diff --git a/README.md b/README.md index e7fc68e3892af532de5ac4d6e52be45c746cb743..a334ce79c43a3154ccbab2e3d5628311de4c9fe5 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,13 @@ configs: - config_name: default data_files: - split: human - path: "data/human/*.csv" + path: "data/human/*.parquet" - split: mouse_BALB_c - path: "data/mouse_BALB_c/*.csv" + path: "data/mouse_BALB_c/*.parquet" - split: mouse_C57BL_6 - path: "data/mouse_C57BL_6/*.csv" + path: "data/mouse_C57BL_6/*.parquet" - split: rat_SD - path: "data/rat_SD/*.csv" + path: "data/rat_SD/*.parquet" license: cc-by-4.0 --- # Dataset Card for OAS Paired Sequence Data @@ -23,10 +23,3 @@ license: cc-by-4.0 ### Dataset Summary Paired heavy- and light-chain sequence information from the Observed Antibody Space (OAS) database, downloaded on September 9, 2023. - -Note: The following files were removed due to data loading errors: - -1a_S1__1_Paired_All.csv ERR4082235_paired.csv ERR4082263_paired.csv ERR4082291_paired.csv SRR10313335_paired.csv -1_S1__1_Paired_All.csv ERR4082243_paired.csv ERR4082267_paired.csv ERR4082299_paired.csv SRR10358523_paired.csv -3d_S6__1_Paired_All.csv ERR4082251_paired.csv ERR4082275_paired.csv ERR4082303_paired.csv SRR10358524_paired.csv -ERR4082227_paired.csv ERR4082259_paired.csv ERR4082283_paired.csv SRR10313332_paired.csv SRR10358525_paired.csv diff --git a/data/human/.gitattributes b/data/human/.gitattributes deleted file mode 100644 index d0c00cb99f3bac2de43698ba13e5340932619dec..0000000000000000000000000000000000000000 --- a/data/human/.gitattributes +++ /dev/null @@ -1,103 +0,0 @@ -1a_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2b_S7__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2_S2__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082283_paired.csv filter=lfs diff=lfs merge=lfs -text -1287192_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287201_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287202_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1e_S5pc__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082267_paired.csv filter=lfs diff=lfs merge=lfs -text -ERR4082275_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12875348_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875350_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287181_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1a_S1mod_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT6md_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT7mb_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082259_paired.csv filter=lfs diff=lfs merge=lfs -text -ERR4082303_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12113363_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875360_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287198_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT7me_S4__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875362_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1c_S3__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287199_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287205_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2a_S3__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT7mc_S2__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875356_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287193_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3d_S7__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT7ma_S7__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082227_paired.csv filter=lfs diff=lfs merge=lfs -text -1a_S1mod2_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3b_S4__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3c_S6__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT6p2c_S5__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -BT4p1_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875353_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875357_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287197_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287189_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287194_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287203_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1e_S5__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT7md_S3__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082243_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12875354_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287183_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287184_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1b_S2mod_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2c_S8__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT6me_S2__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR10358523_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12875349_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287182_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1c_S3mod_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1f_S6__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082251_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12875358_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287207_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2a_S6__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3e_S7__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875352_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287191_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3d_S6__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082299_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12113364_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287196_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287187_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3c_S5__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT6p2a_S3__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -AT6p2b_S4__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -BT4p2_S2__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082291_paired.csv filter=lfs diff=lfs merge=lfs -text -1287185_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287190_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287200_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287204_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1287206_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1b_S2__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1d_S4mod_S1__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082235_paired.csv filter=lfs diff=lfs merge=lfs -text -1287188_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR10313335_paired.csv filter=lfs diff=lfs merge=lfs -text -1287195_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -1d_S4__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -2_S7__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3a_S3__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3a_S4__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -3e_S8__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -ERR4082263_paired.csv filter=lfs diff=lfs merge=lfs -text -1287186_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875355_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875359_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR10313332_paired.csv filter=lfs diff=lfs merge=lfs -text -3b_S5__1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR10358524_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR10358525_paired.csv filter=lfs diff=lfs merge=lfs -text -SRR12875351_1_Paired_All.csv filter=lfs diff=lfs merge=lfs -text -SRR12875361_1_Paired_All.csv filter=lfs diff=lfs 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b/download_and_process_data.py new file mode 100644 index 0000000000000000000000000000000000000000..bbf25127777b65f362ebcc14d63794cfc31a9f73 --- /dev/null +++ b/download_and_process_data.py @@ -0,0 +1,66 @@ +import pandas as pd +import os +from datasets import load_dataset + +data_dir = os.path.join(os.getcwd(), "data") + +species_list = ["rat_SD", "mouse_BALB_c", "mouse_C57BL_6", "human"] + +for species in species_list: + species_url_file = os.path.join(os.getcwd(), species + "_oas_paired.txt") + with open(species_url_file, "r") as f: + for csv_file in f.readlines(): + print(csv_file) + filename = os.path.basename(csv_file) + filename = os.path.splitext(filename)[0] + filename = os.path.splitext(filename)[0] # Not a typo, need to pull off the .gzip AND the .csv + df = pd.read_csv( + csv_file, + header=1, + compression="gzip", + on_bad_lines="warn", + ) + df = df[ + [ + "sequence_id_heavy", + "sequence_heavy", + "locus_heavy", + "stop_codon_heavy", + "productive_heavy", + "rev_comp_heavy", + "sequence_alignment_aa_heavy", + "fwr1_aa_heavy", + "cdr1_aa_heavy", + "fwr2_aa_heavy", + "cdr2_aa_heavy", + "fwr3_aa_heavy", + "cdr3_aa_heavy", + "junction_aa_heavy", + "junction_aa_length_heavy", + "sequence_id_light", + "sequence_light", + "locus_light", + "stop_codon_light", + "productive_light", + "rev_comp_light", + "sequence_alignment_aa_light", + "fwr1_aa_light", + "cdr1_aa_light", + "fwr2_aa_light", + "cdr2_aa_light", + "fwr3_aa_light", + "cdr3_aa_light", + "junction_aa_light", + "junction_aa_length_light", + ] + ] + output_path = os.path.join(data_dir, species) + if not os.path.exists(output_path): + os.makedirs(output_path, exist_ok=True) + df.to_parquet( + os.path.join(output_path, filename + ".parquet"), compression="gzip" + ) + + x = load_dataset(output_path) + print(x.num_rows) + diff --git a/human_oas_paired.txt b/human_oas_paired.txt new file mode 100644 index 0000000000000000000000000000000000000000..eab6d009b6842ffbab80ee97c1fb49fc0da5d411 --- 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