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bloyal
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oas_paired_human_sars_cov_2

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Commit
58411c1
•
1 Parent(s): 2059e42

Add train test data

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Files changed (5) hide show
  1. .gitattributes +2 -0
  2. download_oas_data.py +23 -0
  3. oas_uri_list.txt +63 -0
  4. test.parquet +3 -0
  5. train.parquet +3 -0
.gitattributes CHANGED
@@ -54,3 +54,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  *.jpeg filter=lfs diff=lfs merge=lfs -text
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  *.webp filter=lfs diff=lfs merge=lfs -text
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  data.parquet filter=lfs diff=lfs merge=lfs -text
 
 
 
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  *.jpeg filter=lfs diff=lfs merge=lfs -text
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  *.webp filter=lfs diff=lfs merge=lfs -text
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  data.parquet filter=lfs diff=lfs merge=lfs -text
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+ test.parquet filter=lfs diff=lfs merge=lfs -text
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+ train.parquet filter=lfs diff=lfs merge=lfs -text
download_oas_data.py ADDED
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+ import pandas as pd
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+
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+ # Download data from OAS
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+ list_of_df = []
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+ with open("scripts/oas_uri_list.txt", "r") as f:
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+ for url in f:
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+ print(url)
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+ df = pd.read_csv(url, skiprows=1, compression="gzip")
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+ df = df[df["complete_vdj_heavy"] == "T"]
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+ df = df[df["complete_vdj_light"] == "T"]
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+ df = df[["sequence_alignment_aa_heavy", "sequence_alignment_aa_light"]]
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+ df["sequence_alignment_aa_joint"] = (
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+ df["sequence_alignment_aa_heavy"]
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+ + "-" * 25
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+ + df["sequence_alignment_aa_light"]
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+ )
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+ list_of_df.append(df)
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+ df = pd.concat(list_of_df, ignore_index=True)
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+ train = df.sample(frac=0.8)
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+ test = df.drop(train.index)
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+
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+ train.to_parquet("data/train.parquet")
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+ test.to_parquet("data/test.parquet")
oas_uri_list.txt ADDED
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