Changes to wrapper to integrate with Bibiserv#62
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aweimann
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Why would you replace sort_values with sort_index?
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DataFrame.sort_values() is only available in Pandas 0.17.0 seemingly, and
the version in Ubuntu Trusty is 0.13.0. No backports are available either.
Could build the Docker image with a later Ubuntu release though.
http://pandas.pydata.org/pandas-docs/stable/whatsnew.html#changes-to-sorting-api
http://pandas.pydata.org/pandas-docs/version/0.17.0/generated/pandas.DataFrame.sort_values.html
https://stackoverflow.com/questions/19332171/difference-between-sort-values-and-sort-index
…On 2 August 2017 at 13:58, aweimann ***@***.***> wrote:
***@***.**** commented on this pull request.
Why would you replace sort_values with sort_index?
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aweimann
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Oh I see. The solution is to use bioconda / conda for installing the dependencies. Actually, I'm currently working on making a conda recipe for Traitar itself. Could you use that as well? https://conda.io/docs/install/quick.html
| sample_table = pd.DataFrame(sample_file_names) | ||
| categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist()) | ||
| sample_table['category'] = categories | ||
| sample_table.columns = ["sample_file_name", "category"] |
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thanks for the changes; I think I haven't really properly tested this one!
| with open(out_f, 'w') as out_fo: | ||
| ps.DataFrame(filtered_df.columns).T.to_csv(out_f, sep = "\t", index = False, header = False, mode = 'a') | ||
| filtered_df.sort_values(by = ["target name", "query name"], inplace = True) | ||
| filtered_df.sort_index(by = ["target name", "query name"], inplace = True) |
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Bioconda - sounds good. So, we can just change all the deps in the
Dockerfile (inc. Traitar).
In traitar/traitar_from_archive.py
<#62 (comment)>:
2nd argument for DF was a DF and not a list
In traitar/hmmer2filtered_best.py
<#62 (comment)>:
As discussed - only available in Pandas 0.17.0
…On 2 August 2017 at 14:14, aweimann ***@***.***> wrote:
***@***.**** commented on this pull request.
Oh I see. The solution is to use bioconda / conda for installing the
dependencies. Actually, I'm currently working on making a conda recipe for
Traitar itself. Could you use that as well?
------------------------------
In traitar/traitar_from_archive.py
<#62 (comment)>:
> #replace index with cleaned file names
sample_cat.index.rename(str, dict([(tf, sfn) for sfn, tf in zip(sample_file_names, namelist)]))
- sample_table = pd.DataFrame([sample_file_names, sample_cat.loc[sample_file_names,]])
+ sample_table = pd.DataFrame(sample_file_names)
+ categories = pd.Series(sample_cat.loc[sample_file_names, ]['category'].tolist())
+ sample_table['category'] = categories
sample_table.columns = ["sample_file_name", "category"]
thanks for the changes; I think I haven't really properly tested this one!
------------------------------
In traitar/hmmer2filtered_best.py
<#62 (comment)>:
> @@ -49,7 +49,7 @@ def aggregate_domain_hits(filtered_df, out_f):
#sort by gene identifier and Pfam
with open(out_f, 'w') as out_fo:
ps.DataFrame(filtered_df.columns).T.to_csv(out_f, sep = "\t", index = False, header = False, mode = 'a')
- filtered_df.sort_values(by = ["target name", "query name"], inplace = True)
+ filtered_df.sort_index(by = ["target name", "query name"], inplace = True)
Why would you do this?
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