kssdtree 2.0.0__tar.gz → 2.0.2__tar.gz

{kssdtree-2.0.0/kssdtree.egg-info → kssdtree-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 2.0.0
+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-2.0.0 → kssdtree-2.0.2/kssdtree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 2.0.0
+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-2.0.0 → kssdtree-2.0.2}/kssdtree.egg-info/requires.txt

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

{kssdtree-2.0.0 → kssdtree-2.0.2}/kssdtree.py

@@ -26,12 +26,15 @@ def sketch(shuf_file=None, genome_files=None, output=None, set_opt=None):
                     print('Genome format error for file:', filename)
                     return False
         if not os.path.exists(shuf_file):
-            if shuf_file in ['L3K9.shuf', './L3K9.shuf']:
+            if shuf_file in ['L3K9.shuf', './L3K9.shuf', 'L3K10.shuf', './L3K10.shuf']:
                 print('Downloading...', shuf_file)
                 import http.client
                 http.client.HTTPConnection._http_vsn = 10
                 http.client.HTTPConnection._http_vsn_str = 'HTTP/1.0'
-                url = 'http://www.metakssdcoabundance.link/kssdtree/shuffle/' + shuf_file
+                if shuf_file == 'L3K9.shuf' or shuf_file == './L3K9.shuf':
+                    url = 'https://zenodo.org/records/12699159/files/L3K9.shuf?download=1'
+                else:
+                    url = 'https://zenodo.org/records/12699159/files/L3K10.shuf?download=1'
                 start_time = time.time()
                 response = requests.get(url, stream=True)
                 with open(shuf_file, 'wb') as file:
@@ -41,11 +44,10 @@ 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', 'L3K10.shuf', 'L2K9.shuf', 'L3K11.shuf', './L2K8.shuf', './L3K10.shuf',
-                               './L2K9.shuf', './L3K11.shuf']:
+            elif shuf_file in ['L2K8.shuf', 'L2K9.shuf', 'L3K11.shuf', './L2K8.shuf', './L2K9.shuf', './L3K11.shuf']:
                 print('Shuffling...', shuf_file)
                 file_name = shuf_file.split('.')[0]
                 k = int(file_name[3:])
@@ -74,14 +76,14 @@ def sketch(shuf_file=None, genome_files=None, output=None, set_opt=None):
         return False
 
 
-def dist(ref_sketch=None, qry_sketch=None, output=None, flag=None):
-    if ref_sketch is not None and qry_sketch is not None and output is not None:
-        if not os.path.exists(ref_sketch):
-            print('No such file or directory: ', ref_sketch)
-            return False
-        if not os.path.exists(qry_sketch):
-            print('No such file or directory: ', qry_sketch)
+def dist(genome_sketch=None, output=None, flag=None):
+    if genome_sketch is not None and output is not None:
+        if not os.path.exists(genome_sketch):
+            print('No such file or directory: ', genome_sketch)
             return False
+        # if not os.path.exists(qry_sketch):
+        #     print('No such file or directory: ', qry_sketch)
+        #     return False
         if flag is None:
             flag = 0
         print('Disting...')
@@ -95,7 +97,7 @@ def dist(ref_sketch=None, qry_sketch=None, output=None, flag=None):
         else:
             output_name = output
         if output_name.endswith(".phy") or output_name.endswith(".phylip"):
-            kssd.dist_dispatch(ref_sketch, output, qry_sketch, 2, 0, flag)
+            kssd.dist_dispatch(genome_sketch, output, genome_sketch, 2, 0, flag)
             end = time.time()
             print('Dist spend time：%.2fs' % (end - start))
             print('Dist finished!')
@@ -108,23 +110,26 @@ def dist(ref_sketch=None, qry_sketch=None, output=None, flag=None):
         return False
 
 
-def retrieve(ref_sketch=None, qry_sketch=None, output=None, N=None, method=None):
-    if ref_sketch is not None and qry_sketch is not None and output is not None:
+def retrieve(database=None, genome_sketch=None, output=None, N=None, method=None):
+    if database is not None and genome_sketch is not None and output is not None:
         if method is None:
             method = 'nj'
         if method not in ['nj', 'dnj']:
             print('Only support nj and dnj methods!!!')
             return
-        if not os.path.exists(qry_sketch):
-            print('No such file or directory: ', qry_sketch)
+        if not os.path.exists(genome_sketch):
+            print('No such file or directory: ', genome_sketch)
             return False
-        if ref_sketch == 'gtdbr214_sketch':
+        if database == 'gtdbr214':
             print('Retrieving...')
             start = time.time()
             if not os.path.exists(output):
                 os.makedirs(output)
                 print("Created directory:", output)
-            newick, accession_taxonomy = toolutils.upload_request(qry_sketch=qry_sketch, method=method, N=N)
+            else:
+                print('Output path exist!!!')
+                return False
+            newick, accession_taxonomy = toolutils.upload_request(qry_sketch=genome_sketch, method=method, N=N)
             if newick is None:
                 print('Server error!!!')
                 return False
@@ -138,7 +143,7 @@ def retrieve(ref_sketch=None, qry_sketch=None, output=None, N=None, method=None)
             print('Retrieve finished!')
             return True
         else:
-            print("ref_sketch must be set to 'gtdbr214_sketch'")
+            print("database only support 'gtdbr214'")
             return False
     else:
         print('Args error!!!')
@@ -184,6 +189,12 @@ def build(phylip=None, output=None, method=None):
                 print('Build spend time：%.2fs' % (end - start))
                 print('Build finished!')
                 return True
+            else:
+                print('phylip format error, Check that the phylip format is consistent with NJ or DNJ requirements!!!')
+                return False
+        else:
+            print('Output type error, only supports .newick (.nwk) format:', output_name)
+            return False
     else:
         print('Args error!!!')
         return False
@@ -196,7 +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
@@ -266,9 +282,12 @@ def subtract(ref_sketch=None, genome_sketch=None, output=None, flag=None):
         return False
 
 
-def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxonomy=None, method='nj', mode='r', N=0):
-    if reference is None and taxonomy is 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'
@@ -286,9 +305,9 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 return False
             print('Step2...')
             if method == 'nj':
-                s2 = dist(ref_sketch=temp_sketch, qry_sketch=temp_sketch, output=temp_phy, flag=0)
+                s2 = dist(genome_sketch=temp_sketch, output=temp_phy, flag=0)
             else:
-                s2 = dist(ref_sketch=temp_sketch, qry_sketch=temp_sketch, output=temp_phy, flag=1)
+                s2 = dist(genome_sketch=temp_sketch, output=temp_phy, flag=1)
             if not s2:
                 return False
             print('Step3...')
@@ -297,7 +316,7 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 return False
             print('Step4...')
             print('Tree visualization finished!')
-            visualize(newick=output, taxonomy=taxonomy, mode=mode)
+            visualize(newick=output, mode=mode)
             if platform.system() == 'Linux':
                 current_directory = os.getcwd()
                 temp_dir1 = os.path.join(current_directory, temp_sketch)
@@ -311,11 +330,10 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
         else:
             print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
             return False
-
-    elif reference == 'gtdbr214_sketch' and taxonomy is None:
+    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'")
@@ -325,7 +343,7 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
             s1 = sketch(shuf_file=shuf_file, genome_files=genome_files, output=qry_sketch, set_opt=True)
             if not s1:
                 return False
-            s2 = retrieve(ref_sketch=reference, qry_sketch=qry_sketch, output=output, N=N, method=method)
+            s2 = retrieve(database=database, genome_sketch=qry_sketch, output=output, N=N, method=method)
             if not s2:
                 return False
             print('Tree visualization finished!')
@@ -342,82 +360,88 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
         else:
             print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
             return False
-    else:
+    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(ref_sketch=temp_subtract_sketch, qry_sketch=temp_subtract_sketch, output=temp_phy,
-                              flag=0)
                 else:
-                    s5 = dist(ref_sketch=temp_subtract_sketch, qry_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, taxonomy=taxonomy, 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:
+                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:
-                print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
+                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-2.0.0 → kssdtree-2.0.2}/setup.py

@@ -1,17 +1,15 @@
 import sys
-
 from setuptools import setup, Extension, find_packages
 from os import environ
-import subprocess
 import os
 
-
-def get_gcc_version():
-    gcc_version = subprocess.check_output(['gcc', '--version']).decode('utf-8')
-    version_line = gcc_version.split('\n', 1)[0]
-    version_str = version_line.split()[-1]
-    return version_str
-
+# def get_gcc_version():
+#     gcc_version = subprocess.check_output(['gcc', '--version']).decode('utf-8')
+#     version_line = gcc_version.split('\n', 1)[0]
+#     version_str = version_line.split()[-1]
+#     return version_str
+extra_compile_args = []
+extra_link_args = []
 if 'darwin' in sys.platform:
     target_dirs = ["gcc-9", "gcc-10", "gcc-11", "gcc-12", "gcc-13", "gcc-14", "gcc-15"]
     path = "/opt/homebrew/bin/"
@@ -32,12 +30,10 @@ if 'darwin' in sys.platform:
             gcc_path = "/opt/homebrew/bin/gcc-15"
         else:
             gcc_path = "/opt/homebrew/bin/gcc-13"
-        gcc_command = 'gcc-' + str(gcc_version)
         extra_compile_args = ['-fopenmp']
         extra_link_args = ['-fopenmp']
         os.environ["CC"] = gcc_path
 else:
-    gcc_command = 'gcc'
     if environ.get('CC') and 'clang' in environ['CC']:
         # clang
         extra_compile_args = ['-fopenmp=libomp']
@@ -90,13 +86,13 @@ include_dirs3 = ['dnjheaders']
 require_pakages = [
     'pyqt5',
     'ete3',
-    'requests'
+    'requests',
+    'pandas'
 ]
 
-
 setup(
     name='kssdtree',
-    version='2.0.0',
+    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. ",
@@ -118,5 +114,3 @@ setup(
     zip_safe=False,
     include_package_data=True
 )
-
-

{kssdtree-2.0.0 → 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']