glwinsor

# Rename all *.txt to *.text
for f in *.txt; do 
    mv -- "$f" "${f%.txt}.gbk"
done

glwinsor

#! /usr/bin/python3

from subprocess import Popen,PIPE,STDOUT

pmidString=''

command='/home/glwinsor/edirect/efetch -db pubmed -id 153904'

#captures STDOUT without having to use a redirect to a filename
#note that it captures bytes, not a string. Therefore need to specify universtal_newlines=True in order to retain newlines

glwinsor

#!/usr/bin/python3

f = open('filename.txt', 'w')

f.write()

f.close()

glwinsor

from optparse import OptionParser
import pymysql

# Get options from the command line
parser = OptionParser()
parser.add_option("-d", "--database", dest="database", action="store", type="string", help="Name of database you wish to connect to", metavar="DATABASE")
parser.add_option("-H", "--host", dest="host", action="store", type="string", help="Database host", metavar="HOST")
parser.add_option("-u", "--user", dest="user", action="store", type="string", help="User name", metavar="NAME")
parser.add_option("-p", "--password", dest="password", action="store", type="string", help="Password", metavar="PASSWORD")

glwinsor

from Bio import SeqIO

# read in the fasta file and create seq object. File name is stored in fasta variable and the following "fasta" in quotes means the type of format being input
for seq_record in SeqIO.parse(fasta,"fasta"):
    # Prints the sequence ID
    print(seq_record.id)
    # Prints string representation of the sequence
    print(str(seq_record.seq))

glwinsor

import sys
from optparse import OptionParser

try:    
  	# assumes file was specified as argument in the command line using optparse with --file option
    file=open(options.file, 'r')     
except FileNotFoundError: # works for python3
    print("Could not find file")
    sys.exit()

glwinsor

import os


  
if not os.path.isfile("./file.txt"):
  raise FileNotFoundError("Could not find ./file.txt")


if not os.path.isdir('./dir'):
  raise FileNotFoundError("Could not find ./dir")

glwinsor

from optparse import OptionParser

# Get options from the command line
parser = OptionParser()
parser.add_option("-f", "--flag", dest="flag", action="store", type="string", help="Description of flag", metavar="FLAG")

(options, args) = parser.parse_args()

if options.flag == None:
    parser.error("Missing argument for --flag ")

glwinsor

// vim: syntax=perl
my %CONF;
open my $configfile, '<', 'config.txt' or die $!;

while (<$configfile>) {
	chomp;
	my ( $key, @value ) = split( "=", $_ );
	$CONF{$key} = join '=', @value;
}

glwinsor

#!/usr/bin/perl -w

use strict;
use warnings;
use Getopt::Long;
use DBI;

my $database = '';
my $password = '';
my $user     = '';