Virginie Grosboillot vestalisvirginis
vestalisvirginis
/ asset.py
Last active
November 8, 2023 17:44
add image to Dagster as asset metadata
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| # For metadata | |
| buffer = BytesIO() | |
| _gd_diagram.write(buffer, "png") | |
| image_data = base64.b64encode(buffer.getvalue()) | |
| # Asset metadata | |
| context.add_output_metadata( | |
| metadata={ | |
| "text_metadata": "A synteny diagram had been created.", | |
| "num_sqcs": len(_records), |
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| import numpy as np | |
| from functional import seq | |
| from collections import deque, defaultdict | |
| import time | |
| def RandomNumberGenerator(dna, k): | |
| #return an array (0,t) of random integers, than can be used as starting point for selecting random k-mer along dna strings | |
| return np.random.randint(0, DnaToMatrix(dna).shape[1]+1-k, size = (DnaToMatrix(dna).shape[0], 1)) | |
| def DnaToMatrix(dna): |
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| from itertools import product | |
| from functional import seq | |
| def all_kmers(k): | |
| '''return list of all dna carthesien products of length k''' | |
| all = list(product('ACGT', repeat=k)) | |
| return seq(all).map(lambda x: ''.join(x)).to_list() | |
| def kmer_per_segment(dna_segment, k): | |
| '''return all the dna substrings of length k of the different dna strings in dna list''' |