V1.1.0.20240131

.github/workflows/heatcluster.yml

@@ -5,10 +5,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: install dependencies
-        run: pip3 install pandas numpy pathlib seaborn matplotlib scipy
+        run: pip3 install pandas numpy pathlib seaborn seaborn_polars polars pyarrow matplotlib scipy
 
       - name: test (tab-delimited)
         run: python3 heatcluster.py -i test/small_matrix.csv

Dockerfile

@@ -1,7 +1,7 @@
 FROM ubuntu:jammy as app
 
 # default version
-ARG HEATCLUSTER_VER="1.0.2c"
+ARG HEATCLUSTER_VER="1.1.0.20240131"
 
 # adding labels
 LABEL base.image="ubuntu:jammy"
@@ -27,7 +27,7 @@ RUN apt-get update && apt-get upgrade -y && \
   apt-get autoclean && rm -rf /var/lib/apt/lists/*
 
 # installing python dependencies
-RUN pip3 install --no-cache argparse pandas numpy pathlib seaborn matplotlib scipy --upgrade-strategy=only-if-needed
+RUN pip3 install --no-cache argparse pandas numpy pathlib seaborn seaborn_polars polars pyarrow matplotlib scipy --upgrade-strategy=only-if-needed
 
 # copying files to docker image
 COPY . /heatcluster

heatcluster.py

@@ -1,11 +1,12 @@
 #!/usr/bin/python3
 
 ###########################################
-# heatcluster-1.0.2c                       #
+# heatcluster-1.1.0.20240131              #
 # written by Stephen Beckstrom-Sternberg  #
 # Creates SNP heatmaps                    #
 # from SNP matrices                       #
 # Outputs sorted csv SNP matrix           #
+# Uses Polars instead of Pandas           #
 ###########################################
 
 import argparse
@@ -16,6 +17,10 @@
 import matplotlib
 matplotlib.use('agg')
 import matplotlib.pyplot as plt
+import polars as pl
+import seaborn_polars as snl
+import pyarrow
+
 
 logging.basicConfig(format='%(asctime)s - %(message)s', datefmt='%y-%b-%d %H:%M:%S', level=logging.INFO)
 
@@ -64,18 +69,17 @@ def read_snp_matrix(file):
         file (str): SNP dist output file that should be converted to pandas dataframe
 
     Returns:
-        df (DataFrame): Pandas dataframe of SNP matrix.
+        df (DataFrame): Polars dataframe of SNP matrix.
     """
     logging.debug('Determining if file is comma or tab delimited')
-    tabs   = pd.read_csv(file, nrows=1, sep='\t').shape[1]
-    commas = pd.read_csv(file, nrows=1, sep=',').shape[1]
+    tabs   = pl.scan_csv(file, n_rows=1, separator='\t').shape[1]
+    commas = pl.scan_csv(file, n_rows=1, separator=',').shape[1]
     if tabs > commas:
         logging.debug('The file is tab-delimited')
-        df = pd.read_csv(file, sep='\t', index_col=False)
+        df = pl.scan_csv(file, separator='\t', index_col=False)
     else:
         logging.debug('The file is comma-delimited')
-        df = pd.read_csv(file, sep=',', index_col=False)
-
+        df = pl.scan_csv(file, separator=',', index_col=False)
     return df
 
 def clean_and_read_df(df):
@@ -182,7 +186,8 @@ def create_heatmap(df, fontSize, labelSize, figsize, labels):
     fig,ax = plt.subplots(figsize=figsize)
     logging.debug('Creating heatmap')
 
-    heatmap = sns.heatmap(
+    #heatmap = sns.heatmap(
+    heatmap = snl.heatmap(
         df,
         xticklabels=True,
         yticklabels=True,