peterk87

#!/usr/bin/env python

import argparse
import textwrap
import os
import sys
import json
import re

peterk87

Steps to retrieve table of named serovars with O- and H-antigens

Downloaded "Antigenic Formulae Of The Salmonella Serovars 2007 9th edition" from:

https://www.pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089

Regex Steps

Remove page numbers:

• match

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").

peterk87

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

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

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

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

#!/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

#!/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

_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]}";