<jupyter_start><jupyter_text>Standalone check<jupyter_code>import pandas as pd
import numpy as np
fname = 'latent_dim_3_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95_ranks.txt'
ranks = pd.read_csv(f'summary/{fname}', sep='\t', index_col=0)
microbe_metadata = pd.read_csv('microbe-metadata.txt', sep='\t', index_col=0)
metabolite_metadata = pd.read_csv('metabolite-metadata.txt', sep='\t', index_col=0)
microbe_metadata = microbe_metadata.loc[ranks.columns]
i = microbe_metadata.Taxon.apply(lambda x: 'Pseudomonas' in x)
pseudomonas = microbe_metadata.loc[i].index
metabolite_metadata = metabolite_metadata.dropna(subset=['expert_annotation'])
np.sum(ranks.loc[metabolite_metadata.index, pseudomonas[0]] > 0)<jupyter_output><empty_output><jupyter_text>qiime2 check<jupyter_code>import qiime2
ranks = qiime2.Artifact.load('ranks.qza').view(pd.DataFrame)
microbe_metadata = pd.read_csv('microbe-metadata.txt', sep='\t', index_col=0)
metabolite_metadata = pd.read_csv('metabolite-metadata.txt', sep='\t', index_col=0)
microbe_metadata = microbe_metadata.loc[ranks.columns]
i = microbe_metadata.Taxon.apply(lambda x: 'Pseudomonas' in x)
pseudomonas = microbe_metadata.loc[i].index
metabolite_metadata = metabolite_metadata.dropna(subset=['expert_annotation'])
np.sum(ranks.loc[metabolite_metadata.index, pseudomonas[0]] > 0)<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.13970588235294118, 'fraction_numerical': 0.019852941176470587, 'mean_word_length': 9.389312977099237, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 11, '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}}
{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '317846', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 546, 'n_tokens_neox': 516, 'n_words': 65, 'path': 'examples/cf/check_rhamnolipids.ipynb', 'repo_name': 'mortonjt/mmvec', 'size': '1360'}