chasemc

# Start with Ubuntu base image
FROM ubuntu:22.04

# Set environment variables to prevent prompts during package installation
ENV DEBIAN_FRONTEND=noninteractive

# Update and install dependencies
RUN apt-get update && apt-get install -y \
    software-properties-common \
    build-essential \

chasemc

chasemc

selected_dir<- system('osascript -l JavaScript -e \'a=Application.currentApplication();a.includeStandardAdditions=true;a.chooseFolder({withPrompt:"Please select a file to process:"}).toString()\'', intern = TRUE, ignore.stderr = T)

chasemc

import pandas as pd

from shiny import App, Inputs, Outputs, Session, reactive, render, ui
from shiny.types import FileInfo

app_ui = ui.page_fluid(
    ui.input_file("file1", "Choose CSV File", accept=[".csv"], multiple=False),
    ui.input_checkbox_group(
        "stats",
        "Summary Stats",

chasemc

library(IDBacApp)
library(dplyr)
library(DBI)
library(pool)
library(coop)

# Change this to be the full file path to your sqlite file 
sqlite_filepath <- "/home/chase/Downloads/NK_Library_Full_Up_To_2023-10-02-Copy.sqlite"

chasemc

def parse_fasta(filepath: str) -> Generator[str, str]:
    seq_id = ""
    with open(filepath, "r") as h:
        seq_id = ""
        seq = ""
        for i in h:
            if i[0] == ">":
                if seq_id:
                    yield (seq_id, seq)
                seq_id = i[1:].strip()

chasemc

#!/usr/bin/python3

# MIT License

# Copyright (c) Chase M. Clark

# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

chasemc

https://docs.google.com/presentation/d/1NqwMVOYB2o_sqkOjoPH_AK1zKxrYyYcaUv8ZuAmU8og/edit?usp=sharing

chasemc

chasemc

import json
z=set()
with open("/media/socialgene_nvme/v0.2.3/refseq/socialgene_neo4j/import/antismash_results.jsonl", "r") as h:
    for line in h:
        for record in json.loads(line)['records']:
            for k,v in record.items():
                for i in v:
                    for ii in i['products']:
                        z.add(ii)