<commit_before>#!/usr/bin/env python2.7
import pandas as pd
import numpy as np
import sys
import matplotlib
from scipy.spatial.distance import pdist, squareform
from scipy.cluster.hierarchy import linkage, dendrogram
from matplotlib import pyplot as plt
from scipy.cluster import hierarchy
import sys, getopt

opts, args = getopt.getopt(sys.argv[1:], 'i:o:d:h', ['help', 'input', 'output', 'delimiter'])

def usage():
        print """
Example script for plotting hierarchical clusters on top of heatmap
using various Python modules. Output to SVG. Will need to move axes
around to better suit incoming data.

Assumes row identifiers in first column.
Assumes column identifiers in first row.
Assumes all input data is numerical

Usage: tsv_clustering.py -i <INPUT> -o <fig.svg> [OPTIONS]

OPTIONS:<commit_msg>Forgot to update option parser for log-normalize option<commit_after>#!/usr/bin/env python2.7
import pandas as pd
import numpy as np
import sys
import matplotlib
from scipy.spatial.distance import pdist, squareform
from scipy.cluster.hierarchy import linkage, dendrogram
from matplotlib import pyplot as plt
from scipy.cluster import hierarchy
import sys, getopt

opts, args = getopt.getopt(sys.argv[1:], 'i:o:d:hl', ['help', 'input', 'output', 'delimiter', 'log-normalize'])

def usage():
        print """
Example script for plotting hierarchical clusters on top of heatmap
using various Python modules. Output to SVG. Will need to move axes
around to better suit incoming data.

Assumes row identifiers in first column.
Assumes column identifiers in first row.
Assumes all input data is numerical

Usage: tsv_clustering.py -i <INPUT> -o <fig.svg> [OPTIONS]

OPTIONS:
{'fraction_non_alphanumeric': 0.08522050059594756, 'fraction_numerical': 0.003575685339690107, 'mean_word_length': 4.932862190812721, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2050163', 'n_tokens_mistral': 523, 'n_tokens_neox': 499, 'n_words': 211}