kssdtree 2.0.1__tar.gz → 2.0.2__tar.gz

{kssdtree-2.0.1/kssdtree.egg-info → kssdtree-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 2.0.1
+Version: 2.0.2
 Summary: Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. 
 Home-page: https://github.com/yhlink/kssdtree
 Download-URL: https://pypi.org/project/kssdtree

{kssdtree-2.0.1 → kssdtree-2.0.2/kssdtree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 2.0.1
+Version: 2.0.2
 Summary: Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. 
 Home-page: https://github.com/yhlink/kssdtree
 Download-URL: https://pypi.org/project/kssdtree

{kssdtree-2.0.1 → kssdtree-2.0.2}/kssdtree.egg-info/requires.txt

@@ -1,3 +1,4 @@
 pyqt5
 ete3
 requests
+pandas

{kssdtree-2.0.1 → kssdtree-2.0.2}/kssdtree.py

@@ -44,7 +44,7 @@ def sketch(shuf_file=None, genome_files=None, output=None, set_opt=None):
                 end_time = time.time()
                 if end_time - start_time > 120:
                     print(
-                        "Network timeout, please manually download from github (https://github.com/yhlink/kssdtree/tree/master/shuffle_file)")
+                        "Network timeout, please manually download from https://zenodo.org/records/12699159")
                     return False
                 print('Download finished: ', shuf_file)
             elif shuf_file in ['L2K8.shuf', 'L2K9.shuf', 'L3K11.shuf', './L2K8.shuf', './L2K9.shuf', './L3K11.shuf']:
@@ -207,7 +207,12 @@ def visualize(newick=None, taxonomy=None, mode=None):
             return False
         if mode is None:
             mode = 'r'
-        toolutils.view_tree(newick, taxonomy, mode=mode)
+        if taxonomy is not None and mode == 'c':
+            print('Warning: this pipeline only support 'r' (rectangle) mode !!!')
+            mode = 'r'
+            toolutils.view_tree(newick, taxonomy, mode=mode)
+        else:
+            toolutils.view_tree(newick, taxonomy, mode=mode)
     else:
         print('Args error!!!')
         return False
@@ -280,6 +285,9 @@ def subtract(ref_sketch=None, genome_sketch=None, output=None, flag=None):
 def quick(shuf_file=None, genome_files=None, output=None, reference=None, database=None, method='nj', mode='r', N=0):
     if reference is None and database is None:
         if shuf_file is not None and genome_files is not None and output is not None:
+            if toolutils.is_positive_integer(N) or toolutils.is_negative_integer(N):
+                print("N must = 0 !!!")
+                return False
             timeStamp = int(time.mktime(time.localtime(time.time())))
             temp_sketch = toolutils.rs() + '_sketch_' + str(timeStamp)
             temp_phy = toolutils.rs() + '_temp.phy'
@@ -325,7 +333,7 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, databa
     elif reference is None and database == 'gtdbr214':
         if shuf_file is not None and genome_files is not None and output is not None:
             if not toolutils.is_positive_integer(N):
-                print("N must >0 !!!")
+                print("N must > 0 !!!")
                 return False
             if shuf_file != 'L3K9.shuf':
                 print("shuf_file must be set to 'L3K9.shuf'")
@@ -354,83 +362,86 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, databa
             return False
     elif reference is not None and database is None:
         if shuf_file is not None and genome_files is not None and output is not None and method in ['nj', 'dnj']:
-            if shuf_file is not None and genome_files is not None and output is not None and method in ['nj', 'dnj']:
-                if not toolutils.allowed_file(genome_files):
-                    num = toolutils.get_file_num(genome_files)
-                    if num == 1:
-                        print('genome_files is a folder containing at least two . fasta or .fastq files!!!')
-                        return False
-                else:
-                    print('genome_files is a folder containing at least two . fasta or .fastq files, not a file!!!')
+            if toolutils.is_positive_integer(N) or toolutils.is_negative_integer(N):
+                print("N must = 0 !!!")
+                return False
+            if not toolutils.allowed_file(genome_files):
+                num = toolutils.get_file_num(genome_files)
+                if num == 1:
+                    print('genome_files is a folder containing at least two . fasta or .fastq files!!!')
                     return False
-                timeStamp = int(time.mktime(time.localtime(time.time())))
-                temp_reference_sketch = toolutils.rs() + '_ref_sketch_' + str(timeStamp)
-                temp_genomes_sketch = toolutils.rs() + '_sketch_' + str(timeStamp)
-                if not toolutils.allowed_file(reference):
-                    # cur_path = os.getcwd()
-                    # ref_path = os.path.join(cur_path, reference)
-                    num = toolutils.get_file_num(reference)
-                    if num == 1:
-                        temp_union_sketch = temp_reference_sketch
-                    else:
-                        temp_union_sketch = toolutils.rs() + '_ref_union_sketch_' + str(timeStamp)
-                else:
+            else:
+                print('genome_files is a folder containing at least two . fasta or .fastq files, not a file!!!')
+                return False
+            timeStamp = int(time.mktime(time.localtime(time.time())))
+            temp_reference_sketch = toolutils.rs() + '_ref_sketch_' + str(timeStamp)
+            temp_genomes_sketch = toolutils.rs() + '_sketch_' + str(timeStamp)
+            if not toolutils.allowed_file(reference):
+                # cur_path = os.getcwd()
+                # ref_path = os.path.join(cur_path, reference)
+                num = toolutils.get_file_num(reference)
+                if num == 1:
                     temp_union_sketch = temp_reference_sketch
-                temp_subtract_sketch = toolutils.rs() + '_subtract_sketch_' + str(timeStamp)
-                temp_phy = toolutils.rs() + '_temp.phy'
-                print('Step1...')
-                s1 = sketch(shuf_file=shuf_file, genome_files=reference, output=temp_reference_sketch, set_opt=True)
-                if not s1:
-                    return False
-                s2 = sketch(shuf_file=shuf_file, genome_files=genome_files, output=temp_genomes_sketch, set_opt=True)
-                if not s2:
-                    return False
-                print('Step2...')
-                s3 = union(ref_sketch=temp_reference_sketch, output=temp_union_sketch)
-                if not s3:
-                    return False
-                s4 = subtract(ref_sketch=temp_union_sketch, genome_sketch=temp_genomes_sketch,
-                              output=temp_subtract_sketch, flag=1)
-                if not s4:
-                    return False
-                print('Step3...')
-                if method == 'nj':
-                    s5 = dist(genome_sketch=temp_subtract_sketch, output=temp_phy,
-                              flag=0)
                 else:
-                    s5 = dist(genome_sketch=temp_subtract_sketch, output=temp_phy,
-                              flag=1)
-                if not s5:
-                    return False
-                print('Step4...')
-                s6 = build(phylip=temp_phy, output=output, method=method)
-                if not s6:
-                    return False
-                print('Step5...')
-                print('Tree visualization finished!')
-                visualize(newick=output, mode=mode)
-                if platform.system() == 'Linux':
-                    current_directory = os.getcwd()
-                    temp_dir1 = os.path.join(current_directory, temp_reference_sketch)
-                    temp_dir2 = os.path.join(current_directory, temp_genomes_sketch)
-                    temp_dir3 = os.path.join(current_directory, temp_union_sketch)
-                    temp_dir4 = os.path.join(current_directory, temp_subtract_sketch)
-                    temp_dir5 = os.path.join(current_directory, 'distout')
-                    if os.path.exists(temp_dir1):
-                        shutil.rmtree(temp_dir1)
-                    if os.path.exists(temp_dir2):
-                        shutil.rmtree(temp_dir2)
-                    if os.path.exists(temp_dir3):
-                        shutil.rmtree(temp_dir3)
-                    if os.path.exists(temp_dir4):
-                        shutil.rmtree(temp_dir4)
-                    if os.path.exists(temp_dir5):
-                        shutil.rmtree(temp_dir5)
-                    if os.path.exists(temp_phy):
-                        os.remove(temp_phy)
+                    temp_union_sketch = toolutils.rs() + '_ref_union_sketch_' + str(timeStamp)
             else:
-                print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
+                temp_union_sketch = temp_reference_sketch
+            temp_subtract_sketch = toolutils.rs() + '_subtract_sketch_' + str(timeStamp)
+            temp_phy = toolutils.rs() + '_temp.phy'
+            print('Step1...')
+            s1 = sketch(shuf_file=shuf_file, genome_files=reference, output=temp_reference_sketch, set_opt=True)
+            if not s1:
                 return False
+            s2 = sketch(shuf_file=shuf_file, genome_files=genome_files, output=temp_genomes_sketch, set_opt=True)
+            if not s2:
+                return False
+            print('Step2...')
+            s3 = union(ref_sketch=temp_reference_sketch, output=temp_union_sketch)
+            if not s3:
+                return False
+            s4 = subtract(ref_sketch=temp_union_sketch, genome_sketch=temp_genomes_sketch,
+                          output=temp_subtract_sketch, flag=1)
+            if not s4:
+                return False
+            print('Step3...')
+            if method == 'nj':
+                s5 = dist(genome_sketch=temp_subtract_sketch, output=temp_phy,
+                          flag=0)
+            else:
+                s5 = dist(genome_sketch=temp_subtract_sketch, output=temp_phy,
+                          flag=1)
+            if not s5:
+                return False
+            print('Step4...')
+            s6 = build(phylip=temp_phy, output=output, method=method)
+            if not s6:
+                return False
+            print('Step5...')
+            print('Tree visualization finished!')
+            visualize(newick=output, mode=mode)
+            if platform.system() == 'Linux':
+                current_directory = os.getcwd()
+                temp_dir1 = os.path.join(current_directory, temp_reference_sketch)
+                temp_dir2 = os.path.join(current_directory, temp_genomes_sketch)
+                temp_dir3 = os.path.join(current_directory, temp_union_sketch)
+                temp_dir4 = os.path.join(current_directory, temp_subtract_sketch)
+                temp_dir5 = os.path.join(current_directory, 'distout')
+                if os.path.exists(temp_dir1):
+                    shutil.rmtree(temp_dir1)
+                if os.path.exists(temp_dir2):
+                    shutil.rmtree(temp_dir2)
+                if os.path.exists(temp_dir3):
+                    shutil.rmtree(temp_dir3)
+                if os.path.exists(temp_dir4):
+                    shutil.rmtree(temp_dir4)
+                if os.path.exists(temp_dir5):
+                    shutil.rmtree(temp_dir5)
+                if os.path.exists(temp_phy):
+                    os.remove(temp_phy)
+        else:
+            print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
+            return False
+
     else:
         print('Pipeline error, please see https://kssdtree.readthedocs.io/en/latest!!!')
         return False

{kssdtree-2.0.1 → kssdtree-2.0.2}/setup.py

@@ -2,8 +2,6 @@ import sys
 from setuptools import setup, Extension, find_packages
 from os import environ
 import os
-import platform
-
 
 # def get_gcc_version():
 #     gcc_version = subprocess.check_output(['gcc', '--version']).decode('utf-8')
@@ -85,25 +83,16 @@ include_dirs1 = ['kssdheaders']
 include_dirs2 = ['njheaders']
 include_dirs3 = ['dnjheaders']
 
-if 'darwin' in sys.platform:
-    if platform.machine() == 'arm64':
-        require_pakages = []
-    else:
-        require_pakages = [
-            'pyqt5',
-            'ete3',
-            'requests'
-        ]
-else:
-    require_pakages = [
-        'pyqt5',
-        'ete3',
-        'requests'
-    ]
+require_pakages = [
+    'pyqt5',
+    'ete3',
+    'requests',
+    'pandas'
+]
 
 setup(
     name='kssdtree',
-    version='2.0.1',
+    version='2.0.2',
     author='Hang Yang',
     author_email='yhlink1207@gmail.com',
     description="Kssdtree is a versatile Python package for phylogenetic analysis. It also provides one-stop tree construction and visualization. It can handle DNA sequences of both fasta or fastq format, whether gzipped or not. ",
@@ -125,5 +114,3 @@ setup(
     zip_safe=False,
     include_package_data=True
 )
-
-

{kssdtree-2.0.1 → kssdtree-2.0.2}/toolutils.py

@@ -24,6 +24,11 @@ def is_positive_integer(num):
     else:
         return False
 
+def is_negative_integer(num):
+    if isinstance(num, int) and num < 0:
+        return True
+    else:
+        return False
 
 def randomcolor():
     colorArr = ['1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F']