Indexing pandas data frame with set will be deprecated

[psl-schaefer]

In:

pycistarget/pycistarget/motif_enrichment_cistarget.py

Line 299 in 67a1757

self.regions_to_db = ctx_db.regions_to_db[self.name] if type(ctx_db.regions_to_db) == dict else ctx_db.regions_to_db.loc[set(coord_to_region_names(self.region_set)) & set(ctx_db.regions_to_db['Target'])]

I get the following error:

"Passing a set as an indexer will be deprecated and will raise in a future version. Use a list instead."

Using Pandas version 1.4.3 (the most recent version).

I guess you just have to wrap list around the set.

[SeppeDeWinter]

Hi @schae211

We are aware of this warning message.
Indeed converting to a list will solve it.

However, did the motif enrichment actually crash? (normally it should just print the warning but continue running).

Best,

S

[psl-schaefer]

Hi @SeppeDeWinter

I was looking into this #8, and for a second I thought this issue here might have something to do with it. But this is not the case.

[SeppeDeWinter]

Hi @schae211

Indeed, it's not the case.

Thank you for the nice bug report in #8, I will take a look as soon as possible.

In the mean time I will close this issue.

Best

S

[Gat2018]

I am constructing ancenstral state with pastml package and I got this error any help please

/usr/local/lib/python3.8/dist-packages/pandas/core/computation/expressions.py:20: UserWarning: Pandas requires version '2.7.3' or newer of 'numexpr' (version '2.7.1' currently installed).
from pandas.core.computation.check import NUMEXPR_INSTALLED
Traceback (most recent call last):
File "/home/manager/.local/bin/pastml", line 8, in
sys.exit(main())
File "/home/manager/.local/lib/python3.8/site-packages/pastml/acr.py", line 1227, in main
pastml_pipeline(**vars(params))
File "/home/manager/.local/lib/python3.8/site-packages/pastml/acr.py", line 649, in pastml_pipeline
_validate_input(tree, columns, name_column if html_compressed or html_mixed else None, data, data_sep, id_index,
File "/home/manager/.local/lib/python3.8/site-packages/pastml/acr.py", line 865, in _validate_input
filtered_df = df.loc[common_ids, :]
File "/usr/local/lib/python3.8/dist-packages/pandas/core/indexing.py", line 1091, in getitem
check_dict_or_set_indexers(key)
File "/usr/local/lib/python3.8/dist-packages/pandas/core/indexing.py", line 2611, in check_dict_or_set_indexers
raise TypeError(
TypeError: Passing a set as an indexer is not supported. Use a list instead.

[SeppeDeWinter]

@Gat2018

Could you please elaborate a bit more on what you are trying to do?
I'm not familiar with the pastml package.

All the best,

Seppe

[Gat2018]

Hi, this model for ancestral state reconstruction (ASR) ...pastml -*p*hylogenetic *a*nalysis with *s*pace and *t*ime *m*odel We estimate the associations between pathogens and location and time Gaspary

…

On Tue, Oct 17, 2023 at 6:19 PM Seppe ***@***.***> wrote: @Gat2018 <https://github.com/Gat2018> Could you please elaborate a bit more on what you are trying to do? I'm not familiar with the pastml package. All the best, Seppe — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKW3YOS2VB2I6HG2A5CNUTLX72VXNAVCNFSM57TLZ2BKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZWGY3TIOJXGI2Q> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SeppeDeWinter]

Okay, and with which part of the code do you get this error? Can you show which command you were running?

Best,

Seppe

[Gat2018]

Dear Seppe, Yes, here is the command line and error I got attached

…

On Tue, Oct 17, 2023 at 7:18 PM Seppe ***@***.***> wrote: Okay, and with which part of the code do you get this error? Can you show which command you were running? Best, Seppe — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKW3YOVDIVKXWCLLX4JE6TTX724VVAVCNFSM57TLZ2BKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZWGY4DINZTGM2A> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SeppeDeWinter]

Hi @Gat2018

I'm sorry but I don't see the command ...

Could you please copy-paste it (as text) in a comment on this issue?

Best,

Seppe

[Gat2018]

The first line in the txt doc is the command ?

…

On Wed, Oct 18, 2023 at 4:14 PM Seppe ***@***.***> wrote: Hi @Gat2018 <https://github.com/Gat2018> I'm sorry but I don't see the command ... Could you please copy-paste it (as text) in a comment on this issue? Best, Seppe — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKW3YOQT65TCRMDFPFQT3XDX77P6BAVCNFSM57TLZ2BKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZWHA2TKNRYGEZQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SeppeDeWinter]

I don't see the text file, that is the issue.

So if you could just copy-paste the command and error (as a comment to this github issue) I can try and help you.

[Gat2018]

Hi, The command is pastml -t For_Visualization_tree01.nwk -d tz_metadata2.csv -s , -i 1 -c country --prediction_method MPPA -o OUT_DATA --html HTML --html_compressed HTML_COMPRESSED --verbose --upload_to_itol --itol_tree_name ITOL_TREE The problem for -c country -c flag indicates the column that i want to include in the analysis so in this case I have two columns in the csv file that looks like name (index 0, first column that includes identifiers), country (index 1, second column), date (index 2, third column for years (2010,2015, etc.....) So my csv reads as name,country,date (three columns) When I want to include country and date in the analysis -c country date it does not work gives me this error TypeError:float() argument must be a string or a number not a set? When I just include one column (country) as -c country it does work well So with one column included -c country IT WORKS with two columns included -c county date IT DOES NOT WORK ....gives THIS TypeError:float() argument must be a string or a number not a set?

…

On Wed, Oct 18, 2023 at 6:17 PM Seppe ***@***.***> wrote: I don't see the text file, that is the issue. So if you could just copy-paste the command and error (as a comment to this github issue) I can try and help you. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKW3YOWEDQJYBC3X3OZJ2ILX776HZAVCNFSM57TLZ2BKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZWHA4DQMRYGEZA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[SeppeDeWinter]

Hi @Gat2018

This issue is not related to pycistarget (the repo where you are posting your issue).
I guess you want to open an issue on the pastml repo https://github.com/evolbioinfo/pastml?

All the best,

Seppe