Merge pull request #21 from MannLabs/development

Development

.gitignore

@@ -191,4 +191,5 @@ figures/
 _docs/
 _proc/
 
-sandbox/
+sandbox/
+test_data/unit_tests/input_table_formats/spectronaut.frgions.large.tsv.tmp.longformat.columnfilt.tsv

directlfq/__init__.py

@@ -2,7 +2,7 @@
 
 
 __project__ = "directlfq"
-__version__ = "0.2.13"
+__version__ = "0.2.14"
 __license__ = "Apache"
 __description__ = "An open-source Python package of the AlphaPept ecosystem"
 __author__ = "Mann Labs"

directlfq/config.py

@@ -13,8 +13,8 @@ def set_log_processed_proteins(log_processed_proteins = True):
     LOG_PROCESSED_PROTEINS = log_processed_proteins
 
 
-PROTEIN_ID = None
-QUANT_ID = None
+PROTEIN_ID = 'protein'
+QUANT_ID = 'ion'
 
 def set_global_protein_and_ion_id(protein_id = 'protein', quant_id = 'ion'):
     global PROTEIN_ID

directlfq/normalization.py

@@ -298,7 +298,11 @@ def _shift_remaining_dataframe_to_reference_sample(self):
     @staticmethod
     @njit
     def _get_num_nas_in_row(row):
-        return sum(np.isnan(row))
+        sum = 0
+        isnans = np.isnan(row)
+        for is_nan in isnans:
+            sum+=is_nan
+        return sum
 
 class NormalizationManagerSamples(NormalizationManager):
     def __init__(self, complete_dataframe, num_samples_quadratic):

directlfq/protein_intensity_estimation.py

@@ -184,7 +184,11 @@ def _determine_nansorted_df_index(self):
     @staticmethod
     @njit
     def _get_num_nas_in_row(row):
-        return sum(np.isnan(row))
+        sum = 0
+        isnans = np.isnan(row)
+        for is_nan in isnans:
+            sum+=is_nan
+        return sum
 
 
     def get_dataframe(self):

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.13
+current_version = 0.2.14
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?