vsnp3 version 3.28

stuber · stuber · commit bc085254dd69 · 2025-04-02T13:32:53.000-06:00
diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ This step combines the VCF files from Step 1 to create SNP matrices and construc
 # Installation
 
 ```bash
-conda create -c conda-forge -c bioconda -n vsnp3 vsnp3=3.27
+conda create -c conda-forge -c bioconda -n vsnp3 vsnp3=3.28
 ```
 
 For detailed Miniconda setup instructions, see [conda instructions](./docs/instructions/conda_instructions.md).
diff --git a/bin/vsnp3_alignment_vcf.py b/bin/vsnp3_alignment_vcf.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import subprocess
diff --git a/bin/vsnp3_annotation.py b/bin/vsnp3_annotation.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import shutil
diff --git a/bin/vsnp3_assembly.py b/bin/vsnp3_assembly.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_best_reference_sourmash.py b/bin/vsnp3_best_reference_sourmash.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import subprocess
diff --git a/bin/vsnp3_bruc_mlst.py b/bin/vsnp3_bruc_mlst.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import io
diff --git a/bin/vsnp3_download_GCA_fasta_get_metadata.py b/bin/vsnp3_download_GCA_fasta_get_metadata.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_download_fasta_gbk_gff_by_acc.py b/bin/vsnp3_download_fasta_gbk_gff_by_acc.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import argparse
diff --git a/bin/vsnp3_excel_merge_defining_snps.py b/bin/vsnp3_excel_merge_defining_snps.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/bin/vsnp3_excel_merge_files.py b/bin/vsnp3_excel_merge_files.py
@@ -10,7 +10,7 @@
     python excel_merger.py -i <input_dir> [options]
 """
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import glob
 import os
diff --git a/bin/vsnp3_fasta_to_fastq.py b/bin/vsnp3_fasta_to_fastq.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import gzip
 import os
diff --git a/bin/vsnp3_fasta_to_snps_table.py b/bin/vsnp3_fasta_to_snps_table.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import subprocess
diff --git a/bin/vsnp3_fastq_stats_seqkit.py b/bin/vsnp3_fastq_stats_seqkit.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import subprocess
diff --git a/bin/vsnp3_file_setup.py b/bin/vsnp3_file_setup.py
@@ -1,15 +1,17 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import shutil
 import re
+import sys
 import pandas as pd
 import multiprocessing
 from datetime import datetime
 import svgwrite
 from cairosvg import svg2png
+import yaml
 
 
 class bcolors:
@@ -141,9 +143,26 @@ def __init__(self, title, hexcode="56, 68, 117"):
         self.banner = f'{os.getcwd()}/{title}-banner.png'
     
 class Latex_Report:
-    ''' 
     '''
-    def __init__(self, sample_name, report_description=None):
+    LaTeX report generator with configurable logo from YAML file
+    '''
+    def __init__(self, sample_name, config_file=None, report_description=None):
+        # If no config file is provided, look for one in the dependencies directory
+        if config_file is None:
+            # Get the directory where the script is located (bin folder)
+            script_dir = os.path.dirname(os.path.abspath(sys.argv[0]))
+            # Go up one level to parent directory
+            parent_dir = os.path.dirname(script_dir)
+            # Look for dependencies folder at the same level as bin
+            dependencies_dir = os.path.join(parent_dir, 'dependencies')
+            # Default config filename in dependencies folder
+            default_config_path = os.path.join(dependencies_dir, 'latex_config.yaml')
+            if os.path.exists(default_config_path):
+                config_file = default_config_path
+        
+        # Load configuration from YAML if provided
+        self.config = self._load_config(config_file)
+        
         date_stamp = datetime.now().strftime('%Y-%m-%d_%H-%M-%S')
         tex_file = f'{sample_name}_{date_stamp}_report.tex'
         self.tex_file = tex_file
@@ -159,7 +178,12 @@ def __init__(self, sample_name, report_description=None):
         print(r'\renewcommand\familydefault{\sfdefault}', file=tex)
         print(r'\usepackage[T1]{fontenc}', file=tex)
         print(r'\usepackage{xcolor}', file=tex)
-        print(r'\lhead{\begin{picture}(0,0) \put(0,0){\includegraphics[width=40mm]{/project/bioinformatic_databases/usdalogo.png}} \end{picture}}', file=tex)
+        
+        # Add logo only if specified in config and file exists
+        logo_path = self.config.get('logo_path')
+        if logo_path and os.path.exists(logo_path):
+            print(r'\lhead{\begin{picture}(0,0) \put(0,0){\includegraphics[width=40mm]{' + logo_path + r'}} \end{picture}}', file=tex)
+        
         current_date = datetime.now().strftime('%B %d, %Y')
         print(r'\rhead{\begin{date} \textbf{\large ' + current_date + r'} \end{date}}', file=tex)
         print(r'\begin{adjustbox}{width=1\textwidth} \\', file=tex)
@@ -171,8 +195,25 @@ def __init__(self, sample_name, report_description=None):
         print(r'\vspace{0.5 mm}', file=tex)
         print(r'\begin{document}', file=tex)
         self.tex = tex
-
-    def latex_ending(self,):
+    
+    def _load_config(self, config_file):
+        """Load configuration from YAML file or use defaults"""
+        default_config = {
+            'logo_path': None  # Default is no logo
+        }
+        
+        if config_file and os.path.exists(config_file):
+            try:
+                with open(config_file, 'r') as f:
+                    user_config = yaml.safe_load(f)
+                    if user_config:
+                        default_config.update(user_config)
+            except Exception as e:
+                print(f"Error loading config file: {e}")
+        
+        return default_config
+    
+    def latex_ending(self):
         print(r'\end{document}', file=self.tex)
         self.tex.close()
         os.system(f'pdflatex -interaction=nonstopmode {self.tex_file} > /dev/null 2>&1')
diff --git a/bin/vsnp3_group_on_defining_snps.py b/bin/vsnp3_group_on_defining_snps.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_group_reporter.py b/bin/vsnp3_group_reporter.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import io
diff --git a/bin/vsnp3_html_tree.py b/bin/vsnp3_html_tree.py
@@ -8,7 +8,7 @@
 import os
 import math
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 class Node:
     def __init__(self, name=None):
diff --git a/bin/vsnp3_kernel_plots.py b/bin/vsnp3_kernel_plots.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/bin/vsnp3_kraken2_wrapper.py b/bin/vsnp3_kraken2_wrapper.py
@@ -15,7 +15,7 @@
 
 from krona_lca_all import force_tax_number
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 class Kraken2_Identification:
     ''' 
diff --git a/bin/vsnp3_path_adder.py b/bin/vsnp3_path_adder.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import glob
diff --git a/bin/vsnp3_reference_options.py b/bin/vsnp3_reference_options.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_remove_from_analysis.py b/bin/vsnp3_remove_from_analysis.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
@@ -41,17 +41,12 @@ def __init__(self, working_directory='.', excel_remove=None, extension=None):
 
         # Updated pandas read_excel approach
         # Read the first column with no header
-        df = pd.read_excel(excel_remove, header=None, names=['sample'])
-        
-        remove_list = []
-        for each_sample in df['sample']:
-            # Convert to string in case there are non-string values
-            each_sample = str(each_sample)
-            # Use Path for path joining rather than string concatenation
-            remove_list.append(str(working_dir_path / each_sample))  # If .vcf is supplied with the sample name
-            remove_list.append(str(working_dir_path / f"{each_sample}.{extension}"))  # Most common behavior
-            remove_list.append(str(working_dir_path / f"{each_sample}_zc.{extension}"))  # Allow _zc to not be specified
-            
+        df = pd.read_excel(excel_remove, index_col=0, usecols=[0], header=None)
+        remove_list=[]
+        for each_sample in df.index:
+            remove_list.append(f'{working_directory}/{each_sample}') #if .vcf is supplied with the sample name in remove_from_analysis.xlsx
+            remove_list.append(f'{working_directory}/{each_sample}.{extension}') #most common behavior if sample name without extension is provided in remove_from_analysis.xlsx
+            remove_list.append(f'{working_directory}/{each_sample}_zc.{extension}') #allow _zc to not be specified in remove_from_analysis.xlsx
         self.excel_remove = excel_remove
         self.remove_list = remove_list
 
diff --git a/bin/vsnp3_spoligotype.py b/bin/vsnp3_spoligotype.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import gzip
diff --git a/bin/vsnp3_step1.py b/bin/vsnp3_step1.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_step2.py b/bin/vsnp3_step2.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import sys
diff --git a/bin/vsnp3_table_compare.py b/bin/vsnp3_table_compare.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/bin/vsnp3_vcf_annotation.py b/bin/vsnp3_vcf_annotation.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/bin/vsnp3_vcf_merge_to_fasta.py b/bin/vsnp3_vcf_merge_to_fasta.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/bin/vsnp3_zero_coverage.py b/bin/vsnp3_zero_coverage.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-__version__ = "3.27"
+__version__ = "3.28"
 
 import os
 import re
diff --git a/dependencies/latex_config.yaml b/dependencies/latex_config.yaml
@@ -0,0 +1,2 @@
+# # latex_config.yaml
+logo_path: /path/to/logo.png
