Um5EOfPRbnJYH8fK7z18m_QeC2klxyfHuldD5s_mZstE35kQwNdZ74UwW1edL-OxTIb_WpFYQeUeXflw3RCMtMrZ7e_dLc7ohoMDQhptxLiBAZ3A1XyKq_o3CsGECDt-fK/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADA4OKYNVNYCIWWDRHDVP63WDHT3TANCNFSM6AAAAAAQ5ZYJZE>. You are receiving this because you commented.Message ID: ***@***.***>