From a7f8876fcbdb8d3a020c12b508bd5038422a5745 Mon Sep 17 00:00:00 2001 From: hjulienne <hanna.julienne@gmail.com> Date: Thu, 22 Nov 2018 17:13:50 +0000 Subject: [PATCH] added requirements to the preprocessing --- .gitlab-ci.yml | 1 + .../jass_preprocessing/map_reference.py | 16 ++++++++++++++++ .../jass_preprocessing/requirements.txt | 6 ++++++ 3 files changed, 23 insertions(+) create mode 100644 jass_preprocessing/jass_preprocessing/requirements.txt diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d1b7629..5235271 100644 --- a/.gitlab-ci.yml +++ b/.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 diff --git a/jass_preprocessing/jass_preprocessing/map_reference.py b/jass_preprocessing/jass_preprocessing/map_reference.py index bb049bc..e04589f 100644 --- a/jass_preprocessing/jass_preprocessing/map_reference.py +++ b/jass_preprocessing/jass_preprocessing/map_reference.py @@ -1,3 +1,8 @@ +""" + 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)}) diff --git a/jass_preprocessing/jass_preprocessing/requirements.txt b/jass_preprocessing/jass_preprocessing/requirements.txt new file mode 100644 index 0000000..ffed5c6 --- /dev/null +++ b/jass_preprocessing/jass_preprocessing/requirements.txt @@ -0,0 +1,6 @@ +scipy +pandas +numpy +warnings +seaborn +matplotlib -- GitLab