added requirements to the preprocessing

.gitlab-ci.yml

@@ -14,6 +14,7 @@ pages:
     - yum install -y make
     - pip3 install sphinx
     - pip3 install sphinxcontrib-bibtex
+    - pip3 install -r jass_preprocessing/jass_preprocessing/requirements.txt
     - cd jass_preprocessing/doc
     - make html
     - mv _build/html/ ../../public

jass_preprocessing/jass_preprocessing/map_reference.py

+"""
+    Module of function
+
+
+"""
 import pandas as pd
 import numpy as np
 import jass_preprocessing.dna_utils as dna_u
@@ -19,6 +24,12 @@ def map_on_ref_panel(gw_df , ref_panel):
     Merge Gwas dataframe with the reference panel
     Make sure that the same SNPs are in the reference panel and the gwas
 
+    Args:
+        gw_df (pandas dataframe): GWAS study dataframe
+        ref_panel (pandas dataframe): reference panel dataframe
+
+    Return:
+        merge_GWAS (pandas dataframe): merge studies,
     """
     inter_index = ref_panel.index.intersection(gw_df.index)
 
@@ -46,6 +57,11 @@ def compute_is_flipped(mgwas):
     Check if the reference panel and the GWAS data have the same reference
     allele. return a boolean vector.
 
+    Args:
+        mgwas (pandas dataframe): GWAS study dataframe merged with the reference_panel
+    Return:
+        is_flipped (pandas dataframe): merge studies,
+
     """
     flipped = pd.DataFrame({"ref_flipped" : (mgwas.ref == mgwas.a2), "alt_flipped" : (mgwas.alt == mgwas.a1)})
     flipped_complement = pd.DataFrame({"ref_flippedc" : (mgwas.ref == mgwas.a2c), "alt_flippedc" : (mgwas.alt == mgwas.a1c)})

jass_preprocessing/jass_preprocessing/requirements.txt

+scipy
+pandas
+numpy
+warnings
+seaborn
+matplotlib