Mercurial > repos > rliterman > csp2

comparison CSP2/bin/userSNPDiffs.py @ 0:01431fa12065

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"planemo upload"
author rliterman
date Mon, 02 Dec 2024 10:40:55 -0500
parents
children 792274118b2e
comparison
equal deleted inserted replaced
-1:000000000000 0:01431fa12065
1 #!/usr/bin/env python3
2
3 import os
4 import sys
5 import pandas as pd
6 import hashlib
7 import argparse
8
9 def checkLineExists(file_path, sha256):
10 if not os.path.exists(file_path):
11 return False
12 try:
13 with open(file_path, 'rb') as file:
14 file_hash = hashlib.sha256()
15 chunk_size = 8192 # Read in 8KB chunks
16 while chunk := file.read(chunk_size):
17 file_hash.update(chunk)
18 return file_hash.hexdigest() == sha256
19 except Exception as e:
20 print(f"Error reading file: {file_path}: {str(e)}")
21 return False
22
23 def processHeader(header_row,snpdiffs_path):
24 header_cols = [item.split(':')[0] for item in header_row]
25 header_vals = [item.split(':')[1] for item in header_row]
26
27 header_data = pd.DataFrame(columns = header_cols)
28 header_data.loc[0] = header_vals
29 header_data['SNPDiffs_File'] = snpdiffs_path
30 return header_data
31
32 parser = argparse.ArgumentParser()
33 parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file")
34 parser.add_argument("--trim_name", help="Trim name")
35 args = parser.parse_args()
36
37 snpdiffs_list_file = args.snpdiffs_file
38 trim_name = args.trim_name
39 header_rows = []
40
41 # Read in all files, and if they exist, read in the header
42 try:
43 snpdiffs_list = [line.strip() for line in open(snpdiffs_list_file, 'r')]
44 except:
45 sys.exit("Error: Unable to read file: " + snpdiffs_list_file)
46
47 for snpdiffs_file in snpdiffs_list:
48 try:
49 snpdiffs_path = os.path.abspath(snpdiffs_file)
50 with open(snpdiffs_path, 'r') as file:
51 top_line = file.readline().lstrip('#').strip().split('\t')
52 header_rows.append(processHeader(top_line,snpdiffs_path))
53 except:
54 sys.exit("Error: Unable to read file: " + snpdiffs_file)
55
56 # Create header df
57 try:
58 all_snpdiffs_data = pd.concat(header_rows,ignore_index=True)
59 all_snpdiffs_data['Reference_ID'] = all_snpdiffs_data['Reference_ID'].str.replace(trim_name,'',regex=False)
60 all_snpdiffs_data['Query_ID'] = all_snpdiffs_data['Query_ID'].str.replace(trim_name,'',regex=False)
61 except:
62 sys.exit("Error: Unable to create header dataframe")
63
64 query_sha_counts = all_snpdiffs_data.groupby('Query_ID')['Query_SHA256'].nunique()
65 reference_sha_counts = all_snpdiffs_data.groupby('Reference_ID')['Reference_SHA256'].nunique()
66 file_counts = all_snpdiffs_data['SNPDiffs_File'].value_counts()
67
68 if ((query_sha_counts > 1).any() or (reference_sha_counts > 1).any()):
69 print(all_snpdiffs_data[all_snpdiffs_data['Query_ID'].isin(query_sha_counts[query_sha_counts > 1].index)])
70 print(all_snpdiffs_data[all_snpdiffs_data['Reference_ID'].isin(reference_sha_counts[reference_sha_counts > 1].index)])
71 sys.exit("Multiple SHA256 values found for the same Query_ID/Reference_ID")
72 elif (file_counts > 1).any():
73 print(all_snpdiffs_data[all_snpdiffs_data['SNPDiffs_File'].isin(file_counts[file_counts > 1].index)])
74 sys.exit("The same SNPDiffs file is listed multiple times")
75 else:
76 results = []
77 for index, row in all_snpdiffs_data.iterrows():
78
79 query_assembly = os.path.abspath(row['Query_Assembly']) if checkLineExists(row['Query_Assembly'], row['Query_SHA256']) else "null"
80 reference_assembly = os.path.abspath(row['Reference_Assembly']) if checkLineExists(row['Reference_Assembly'], row['Reference_SHA256']) else "null"
81
82 result = ",".join([row['SNPDiffs_File'],
83 row['Query_ID'], query_assembly,str(row['Query_Contig_Count']),str(row['Query_Assembly_Bases']),
84 str(row['Query_N50']),str(row['Query_N90']),str(row['Query_L50']),str(row['Query_L90']),row['Query_SHA256'],
85 row['Reference_ID'],reference_assembly,str(row['Reference_Contig_Count']),str(row['Reference_Assembly_Bases']),
86 str(row['Reference_N50']),str(row['Reference_N90']),str(row['Reference_L50']),str(row['Reference_L90']),row['Reference_SHA256']])
87 results.append(result)
88 for result in results:
89 print(result)