kssdtree 1.1.6__tar.gz → 1.1.8__tar.gz

{kssdtree-1.1.6/kssdtree.egg-info → kssdtree-1.1.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 1.1.6
+Version: 1.1.8
 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-1.1.6 → kssdtree-1.1.8}/command_dist.c

@@ -32,6 +32,7 @@
 #include <zlib.h>
 #include <stdbool.h>
 #include <libgen.h>
+
 #ifdef _WIN32
     #include <malloc.h>
 #elif __linux__
@@ -41,9 +42,7 @@
 #endif
 
 #ifdef _WIN32
-
 #include <windows.h>
-
 #endif
 
 #ifdef _WIN32

{kssdtree-1.1.6 → kssdtree-1.1.8}/kssdheaders/global_basic.h

@@ -166,6 +166,8 @@ static inline int isOK_fmt_infile (char* fname, const char *test_fmt[], int test
 #endif
 #include <fcntl.h>
 #include <unistd.h>
+
+
 static inline void check (int test, const char * message, ...)
 {
     if (test) {

{kssdtree-1.1.6 → kssdtree-1.1.8/kssdtree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 1.1.6
+Version: 1.1.8
 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-1.1.6 → kssdtree-1.1.8}/kssdtree.py

@@ -44,7 +44,8 @@ def sketch(shuf_file=None, genome_files=None, output=None, set_opt=None):
                         "Network timeout, please manually download from github (https://github.com/yhlink/kssdtree/tree/master/shuffle_file)")
                     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', 'L3K10.shuf', 'L2K9.shuf', 'L3K11.shuf', './L2K8.shuf', './L3K10.shuf',
+                               './L2K9.shuf', './L3K11.shuf']:
                 print('Shuffling...', shuf_file)
                 file_name = shuf_file.split('.')[0]
                 k = int(file_name[3:])
@@ -124,6 +125,9 @@ def retrieve(ref_sketch=None, qry_sketch=None, output=None, N=None, method=None)
                 os.makedirs(output)
                 print("Created directory:", output)
             newick, accession_taxonomy = toolutils.upload_request(qry_sketch=qry_sketch, method=method, N=N)
+            if newick is None:
+                print('Server error!!!')
+                return False
             with open(os.path.join(output, 'output.newick'), 'w') as f:
                 f.write(newick)
             with open(os.path.join(output, 'output_accession_taxonomy.txt'), 'w') as f:
@@ -283,6 +287,9 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
             s3 = build(phylip=temp_phy, output=output, method=method)
             if not s3:
                 return False
+            print('Step4...')
+            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_sketch)
@@ -293,13 +300,6 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                     shutil.rmtree(temp_dir2)
                 if os.path.exists(temp_phy):
                     os.remove(temp_phy)
-                print('Step4...')
-                print('Tree visualization finished!')
-                visualize(newick=output, taxonomy=taxonomy, mode=mode)
-            else:
-                print('Step4...')
-                print('Tree visualization finished!')
-                visualize(newick=output, taxonomy=taxonomy, mode=mode)
         else:
             print('Args error!!!')
             return False
@@ -313,29 +313,24 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 print("shuffle file must be set to 'L3K9.shuf'")
                 return False
             timeStamp = int(time.mktime(time.localtime(time.time())))
-            qry_sketch =  'sketch_' + str(timeStamp)
+            qry_sketch = 'sketch_' + str(timeStamp)
             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)
             if not s2:
                 return False
+            print('Tree visualization finished!')
+            visualize(newick=os.path.join(output, 'output.newick'),
+                      taxonomy=os.path.join(output, 'output_accession_taxonomy.txt'), mode=None)
             if platform.system() == 'Linux':
-                if platform.system() == 'Linux':
-                    current_directory = os.getcwd()
-                    temp_dir1 = os.path.join(current_directory, qry_sketch)
-                    temp_dir2 = os.path.join(current_directory, qry_sketch + '.zip')
-                    if os.path.exists(temp_dir1):
-                        shutil.rmtree(temp_dir1)
-                    if os.path.exists(temp_dir2):
-                        os.remove(temp_dir2)
-                print('Tree visualization finished!')
-                visualize(newick=os.path.join(output, 'output.newick'),
-                          taxonomy=os.path.join(output, 'output_accession_taxonomy.txt'), mode=None)
-            else:
-                print('Tree visualization finished!')
-                visualize(newick=os.path.join(output, 'output.newick'),
-                          taxonomy=os.path.join(output, 'output_accession_taxonomy.txt'), mode=None)
+                current_directory = os.getcwd()
+                temp_dir1 = os.path.join(current_directory, qry_sketch)
+                temp_dir2 = os.path.join(current_directory, qry_sketch + '.zip')
+                if os.path.exists(temp_dir1):
+                    shutil.rmtree(temp_dir1)
+                if os.path.exists(temp_dir2):
+                    os.remove(temp_dir2)
         else:
             print('Args error!!!')
             return False
@@ -385,6 +380,9 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 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)
@@ -404,13 +402,6 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                         shutil.rmtree(temp_dir5)
                     if os.path.exists(temp_phy):
                         os.remove(temp_phy)
-                    print('Step5...')
-                    print('Tree visualization finished!')
-                    visualize(newick=output, taxonomy=taxonomy, mode=mode)
-                else:
-                    print('Step5...')
-                    print('Tree visualization finished!')
-                    visualize(newick=output, taxonomy=taxonomy, mode=mode)
             else:
                 print('Args error!!!')
                 return False

{kssdtree-1.1.6 → kssdtree-1.1.8}/setup.py

@@ -12,24 +12,20 @@ def get_gcc_version():
     version_str = version_line.split()[-1]
     return version_str
 
-
-gcc_version = get_gcc_version()
-if '9.' in gcc_version:
-    gcc_path = "/opt/homebrew/bin/gcc-9"
-elif '10.' in gcc_version:
-    gcc_path = "/opt/homebrew/bin/gcc-10"
-elif '11.' in gcc_version:
-    gcc_path = "/opt/homebrew/bin/gcc-11"
-elif '12.' in gcc_version:
-    gcc_path = "/opt/homebrew/bin/gcc-12"
-elif '14.' in gcc_version:
-    gcc_path = "/opt/homebrew/bin/gcc-14"
-else:
-    gcc_path = "/opt/homebrew/bin/gcc-13"
-
-
 if 'darwin' in sys.platform:
-    # MacOS
+    gcc_version = get_gcc_version()
+    if '9.' in gcc_version:
+        gcc_path = "/opt/homebrew/bin/gcc-9"
+    elif '10.' in gcc_version:
+        gcc_path = "/opt/homebrew/bin/gcc-10"
+    elif '11.' in gcc_version:
+        gcc_path = "/opt/homebrew/bin/gcc-11"
+    elif '12.' in gcc_version:
+        gcc_path = "/opt/homebrew/bin/gcc-12"
+    elif '14.' in gcc_version:
+        gcc_path = "/opt/homebrew/bin/gcc-14"
+    else:
+        gcc_path = "/opt/homebrew/bin/gcc-13"
     gcc_command = 'gcc-' + str(gcc_version)
     extra_compile_args = ['-fopenmp']
     extra_link_args = ['-fopenmp']
@@ -94,7 +90,7 @@ require_pakages = [
 
 setup(
     name='kssdtree',
-    version='1.1.6',
+    version='1.1.8',
     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. ",

{kssdtree-1.1.6 → kssdtree-1.1.8}/toolutils.py

@@ -78,7 +78,7 @@ def upload_request(qry_sketch, method, N):
         accession_taxonomy = json_data['accession_taxonomy']
         return newick, accession_taxonomy
     else:
-        return None
+        return None, None
 
 def view_tree(newick, taxonomy, mode):
     if taxonomy is None: