# HG changeset patch
# User estrain
# Date 1707416327 0
# Node ID 412d55f097555686c36457396775d65187d5fa38
# Parent 57d1d335ce8898f49a5c4add12f2ae6429465b4c
Uploaded
diff -r 57d1d335ce88 -r 412d55f09755 lissero.xml
--- a/lissero.xml Tue Dec 13 18:43:42 2022 +0000
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- lissero
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- '$output1';
- ]]>
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- 10.1128/JCM.42.8.3819-3822.2004
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diff -r 57d1d335ce88 -r 412d55f09755 lissero/lissero.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lissero/lissero.xml Thu Feb 08 18:18:47 2024 +0000
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+ lissero
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+ output1;
+ python $__tool_directory__/variant4b.py output1 output2.txt;
+ ]]>
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+ 10.1128/JCM.42.8.3819-3822.2004
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diff -r 57d1d335ce88 -r 412d55f09755 lissero/variant4b.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/lissero/variant4b.py Thu Feb 08 18:18:47 2024 +0000
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+import sys
+
+def identify_variants_with_genes(input_file_path, output_file_path):
+ # Define the genes of interest
+ genes_of_interest = ['LMO0737', 'ORF2110', 'ORF2819']
+
+ # Open the input file and read its lines
+ with open(input_file_path, 'r') as file:
+ lines = file.readlines()
+
+ # Check if the file has more than just the header
+ if len(lines) <= 1:
+ print("Input file does not contain enough data.")
+ return
+
+ # Extract the column headers and find the indices of the genes of interest
+ headers = lines[0].strip().split('\t')
+ gene_indices = [headers.index(gene) for gene in genes_of_interest]
+ serotype_index = headers.index('SEROTYPE')
+
+ # Initialize a list to hold the modified lines
+ modified_lines = [lines[0]] # Start with the header
+
+ # Process each data line in the input file
+ for line in lines[1:]:
+ data = line.strip().split('\t')
+ # Check if the genes of interest are all present (marked as "FULL")
+ if all(data[index] == 'FULL' for index in gene_indices):
+ # Modify the SEROTYPE column to "4b variant"
+ data[serotype_index] = "4b variant"
+ # Rejoin the modified data into a single string and add it to the list
+ modified_lines.append('\t'.join(data) + '\n')
+
+ # Write the modified lines to the output file
+ with open(output_file_path, 'w') as file:
+ file.writelines(modified_lines)
+
+ print(f'Results written to {output_file_path}')
+
+if __name__ == "__main__":
+ if len(sys.argv) != 3:
+ print("Usage: python script.py ")
+ sys.exit(1)
+
+ input_file_path = sys.argv[1]
+ output_file_path = sys.argv[2]
+ identify_variants_with_genes(input_file_path, output_file_path)
+