chasemc’s gists

chasemc / download_all_refseq_gbff.py

Last active March 2, 2023 18:01

If you do this follow NCBI's guidelines of when to do large downloads. This script won't to check your available hard drive space and **RefSeq** alone will require > 1 Terabyte**

	#!/usr/bin/env python
	# Import Module
	import argparse
	import ftplib
	from tqdm import tqdm
	import requests
	from pathlib import Path
	import logging
	import multiprocessing
	import csv

chasemc / a

Last active March 2, 2023 16:21

	# See ftp://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt for a description of the columns in this file.
	# assembly_accession bioproject biosample wgs_master refseq_category taxid species_taxid organism_name infraspecific_name isolate version_status assembly_level release_type genome_rep seq_rel_date asm_name submitter gbrs_paired_asm paired_asm_comp ftp_path excluded_from_refseq relation_to_type_material asm_not_live_date
	GCF_000001215.4 PRJNA164 SAMN02803731 reference genome 7227 7227 Drosophila melanogaster latest Chromosome Major Full 2014/08/01 Release 6 plus ISO1 MT The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics GCA_000001215.4 identical https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT na
	GCF_000001405.40 PRJNA168 reference genome 9606 9606 Homo sapiens latest Chromosome Patch Full 2022/02/03 GRCh38.p14 Genome Reference Consortium GCA_000001405.29 different https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001

chasemc / download_mibig_genomes.py

Created February 2, 2023 16:54

	#!/usr/bin/env python3

	# script to find and download genomes associated with mibig

	from pathlib import Path
	import os
	import hashlib
	import requests
	import csv
	import argparse

chasemc / day7.py

Created December 7, 2022 18:57

	from collections import defaultdict
	from pathlib import Path

	prompt_data = "/home/chase/Downloads/input.txt"

	with open(prompt_data) as fp:
	lines = fp.readlines()

	cleaned=[]

chasemc / b

Created November 8, 2022 20:28

<?xml version='1.0' encoding='UTF-8'?>

<rdf:RDF xml:base="http://purl.uniprot.org/uniprot/" xmlns="http://purl.uniprot.org/core/" xmlns:ECO="http://purl.obolibrary.org/obo/ECO_" xmlns:annotation="http://purl.uniprot.org/annotation/" xmlns:citation="http://purl.uniprot.org/citations/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:disease="http://purl.uniprot.org/diseases/" xmlns:enzyme="http://purl.uniprot.org/enzyme/" xmlns:faldo="http://biohackathon.org/resource/faldo#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:go="http://purl.obolibrary.org/obo/GO_" xmlns:isoform="http://purl.uniprot.org/isoforms/" xmlns:keyword="http://purl.uniprot.org/keywords/" xmlns:location="http://purl.uniprot.org/locations/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:position="http://purl.uniprot.org/position/" xmlns:pubmed="http://purl.uniprot.org/pubmed/" xmlns:range="http://purl.uniprot.org/range/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="htt

chasemc / a

Created November 8, 2022 20:23

This file has been truncated, but you can view the full file.

	<?xml version='1.0' encoding='UTF-8'?>
	<rdf:RDF xmlns="http://purl.uniprot.org/core/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#">
	<owl:Ontology rdf:about="">
	<owl:imports rdf:resource="http://purl.uniprot.org/core/"/>
	</owl:Ontology>
	<rdf:Description rdf:about="http://purl.uniprot.org/enzyme/1.-.-.-">
	<rdf:type rdf:resource="http://purl.uniprot.org/core/Enzyme"/>
	<skos:prefLabel>Oxidoreductases</skos:prefLabel>
	<rdfs:subClassOf rdf:resource="http://purl.uniprot.org/core/Enzyme"/>
	<skos:narrowerTransitive rdf:resource="http://purl.uniprot.org/enzyme/1.1.-.-"/>

chasemc / create_metadata_csv.R

Created October 27, 2022 17:23

	#!/usr/bin/env Rscript
	if (!require("remotes")) {
	install.packages("remotes")
	library(remotes)
	}
	if (!require("DBI")) {
	install.packages("DBI")
	library(DBI)
	}
	if (!require("RSQLite")) {

chasemc / pfam_subset.hmm

Created October 17, 2022 22:23

This file has been truncated, but you can view the full file.

	HMMER3/f [3.1b2 \| February 2015]
	NAME adh_short
	ACC PF00106.28
	DESC short chain dehydrogenase
	LENG 195
	ALPH amino
	RF no
	MM no
	CONS yes
	CS yes

chasemc / skimr.r

Created September 20, 2022 18:26

	library(data.table)
	library(skimr)
	temp <- fread(
	"curl -s https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt \| head -n 20",
	sep = "\t",
	header = T
	)
	skim(temp)

chasemc / sgpy_example.ipynb

Created September 20, 2022 14:43

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Chase Clark chasemc