Adding script to create cov, counts, contigID matrix

workflow/scripts/create_matrix.py

@@ -0,0 +1,264 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 -*-
+# Author: Skyler Kuhn
+
+# Standard Library
+from __future__ import print_function
+import sys, os
+import textwrap
+
+# 3rd party packages,
+# installed from pypi
+import argparse
+import pandas as pd
+
+
+_help = textwrap.dedent("""create_matrix.py: Wake up Neo...
+@Usage:
+    $ ./create_matrix.py [-h] [--version] \\
+            [--clean-suffix CLEAN_SUFFIX] \\
+            [--nan-values NAN_VALUES] \\
+            --join-on JOIN_ON \\
+            --extract EXTRACT \\
+            --output OUTPUT \\
+            --input FILE_1 [FILE_2 ...]
+
+@About:
+    Given a list of files, an output file name, 
+    a column name to join on, and a column name 
+    containing features to extract, this script 
+    will create a counts matrix for N sample by 
+    M features. By default, sample column names
+    in the resulting matrix will be the basename 
+    of the X file that was provided; however, you 
+    can provide string to strip any suffices from 
+    the sample's filename.  
+
+@Required Arguments:
+    --input FILE_1 [FILE_2 ...]
+                   One or more files to create the 
+                   matrix from. Multiple files are 
+                   joined on the `--join-on` column.
+    --output OUTPUT  
+                   Output file name. The file name of 
+                   the resulting matrix file. Please
+                   note that is resulting output file
+                   will be tab-delimited. 
+    --join-on JOIN_ON
+                   Joins multiple files on this column
+                   name. Please note this column name 
+                   must exist in each `--input` file.  
+    --extract EXTRACT 
+                   Extracts features from this column 
+                   to create the resulting matrix.
+
+@Options
+    --clean-suffix CLEAN_SUFFIX
+                    Cleans each sample name in matrix to 
+                    remove this suffix.
+    --nan-values NAN_VALUES
+                    Set missing feature values to this 
+                    instead of the default. By default,
+                    any missing fields are set to an
+                    empty string, i.e ''. 
+    --h, --help     Shows this help message and exits.
+
+
+'The Matrix is everywhere. It is all around us. Even 
+now in this very room' 
+    - Morpheus 
+"""
+)
+
+
+def err(*message, **kwargs):
+    """Prints any provided args to standard error.
+    kwargs can be provided to modify print functions 
+    behavior.
+    @param message <any>:
+        Values printed to standard error
+    @params kwargs <print()>
+        Key words to modify print function behavior
+    """
+    print(*message, file=sys.stderr, **kwargs)
+
+
+
+def fatal(*message, **kwargs):
+    """Prints any provided args to standard error
+    and exits with an exit code of 1.
+    @param message <any>:
+        Values printed to standard error
+    @params kwargs <print()>
+        Key words to modify print function behavior
+    """
+    err(*message, **kwargs)
+    sys.exit(1)
+
+
+def build_matrix(file, matrix_dict, join_index, parse_index, clean_suffix=None):
+    """Creates a 2-D matrix, represented as a dictionary, where
+    each key is N sample and its value is a nested dictionary 
+    containing M feature and its extracted value.
+    @param file <str>: 
+        Path to input file with values to extract via `parse_index`.
+    @param matrix_dict <dict[str][str]=[str]>: 
+        Matrix dictionary to create where:
+            [sample][feature] = feature_value
+    @param join_index <int>: 
+        Index of the field to join multiple files, usually the first column.
+    @param parse_index <int>: 
+        Index of field of interest to extract, could be counts.
+    @param clean_suffix <str>:
+        A suffix to remove from a sample name, could be a file extension.
+        Default: None
+	"""
+    # Parse the input file to extract 
+    # M features of interest for N sample
+    with open(file, 'r') as fh:
+        header = next(fh)               # skip over header 
+        sample = os.path.basename(file) # remove path from sample
+        if clean_suffix:
+            # maybe replace with regex later
+            sample = sample.split(clean_suffix)[0]   
+        for line in fh:
+            linelist = line.lstrip().rstrip().split('\t')
+            j_field = linelist[join_index]
+            j_value = linelist[parse_index]
+            if sample not in matrix_dict:
+                matrix_dict[sample] = {}
+            matrix_dict[sample][j_field] = j_value
+    return matrix_dict
+
+
+def main():
+    """Collect command line args and build the matrix."""
+	# Parse command-line arguments
+    # Create a top-level parser
+    parser = argparse.ArgumentParser(
+        usage = argparse.SUPPRESS,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description = _help,
+        add_help=False
+    )
+
+    # Required Positional Arguments
+    # List of input files
+    parser.add_argument(
+        '--input',
+        required=True,
+        nargs = '+',
+        help = argparse.SUPPRESS
+    )
+    # Output file name
+    parser.add_argument(
+        '--output',
+        required=True,
+        type=str,
+        help = argparse.SUPPRESS
+    )
+    # Join-on column name
+    parser.add_argument(
+        '--join-on',
+        required=True,
+        type=str,
+        help = argparse.SUPPRESS
+    )
+    # Extract column name
+    parser.add_argument(
+        '--extract',
+        required=True,
+        type=str,
+        help = argparse.SUPPRESS
+    )
+
+    # Options
+    # Adding verison information
+    parser.add_argument(
+        '--clean-suffix', 
+        required=False,
+        default=None,
+        type=str,
+        help = argparse.SUPPRESS
+    )
+
+    # Set missing values to this
+    # value instead of an empty 
+    # string 
+    parser.add_argument(
+        '--nan-values', 
+        required=False,
+        default='',
+        type=str,
+        help = argparse.SUPPRESS
+    )
+
+    # Add custom help message
+    parser.add_argument(
+        '-h', '--help', 
+        action='help', 
+        help=argparse.SUPPRESS
+    )
+
+    # Collect parsed arguments
+    args = parser.parse_args()
+
+    # Sanity check for usage
+    if len(sys.argv) == 1:
+        # Nothing was provided
+        fatal('Invalid usage: create_matrix.py [-h] ...')
+
+    # Parse N sample's column 
+    # of interest for M features  
+    matrix = {}
+    # Sort input file names to 
+    # create more deterministic 
+    # output regardless of the 
+    # input order the files  
+    for file in sorted(args.input):
+        # Get first line of file
+        # to get column indices 
+        with open(file, 'r') as fh:
+            header = fh.readline().lstrip().rstrip().split('\t')
+            try:
+                extract_field = header.index(args.extract)
+                join_on = header.index(args.join_on)
+            except ValueError:
+                err(
+                    'Error: Missing one of the follow fields: {} or {}'.format(
+                        args.extract,
+                        args.join_on
+                    )
+                )
+                err('in the following --input {} file'.format(file))
+                fatal('Please check that each file contains each column name!')
+
+        # Create a matrix of N samples 
+        # by M features 
+        matrix = build_matrix(
+            file=file, 
+            matrix_dict=matrix,
+            join_index=join_on,
+            parse_index=extract_field,
+            clean_suffix=args.clean_suffix
+        )
+
+
+    # Write matrix to output file
+    df = pd.DataFrame(matrix)
+    df.to_csv(
+        args.output, 
+        sep="\t", 
+        header=True, 
+        index=True, 
+        index_label = args.join_on,
+        na_rep=args.nan_values
+    )
+
+
+if __name__ == '__main__':
+    # Create the matrix
+    try:
+        main()
+    except BrokenPipeError:
+        pass