kssdtree 1.1.8__tar.gz → 1.1.9__tar.gz

{kssdtree-1.1.8/kssdtree.egg-info → kssdtree-1.1.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 1.1.8
+Version: 1.1.9
 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-1.1.8 → kssdtree-1.1.9/kssdtree.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: kssdtree
-Version: 1.1.8
+Version: 1.1.9
 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-1.1.8 → kssdtree-1.1.9}/kssdtree.py

@@ -270,9 +270,17 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
     if reference is None and taxonomy is None:
         if shuf_file is not None and genome_files is not None and output is not None:
             timeStamp = int(time.mktime(time.localtime(time.time())))
-            temp_sketch = genome_files + '_sketch_' + str(timeStamp)
-            temp_phy = 'temp.phy'
+            temp_sketch = toolutils.rs() + '_sketch_' + str(timeStamp)
+            temp_phy = toolutils.rs() + '_temp.phy'
             print('Step1...')
+            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!!!')
+                return False
             s1 = sketch(shuf_file=shuf_file, genome_files=genome_files, output=temp_sketch, set_opt=False)
             if not s1:
                 return False
@@ -301,7 +309,7 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 if os.path.exists(temp_phy):
                     os.remove(temp_phy)
         else:
-            print('Args error!!!')
+            print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
             return False
 
     elif reference == 'gtdbr214_sketch' and taxonomy is None:
@@ -310,10 +318,10 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 print("N must >0 !!!")
                 return False
             if shuf_file != 'L3K9.shuf':
-                print("shuffle file must be set to 'L3K9.shuf'")
+                print("shuf_file must be set to 'L3K9.shuf'")
                 return False
             timeStamp = int(time.mktime(time.localtime(time.time())))
-            qry_sketch = 'sketch_' + str(timeStamp)
+            qry_sketch = toolutils.rs() + '_sketch_' + str(timeStamp)
             s1 = sketch(shuf_file=shuf_file, genome_files=genome_files, output=qry_sketch, set_opt=True)
             if not s1:
                 return False
@@ -332,26 +340,34 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                 if os.path.exists(temp_dir2):
                     os.remove(temp_dir2)
         else:
-            print('Args error!!!')
+            print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
             return False
     else:
         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!!!')
+                    return False
                 timeStamp = int(time.mktime(time.localtime(time.time())))
-                temp_reference_sketch = 'ref_sketch_' + str(timeStamp)
-                temp_genomes_sketch = genome_files + '_sketch_' + str(timeStamp)
+                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(ref_path)
+                    # 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 = 'ref_union_sketch_' + str(timeStamp)
+                        temp_union_sketch = toolutils.rs() + '_ref_union_sketch_' + str(timeStamp)
                 else:
                     temp_union_sketch = temp_reference_sketch
-                temp_subtract_sketch = genome_files + '_subtract_sketch_' + str(timeStamp)
-                temp_phy = 'temp.phy'
+                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:
@@ -403,5 +419,5 @@ def quick(shuf_file=None, genome_files=None, output=None, reference=None, taxono
                     if os.path.exists(temp_phy):
                         os.remove(temp_phy)
             else:
-                print('Args error!!!')
+                print('Args error, please see https://kssdtree.readthedocs.io/en/latest!!!')
                 return False

{kssdtree-1.1.8 → kssdtree-1.1.9}/setup.py

@@ -90,7 +90,7 @@ require_pakages = [
 
 setup(
     name='kssdtree',
-    version='1.1.8',
+    version='1.1.9',
     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-1.1.8 → kssdtree-1.1.9}/toolutils.py

@@ -5,12 +5,18 @@ import requests
 import json
 import zipfile
 import pandas as pd
-
+import string
 
 def allowed_file(filename):
     allowed_extensions = ['.fa', '.fa.gz', '.fasta', '.fasta.gz', '.fna', '.fna.gz', '.fastq', '.fastq.gz']
     return any(filename.endswith(ext) for ext in allowed_extensions)
 
+def rs():
+    letters = string.ascii_lowercase
+    numbers = string.digits
+    random_letters = ''.join(random.choice(letters) for i in range(6))
+    random_numbers = ''.join(random.choice(numbers) for i in range(3))
+    return random_letters + random_numbers
 
 def is_positive_integer(num):
     if isinstance(num, int) and num > 0: