infer_fitness.py

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High-level description

This script performs fitness inference on a given sequence alignment to predict evolutionary relationships and rank sequences based on their inferred fitness. It uses a phylogenetic approach, considering an outgroup sequence to root the tree and inferring ancestral states.

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Code Structure

The code first parses command-line arguments, reads and processes the input alignment, and identifies the outgroup sequence. Then, it instantiates a sequence_ranking object from the imported module and uses it to perform the fitness inference. Finally, it outputs the inferred tree, ancestral sequences, and sequence rankings.

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References

This script references the following code symbols:

• alignment (from sequence_ranking module)
• sequence_ranking (from sequence_ranking module)
• tree_utils (imported module)

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Symbols

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ofunc

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Description

This function determines the appropriate file opening method based on the file extension. It uses gzip.open for ‘.gz’ files and the built-in open function otherwise.

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Inputs

Name	Type	Description
fname	str	The name of the file to open.
mode	str	The mode in which to open the file (e.g., ‘r’ for reading, ‘w’ for writing).

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Outputs

Name	Type	Description
file object	file	A file object representing the opened file.

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main execution block

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Description

This block of code executes the main functionality of the script. It reads the alignment file, identifies the outgroup sequence, performs fitness inference, and writes the results to files.

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Internal Logic

1. Read alignment and outgroup:
   • Reads the alignment file in FASTA format.
   • Identifies the outgroup sequence based on the provided --outgroup argument.
2. Set up sequence data and perform prediction:
   • Creates an alignment object from the input alignment and outgroup.
   • Instantiates a sequence_ranking object with specified parameters.
   • Predicts the best node using the predict() method of the sequence_ranking object.
3. Output results:
   • Creates a directory for output files based on the current date and time.
   • Writes the reconstructed tree in Newick format to reconstructed_tree.nwk.
   • Writes inferred ancestral sequences to ancestral_sequences.fasta.
   • Writes sequence rankings for terminal and non-terminal nodes to separate files.
   • Optionally plots the marked-up tree if the --plot flag is set.

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Dependencies

Dependency	Purpose
argparse	Parsing command-line arguments.
matplotlib	Plotting the marked-up tree (optional).
Bio	Handling sequence alignments and phylogenetic trees.
numpy	Numerical operations.
tree_utils	Utility functions for tree manipulation and visualization.
sequence_ranking	Module containing classes and functions for sequence ranking and fitness inference.

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Configuration

This script uses command-line arguments for configuration. See the “parse the command line arguments” section for details on available options and their descriptions.

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Error Handling

The script includes a basic check for the presence of the outgroup sequence in the alignment. If not found, it prints an error message and exits.

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Logging

This script does not implement specific logging mechanisms.

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TODOs

This script does not contain any TODOs or notes.