Chase Clark chasemc
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| 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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| name: socialgene_nf | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - conda-forge::python>=3.10 | |
| - bioconda::hmmer>=3.3.2 |
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| include common_parameters.env | |
| export | |
| SHELL = /bin/bash | |
| CURRENT_UID := $(shell id -u) | |
| CURRENT_GID := $(shell id -g) | |
| export CURRENT_UID | |
| export CURRENT_GID |
chasemc
/ gist:45ed264dcc53b1a5d4b77e034a329d36
Created
September 2, 2022 01:53
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| Sep-01 20:50:45.862 [main] DEBUG nextflow.cli.Launcher - $> nextflow run . -profile ultraquickstart,conda --single_outdir /home/chase/Documents/ultraqsauickstart/test -resume | |
| Sep-01 20:50:45.917 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.0 | |
| Sep-01 20:50:46.711 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/chase/Documents/github/kwan_lab/socialgene/sgnf/nextflow.config | |
| Sep-01 20:50:46.712 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/chase/Documents/github/kwan_lab/socialgene/sgnf/nextflow.config | |
| Sep-01 20:50:46.718 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `ultraquickstart,conda` | |
| Sep-01 20:50:46.942 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager | |
| Sep-01 20:50:46.949 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] | |
| Sep-01 20:50:46.949 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] | |
| Sep-01 20:50:46.951 [main] INFO org.pf4j.DefaultPlug |
chasemc
/ dl_subsequence_gbk.py
Created
August 7, 2022 14:27
Download an NCBI genbank file for a subset of a nucleotide sequence
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| import requests | |
| from pathlib import Path | |
| def dl_subsequence_gbk(outdir, accession, n_start, n_stop): | |
| response = requests.post( | |
| "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", | |
| params={ | |
| "db": "nuccore", | |
| "rettype": "gb", | |
| "from": str(n_start), |
chasemc
/ chtc_submission.sub
Created
July 15, 2022 01:21
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| # template.sub | |
| # starter submit file for CHTC jobs | |
| universe = vanilla | |
| log = logs/job_$(Cluster).log | |
| error = errors/job_$(Cluster)_$(Process).err | |
| output = outputs/job_$(Cluster)_$(Process).out | |
| executable = hmmsearch.sh | |
| arguments = $(hmm_model_basename) $(fasta_file_basename) |
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| /* | |
| ======================================================================================== | |
| Nextflow minimal test | |
| ======================================================================================== | |
| Defines input files and everything required to run a fast and simple pipeline test. | |
| Use as follows: | |
| outdir='/home/chase/Documents/socialgene_data/buchnera' |
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| import zstandard as zstd | |
| def decompress_zstd(bytes_input): | |
| dctx = zstd.ZstdDecompressor() | |
| decompressed_domtblout = dctx.decompress(bytes_input) | |
| return decompressed_domtblout.decode("utf-8").splitlines() | |
| cctx = zstandard.ZstdCompressor() | |
| compressed = cctx.compress(b"data to compress") |
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| FROM mambaorg/micromamba:0.23.3 | |
| COPY --chown=$MAMBA_USER:$MAMBA_USER antismash.yml /tmp/env.yaml | |
| RUN micromamba create -n antismash | |
| RUN micromamba install --yes --file /tmp/env.yaml && \ | |
| micromamba clean --all --yes | |
| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | |
| ENV ENV_NAME=antismash |