peterk87

#!/usr/bin/env python

from pathlib import Path
import logging

import typer
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.gridspec as gridspec

peterk87

peterk87

_conda(){
    if (( ${#COMP_WORDS[@]} < 3 )); then
      COMPREPLY=( $(compgen -W "activate deactivate clean config create help info init install list package remove uninstall run search update upgrade env -h --help -V --version" -- $2 ) );
    else
        if [[ $3 == "activate" ]]; then
            local cur="${COMP_WORDS[COMP_CWORD]}";
            local envs=( $(ls "$HOME/miniconda3/envs/") );
            COMPREPLY=( $(compgen -W "${envs[*]}" -- $cur) );
        elif [[ $3 == "env" ]]; then 
            local cur="${COMP_WORDS[COMP_CWORD]}";

peterk87

#!/usr/bin/env python
'''
This script converts a GenBank file (.gbk or .gb) from Stdin into a Sequin feature table (.tbl), which is an input file of tbl2asn used for creating an ASN.1 file (.sqn).

Package requirement: BioPython and argparse

Usage:
    Simple command:
        python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt < annotation.gbk
        cat annotation.gbk | python gbk2tbl.py --mincontigsize 200 --prefix any_prefix --modifiers modifier_file.txt  # pipeline form

peterk87

#!/usr/bin/env python
# coding: utf-8
import os
import logging
from glob import glob
from io import StringIO

import click
import pandas as pd
from Bio import SeqIO

peterk87

peterk87

import argparse
import re
import logging
import pandas as pd
import numpy as np
import sys

from utils import init_console_logger

PROGRAM_NAME = 'to_excel'

peterk87

peterk87

#######################################################################
#                              tmux.conf                              #
#######################################################################

#######################################################################
#                 Setting the prefix from C-b to C-a                  #
#######################################################################
set -g prefix C-a  

#######################################################################

peterk87

#! /usr/bin/Rscript --vanilla

library(getopt)

spec <- matrix(c(
    'msa_dir_path','d',1,'character','MSA directory path (required)'
    ,'msa_file_ext','e',2,'character','MSA file extension (optional; default: "aln")'
    ,'out','o',2,'character','Output core SNP matrix CSV filename (optional; default: "core_distance_matrix.csv")'
    ,'n_cores','c',2,'integer','Number of cores to use for computation (optional; default: 2)'
    ,'dna_distance_model','m',2,'character','DNA distance model (default: "N").