🎨 string format

Multiomics-Analytics-Group · Oct 9, 2024 · d493c3c · d493c3c
1 parent fc152b8
commit d493c3c
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Showing 3 changed files with 18 additions and 14 deletions.
diff --git a/acore/differential_regulation.py b/acore/differential_regulation.py
@@ -265,9 +265,8 @@ def calculate_repeated_measures_anova(df, column, subject="subject", within="gro
         df1, df2 = aov_result["DF"]
     except Exception as e:
         print(
-            "Repeated measurements Anova for column: {} could not be calculated. Error {}".format(
-                column, e
-            )
+            "Repeated measurements Anova for column: {} could not be calculated."
+            " Error {}".format(column, e)
         )
 
     return (column, df1, df2, t, pvalue)

diff --git a/acore/kaplan_meier_analysis.py b/acore/kaplan_meier_analysis.py
@@ -50,16 +50,14 @@ def group_data_based_on_marker(df, marker, index_col, how, value):
                     labels.extend([str(marker) + "-"] * (num_values - value))
                 else:
                     print(
-                        "Invalid value provided. Exceeded maximun number of samples {}".format(
-                            num_values
-                        )
+                        "Invalid value provided. Exceeded maximun number of samples {}"
+                        .format(num_values)
                     )
                 mdf["new_grouping"] = labels
             else:
                 print(
-                    "Grouping method {} not implemented. Try with 'cutoff' or 'top'".format(
-                        how
-                    )
+                    "Grouping method {} not implemented. Try with 'cutoff' or 'top'"
+                    .format(how)
                 )
 
     return mdf

diff --git a/acore/publications_analysis.py b/acore/publications_analysis.py
@@ -3,7 +3,8 @@
 import pandas as pd
 from Bio import Entrez, Medline
 
-Entrez.email = "[email protected]"  # TODO: This should probably be changed to the email of the person installing ckg?
+# TODO: This should probably be changed to the email of the person installing ckg?
+Entrez.email = "[email protected]"
 
 
 def getMedlineAbstracts(idList):
@@ -54,17 +55,23 @@ def get_publications_abstracts(
     index="PMID",
 ):
     """
-    Accesses NCBI PubMed over the WWW and retrieves the abstracts corresponding to a list of one or more PubMed IDs.
+    Accesses NCBI PubMed over the WWW and retrieves the abstracts corresponding
+    to a list of one or more PubMed IDs.
 
-    :param data: pandas dataframe of diseases and publications linked to a list of proteins (columns: 'Diseases', 'Proteins', 'linkout' and 'publication').
+    :param data: pandas dataframe of diseases and publications linked to a list of
+                proteins (columns: 'Diseases', 'Proteins', 'linkout' and 'publication').
     :param str publication_col: column label containing PubMed ids.
     :param list join_by: column labels to be kept from the input dataframe.
     :param str index: column label containing PubMed ids from the NCBI retrieved data.
-    :return: Pandas dataframe with publication information and columns 'PMID', 'abstract', 'authors', 'date', 'journal', 'keywords', 'title', 'url', 'Proteins' and 'Diseases'.
+    :return: Pandas dataframe with publication information and columns 'PMID', 'abstract',
+     'authors', 'date', 'journal', 'keywords', 'title', 'url', 'Proteins' and 'Diseases'.
 
     Example::
 
-        result = get_publications_abstracts(data, publication_col='publication', join_by=['publication','Proteins','Diseases'], index='PMID')
+        result = get_publications_abstracts(data,
+                    publication_col='publication',
+                    join_by=['publication','Proteins','Diseases'],
+                    index='PMID')
     """
     abstracts = pd.DataFrame()
     if not data.empty: