cvmcore 0.2.0__tar.gz → 0.2.2__tar.gz

{cvmcore-0.2.0 → cvmcore-0.2.2}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: cvmcore
-Version: 0.2.0
+Version: 0.2.2
 Summary: SZQ lab data analysis core function
-Home-page: https://github.com/hbucqp/cvmcore
+Home-page: https://github.com/hbucqp/cvmplot
 Author: Qingpo Cui
 Author-email: cqp@cau.edu.cn
 License: MIT Licence

cvmcore-0.2.2/cvmcore/__init__.py

@@ -0,0 +1,10 @@
+# -*- coding:utf-8 -*-
+
+__title__ = 'cvmplot'
+__description__ = 'Major plot function used by SZQ lab from China Agricultural University'
+__url__ = 'https://github.com/hbucqp/cvmplot'
+__version__ = "0.2.2"
+__author__ = 'Qingpo Cui'
+__author_email__ = 'cqp@cau.edu.cn'
+__license__ = 'MIT'
+__copyright__ = 'Copyright 2023 Qingpo Cui'

cvmcore-0.2.2/cvmcore/cvmcore.py

@@ -0,0 +1,141 @@
+import os
+import sys
+import time
+
+# data process
+import numpy as np
+import pandas as pd
+from scipy.cluster.hierarchy import linkage, dendrogram, complete, to_tree
+from scipy.spatial.distance import squareform
+from tabulate import tabulate
+from io import StringIO
+import warnings
+# from Bio.Blast import NCBIWWW
+with warnings.catch_warnings():
+    warnings.simplefilter('ignore', category=DeprecationWarning)
+    from Bio import SeqIO
+    from Bio import Phylo
+    from Bio.Seq import Seq
+    from Bio.SeqRecord import SeqRecord
+    from Bio.Blast import NCBIXML
+
+
+# matplotlib
+import matplotlib
+import matplotlib as mpl
+from matplotlib import pyplot as plt
+from matplotlib.lines import Line2D
+from matplotlib.patches import Patch, FancyArrow
+from matplotlib.transforms import Affine2D
+from matplotlib.colors import LinearSegmentedColormap
+import matplotlib.collections as mpcollections
+from mpl_toolkits.axes_grid1.inset_locator import inset_axes
+from typing import Optional, List, Dict, Union, Tuple
+
+plt.rcParams['font.family'] = 'sans-serif'
+plt.rcParams['font.sans-serif'] = ['Arial']
+plt.rcParams['svg.fonttype'] = 'none'
+
+
+class cfunc():
+    pass
+
+    @staticmethod
+    def is_fasta(file):
+        """
+        chcek if the input file is fasta format
+        """
+        try:
+            with open(file, "r") as handle:
+                fasta = SeqIO.parse(handle, "fasta")
+                # False when `fasta` is empty, i.e. wasn't a FASTA file
+                return any(fasta)
+        except:
+            print(f'The input file {file} is not a valid fasta file.')
+            return False
+
+    def get_mod_time(file):
+        """
+        Return the last modified time of file as YYYY-MM-DD string format.
+        Parameters
+        ----------
+        file :
+            file path string
+        Returns
+        ----------
+        Raises
+        ----------
+        Notes
+        ----------
+        References
+        ----------
+        See Also
+        ----------
+        Examples
+        ----------
+        """
+        file = os.path.abspath(file)
+        md_time = os.stat(file).st_mtime
+        lst_mod_time = time.strftime("%Y-%m-%d", time.localtime(md_time))
+        return lst_mod_time
+
+    def check_sequence_type(file_path):
+        """
+        Check the input file type (DNA or Amino Acid)
+        """
+        try:
+            # Read the sequence from the file
+            records = list(SeqIO.parse(file_path, "fasta"))
+            if not records:
+                return "Unknown"
+
+            sequence = str(records[0].seq).upper()
+
+            # Define sets of characters for DNA and amino acids
+            dna_chars = set("ATCG")
+            amino_acid_chars = set("ACDEFGHIKLMNPQRSTVWY")
+
+            # Check if the sequence contains only DNA characters
+            if set(sequence).issubset(dna_chars):
+                return "DNA"
+            # Check if the sequence contains only amino acid characters
+            elif set(sequence).issubset(amino_acid_chars):
+                return "Amino Acid"
+            else:
+                return "Unknown"
+        except Exception as e:
+            return f"Error: {e}"
+
+    @staticmethod
+    def alleles2ref(files_dir: str, outpath: str, outname: str):
+        """
+        Create cgMLST reference sequences using fasta files downloaded from "https://www.cgmlst.org/"
+        """
+        files_dir = os.path.abspath(files_dir)
+        new_records = []
+        for file in os.listdir(files_dir):
+            # print(file)
+            if file.endswith('.fasta'):
+                file_base = file.split('.')[0]
+                # print(file_base)
+                file = os.path.join(files_dir, file)
+                records = SeqIO.parse(file, 'fasta')
+                for record in records:
+                    record.id = file_base + "_" + record.id
+                    record.name = file_base + "_" + record.name
+                    record.description = ''
+                    # print(record.id)
+                    # print(record)
+                    new_records.append(record)
+
+        # check if outpath exists
+        outdir = os.path.abspath(outpath)
+        if not os.path.exists(outdir):
+            os.makedirs(outdir, exist_ok=True)
+
+        # Specify the output file nameå
+        output_file = f'{outname}.fsa'
+        output_file = os.path.join(outdir, output_file)
+        # Write the modified sequences to the new fasta file
+        with open(output_file, "w") as output_handle:
+            SeqIO.write(new_records, output_handle, "fasta")

{cvmcore-0.2.0 → cvmcore-0.2.2}/cvmcore.egg-info/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: cvmcore
-Version: 0.2.0
+Version: 0.2.2
 Summary: SZQ lab data analysis core function
-Home-page: https://github.com/hbucqp/cvmcore
+Home-page: https://github.com/hbucqp/cvmplot
 Author: Qingpo Cui
 Author-email: cqp@cau.edu.cn
 License: MIT Licence

{cvmcore-0.2.0 → cvmcore-0.2.2}/cvmcore.egg-info/SOURCES.txt

@@ -3,15 +3,11 @@ requirements.txt
 setup.py
 cvmcore/__init__.py
 cvmcore/cvmcore.py
-cvmcore/test.py
 cvmcore.egg-info/PKG-INFO
 cvmcore.egg-info/SOURCES.txt
 cvmcore.egg-info/dependency_links.txt
 cvmcore.egg-info/requires.txt
 cvmcore.egg-info/top_level.txt
-cvmcore/inputdir/CPF_RS14355.fasta
-cvmcore/inputdir/CPF_RS14360.fasta
-cvmcore/inputdir/CPF_RS14365.fasta
 demodata/demo.ipynb
 demodata/gene_feature.csv
 demodata/screenshots/circular_dendrogram.png

{cvmcore-0.2.0 → cvmcore-0.2.2}/cvmcore.egg-info/requires.txt

@@ -5,4 +5,3 @@ matplotlib
 numpy
 scipy
 tabulate
-dask

{cvmcore-0.2.0 → cvmcore-0.2.2}/setup.py

@@ -18,7 +18,13 @@ except ImportError:
 
 
 requirements = [
-    'Bio', 'pandas', 'setuptools', 'matplotlib', 'numpy', 'scipy', 'tabulate', 'dask'
+    'Bio',
+    'pandas',
+    'setuptools',
+    'matplotlib',
+    'numpy',
+    'scipy',
+    'tabulate'
 ]
 
 about = {}

cvmcore-0.2.0/cvmcore/__init__.py

@@ -1,10 +0,0 @@
-# -*- coding:utf-8 -*-
-
-__title__ = 'cvmbcore'
-__description__ = 'core function of data analysis used by SZQ lab from China Agricultural University'
-__url__ = 'https://github.com/hbucqp/cvmcore'
-__version__ = "0.2.0"
-__author__ = 'Qingpo Cui'
-__author_email__ = 'cqp@cau.edu.cn'
-__license__ = 'MIT'
-__copyright__ = 'Copyright 2023 Qingpo Cui'