Chase Clark chasemc
chasemc
/ hashing_uniparc.py
Created
June 29, 2023 14:10
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| import base64 | |
| import hashlib | |
| from Bio.SeqUtils import CheckSum | |
| import sys | |
| def sha512t24u(input): | |
| # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714221/ | |
| # To standardize to caps-only input, use hash_aminos() | |
| sha512_digest = hashlib.sha512(bytes(input,"utf8")).digest()[:24] |
chasemc
/ gist:270ec6eaaa864269b9bed2f12816d55f
Last active
May 16, 2023 12:54
hmmsearch a model with --cut_ga when the model has no defined cutoffs
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| hmmsearch --domtblout "a.dom" -Z 100 --cut_ga '/socialgene_nr_hmms_file_without_cutoffs_1_of_1.hmm' /example.fa | |
| # hmmsearch :: search profile(s) against a sequence database | |
| # HMMER 3.3.2 (Nov 2020); http://hmmer.org/ | |
| # Copyright (C) 2020 Howard Hughes Medical Institute. | |
| # Freely distributed under the BSD open source license. | |
| # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | |
| # query HMM file: /socialgene_nr_hmms_file_without_cutoffs_1_of_1.hmm | |
| # target sequence database: /example.fa |
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| BGC0000001 | antibacterial | |
|---|---|---|
| BGC0000001 | cytotoxic | |
| BGC0000001 | antibacterial | |
| BGC0000001 | cytotoxic | |
| BGC0000002 | antibacterial | |
| BGC0000002 | antifungal | |
| BGC0000014 | antifungal | |
| BGC0000016 | antifungal | |
| BGC0000017 | neurotoxic | |
| BGC0000017 | neurotoxic |
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| PF10417 | |
| PF12574 | |
| PF09847 | |
| PF00244 | |
| PF16998 | |
| PF00389 | |
| PF02826 | |
| PF00198 | |
| PF16078 | |
| PF04029 |
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| # Bio::Pfam::HMM::HMMResults.pm | |
| # | |
| # Author: finnr | |
| # Maintainer: $Id: HMMResults.pm,v 1.3 2009-12-15 14:38:08 jt6 Exp $ | |
| # Version: $Revision: 1.3 $ | |
| # Created: Nov 19, 2008 | |
| # Last Modified: $Date: 2009-12-15 14:38:08 $ | |
| =head1 NAME |
chasemc
/ antismash_minimal_json.py
Created
April 28, 2023 12:50
Extract minimal BGC region info from antismash json
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| #!/usr/bin/env python | |
| # -*- encoding: utf-8 -*- | |
| import json | |
| import argparse | |
| from multiprocessing import Pool | |
| import tarfile | |
| from pathlib import Path | |
| parser = argparse.ArgumentParser(description="Extract from antismash json") | |
| parser.add_argument( |
chasemc
/ find_duplicate_files.py
Created
April 3, 2023 18:10
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| #!/usr/bin/env python | |
| # -*- encoding: utf-8 -*- | |
| import os | |
| import hashlib | |
| from pathlib import Path | |
| import argparse | |
| from collections import defaultdict | |
| import glob, os | |
| from rich.progress import ( |
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| {"import_files": {"/socialgene_neo4j/import/antismash_gbk_to_table.tsv.gz": "d7a8d113e8ed1412e48f8f02c345de58", "/socialgene_neo4j/import/versions.yml": "550ae99b30e769987a5ebb3be53ba196", "/socialgene_neo4j/import/taxdump_process/ea36b0a2f07c7f730058510f39656e70.nodes_taxid.gz": "ea36b0a2f07c7f730058510f39656e70", "/socialgene_neo4j/import/taxdump_process/versions.yml": "2a5caa6b018bbc8b5c9e3fa58591bfad", "/socialgene_neo4j/import/taxdump_process/8a3145f4e2f529124636f99dcc999878.taxid_to_taxid.gz": "8a3145f4e2f529124636f99dcc999878", "/socialgene_neo4j/import/protein_info/7fade5e885cd59d8493ae15b8e9ce1e3.protein_ids.gz": "7fade5e885cd59d8493ae15b8e9ce1e3", "/socialgene_neo4j/import/protein_info/8bcd5f910b49a24b4b36b66a147679d4.protein_info.gz": "8bcd5f910b49a24b4b36b66a147679d4", "/socialgene_neo4j/import/diamond_blastp/versions.yml": "45a30218f36138d65326e1332e1338f2", "/socialgene_neo4j/import/diamond_blastp/36063c1222c951511061b9fdc75fd8f3.blast6.gz": "36063c1222c951511061b9fdc75fd8f3", "/socialgene_neo4j |
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| >NZ_CP070290.1_1-5000 | |
| GTGTCACTTTCGCTTTGGCAGCAGTGTCTTGCCCGATTGCAGGATGAGTTACCAGCCACA | |
| GAATTCAGTATGTGGATACGCCCGTTGCAGGCGGAACTGAGCGATAACACGCTGGCCTTG | |
| TACGCGCCAAATCGTTTTGTCCTCGATTGGGTACGGGACAAGTACCTCAATAATATCAAT | |
| GGACTGCTAACCAGCTTCTGTGGCGCGGATGCCCCACAGTTGCGCTTTGAAGTTGGCACC | |
| AGGCCGGTGACGAAAACCTCTCAGGCCGCAGTGACGAGCAACGTTACAGCGCCAGCTCAG | |
| GTGGCGCAAATGCAACCGCAGCGCGCTGCGCCTGCAGCGCGTTCGGGTTGGGATAACGTT | |
| CCTGCTCCGGCGGAACCGACCTATCGTTCCAACGTCAACGTCAAACATACGTTTGATAAC | |
| TTCGTCGAAGGTAAATCTAACCAACTGGCGCGCGCGGCGGCTCGCCAGGTGGCGGATAAC | |
| CCCGGTGGCGCTTATAACCCGCTGTTCCTTTATGGCGGCACGGGTCTGGGTAAAACTCAC |
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| >NZ_JADOTX010000001.1_1-5000_1 | |
| PGPHRRYGADLVVPRLVRAQCALLKGIALRYVMRRSGFRGRYERQRTMLAEVVAALVRRA | |
| PEGLDPIFAPLWRAAPDDTARLRVVIDQVASLTDPAAVTWHTRLVGNGTPLTDN* | |
| >NZ_JADOTX010000001.1_1-5000_2 | |
| MTERPRNVTSAQVLRTERPTPHLIRLVLGGDELVGLPVGEFTDHYIKVVFPQPGVAYPQP | |
| LDLAAIRRDLPREQWPRLRAYTVRRWDPLAGELTVDVVHHGDEGLAGPWAAALRPGDPVH | |
| FVGPGGAYAPSPDADWHLLVGDESALPAIAAALERLPLGARAHVFVEIADPAEEQKLLSP | |
| GAVELTWLHRGDRPVGEALVAAVRALEFPAGQVHAFVHGEAAFVRELRRLLRGERGIPLG | |
| QLSISGYWRRGMDDEGWRSTKADWNQQVAAEEVAVAAA* | |
| >NZ_JADOTX010000001.1_1-5000_3 |