Initial commit
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Zhongwei Li
299
skills/biogeobears/scripts/validate_geography_file.py
Executable file
299
skills/biogeobears/scripts/validate_geography_file.py
Executable file
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#!/usr/bin/env python3
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"""
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Validates and optionally reformats a BioGeoBEARS geography file.
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Geography files must follow the PHYLIP-like format:
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Line 1: n_species [TAB] n_areas [TAB] (area1 area2 area3 ...)
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Lines 2+: species_name [TAB] binary_string (e.g., 011 for absent in area1, present in area2 and area3)
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Common errors:
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- Spaces instead of tabs
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- Spaces in species names
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- Spaces within binary strings
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- Species names not matching tree tip labels
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"""
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import sys
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import argparse
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import re
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from pathlib import Path
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def validate_geography_file(filepath, tree_tips=None):
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"""
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Validate geography file format.
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Args:
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filepath: Path to geography file
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tree_tips: Optional set of tree tip labels to validate against
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Returns:
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dict with validation results and any errors/warnings
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"""
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errors = []
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warnings = []
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info = {}
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with open(filepath, 'r') as f:
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lines = [line.rstrip('\n\r') for line in f.readlines()]
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if not lines:
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errors.append("File is empty")
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return {'valid': False, 'errors': errors, 'warnings': warnings, 'info': info}
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# Parse header line
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header = lines[0]
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if '\t' not in header:
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errors.append("Line 1: Missing tab delimiter (should be: n_species [TAB] n_areas [TAB] (area_names))")
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else:
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parts = header.split('\t')
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if len(parts) < 3:
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errors.append("Line 1: Expected format 'n_species [TAB] n_areas [TAB] (area_names)'")
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else:
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try:
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n_species = int(parts[0])
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n_areas = int(parts[1])
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# Parse area names
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area_part = parts[2].strip()
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if not (area_part.startswith('(') and area_part.endswith(')')):
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errors.append("Line 1: Area names should be in parentheses: (A B C)")
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else:
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areas = area_part[1:-1].split()
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if len(areas) != n_areas:
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errors.append(f"Line 1: Declared {n_areas} areas but found {len(areas)} area names")
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info['n_species'] = n_species
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info['n_areas'] = n_areas
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info['areas'] = areas
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# Validate species lines
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species_found = []
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for i, line in enumerate(lines[1:], start=2):
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if not line.strip():
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continue
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if '\t' not in line:
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errors.append(f"Line {i}: Missing tab between species name and binary code")
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continue
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parts = line.split('\t')
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if len(parts) != 2:
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errors.append(f"Line {i}: Expected exactly one tab between species name and binary code")
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continue
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species_name = parts[0]
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binary_code = parts[1]
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# Check for spaces in species name
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if ' ' in species_name:
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errors.append(f"Line {i}: Species name '{species_name}' contains spaces (use underscores instead)")
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# Check for spaces in binary code
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if ' ' in binary_code or '\t' in binary_code:
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errors.append(f"Line {i}: Binary code '{binary_code}' contains spaces or tabs (should be like '011' with no spaces)")
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# Check binary code length
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if len(binary_code) != n_areas:
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errors.append(f"Line {i}: Binary code length ({len(binary_code)}) doesn't match number of areas ({n_areas})")
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# Check binary code characters
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if not all(c in '01' for c in binary_code):
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errors.append(f"Line {i}: Binary code contains invalid characters (only 0 and 1 allowed)")
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species_found.append(species_name)
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# Check species count
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if len(species_found) != n_species:
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warnings.append(f"Header declares {n_species} species but found {len(species_found)} data lines")
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info['species'] = species_found
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# Check against tree tips if provided
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if tree_tips:
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species_set = set(species_found)
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tree_set = set(tree_tips)
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missing_in_tree = species_set - tree_set
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missing_in_geog = tree_set - species_set
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if missing_in_tree:
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errors.append(f"Species in geography file but not in tree: {', '.join(sorted(missing_in_tree))}")
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if missing_in_geog:
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errors.append(f"Species in tree but not in geography file: {', '.join(sorted(missing_in_geog))}")
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except ValueError:
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errors.append("Line 1: First two fields must be integers (n_species and n_areas)")
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return {
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'valid': len(errors) == 0,
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'errors': errors,
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'warnings': warnings,
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'info': info
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}
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def reformat_geography_file(input_path, output_path, delimiter=','):
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"""
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Attempt to reformat a geography file from common formats.
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Args:
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input_path: Path to input file
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output_path: Path for output file
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delimiter: Delimiter used in input file (default: comma)
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"""
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with open(input_path, 'r') as f:
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lines = [line.strip() for line in f.readlines()]
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# Detect if first line is a header
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header_line = lines[0]
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has_header = not header_line[0].isdigit()
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if has_header:
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# Parse area names from header
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parts = header_line.split(delimiter)
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species_col = parts[0]
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area_names = [p.strip() for p in parts[1:]]
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data_lines = lines[1:]
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else:
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# No header, infer from first data line
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parts = lines[0].split(delimiter)
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n_areas = len(parts) - 1
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area_names = [chr(65 + i) for i in range(n_areas)] # A, B, C, ...
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data_lines = lines
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# Parse species data
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species_data = []
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for line in data_lines:
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if not line:
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continue
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parts = line.split(delimiter)
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if len(parts) < 2:
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continue
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species_name = parts[0].strip().replace(' ', '_')
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presence = ''.join(['1' if p.strip() in ['1', 'present', 'Present', 'TRUE', 'True'] else '0'
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for p in parts[1:]])
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species_data.append((species_name, presence))
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# Write output
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with open(output_path, 'w') as f:
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# Header line
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n_species = len(species_data)
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n_areas = len(area_names)
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f.write(f"{n_species}\t{n_areas}\t({' '.join(area_names)})\n")
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# Species lines
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for species_name, binary_code in species_data:
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f.write(f"{species_name}\t{binary_code}\n")
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print(f"Reformatted {n_species} species across {n_areas} areas")
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print(f"Output written to: {output_path}")
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def main():
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parser = argparse.ArgumentParser(
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description='Validate and reformat BioGeoBEARS geography files',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Validate a geography file
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python validate_geography_file.py input.txt --validate
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# Reformat from CSV to PHYLIP format
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python validate_geography_file.py input.csv --reformat -o output.data
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# Reformat with tab delimiter
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python validate_geography_file.py input.txt --reformat --delimiter tab -o output.data
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"""
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)
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parser.add_argument('input', help='Input geography file')
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parser.add_argument('--validate', action='store_true',
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help='Validate the file format')
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parser.add_argument('--reformat', action='store_true',
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help='Reformat file to BioGeoBEARS format')
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parser.add_argument('-o', '--output',
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help='Output file path (required for --reformat)')
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parser.add_argument('--delimiter', default=',',
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help='Delimiter in input file (default: comma). Use "tab" for tab-delimited.')
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parser.add_argument('--tree',
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help='Newick tree file to validate species names against')
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args = parser.parse_args()
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if args.delimiter.lower() == 'tab':
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args.delimiter = '\t'
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# Parse tree tips if provided
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tree_tips = None
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if args.tree:
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try:
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with open(args.tree, 'r') as f:
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tree_string = f.read().strip()
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# Extract tip labels using regex
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tree_tips = re.findall(r'([^(),:\s]+):', tree_string)
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if not tree_tips:
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tree_tips = re.findall(r'([^(),:\s]+)[,)]', tree_string)
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print(f"Found {len(tree_tips)} tips in tree file")
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except Exception as e:
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print(f"Warning: Could not parse tree file: {e}")
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if args.validate:
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result = validate_geography_file(args.input, tree_tips)
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print(f"\nValidation Results for: {args.input}")
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print("=" * 60)
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if result['info']:
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print(f"\nFile Info:")
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print(f" Species: {result['info'].get('n_species', 'unknown')}")
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print(f" Areas: {result['info'].get('n_areas', 'unknown')}")
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if 'areas' in result['info']:
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print(f" Area names: {', '.join(result['info']['areas'])}")
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if result['warnings']:
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print(f"\nWarnings ({len(result['warnings'])}):")
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for warning in result['warnings']:
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print(f" ⚠️ {warning}")
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if result['errors']:
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print(f"\nErrors ({len(result['errors'])}):")
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for error in result['errors']:
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print(f" ❌ {error}")
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else:
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print(f"\n✅ File is valid!")
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return 0 if result['valid'] else 1
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elif args.reformat:
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if not args.output:
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print("Error: --output required when using --reformat")
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return 1
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try:
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reformat_geography_file(args.input, args.output, args.delimiter)
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# Validate reformatted file
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result = validate_geography_file(args.output, tree_tips)
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if result['valid']:
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print("✅ Reformatted file is valid!")
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else:
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print("\n⚠️ Reformatted file has validation errors:")
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for error in result['errors']:
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print(f" ❌ {error}")
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return 1
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except Exception as e:
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print(f"Error during reformatting: {e}")
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return 1
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else:
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parser.print_help()
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return 1
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return 0
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if __name__ == '__main__':
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sys.exit(main())
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