azalea

#!/bin/bash

OPENSSL_VERSION="1.0.1g"

curl -O http://www.openssl.org/source/openssl-$OPENSSL_VERSION.tar.gz
tar -xvzf openssl-$OPENSSL_VERSION.tar.gz
mv openssl-$OPENSSL_VERSION openssl_i386
tar -xvzf openssl-$OPENSSL_VERSION.tar.gz
mv openssl-$OPENSSL_VERSION openssl_x86_64
cd openssl_i386

azalea

!macro ProcessEnvPrependPath UN
    ;; ref: http://stackoverflow.com/a/32384667/1292238
    !ifndef ERROR_ENVVAR_NOT_FOUND
        !define ERROR_ENVVAR_NOT_FOUND 203
    !endif
    !if "${NSIS_PTR_SIZE}" <= 4
    !include LogicLib.nsh
    Function ${UN}ProcessEnvPrependPath ; IN:Path OUT:N/A
    System::Store S
    Pop $1

azalea

!macro ProcessEnvPrependPath UN
    ;; ref: http://stackoverflow.com/a/32384667/1292238
    !ifndef ERROR_ENVVAR_NOT_FOUND
        !define ERROR_ENVVAR_NOT_FOUND 203
    !endif
    !if "${NSIS_PTR_SIZE}" <= 4
    !include LogicLib.nsh
    Function ${UN}ProcessEnvPrependPath ; IN:Path OUT:N/A
    System::Store S
    Pop $1

azalea

;; Requisites: Emacs >= 24

;; INSTALL PACKAGES
;; --------------------------------------
(prefer-coding-system 'utf-8)
(require 'package)
(add-to-list 'package-archives
	     '("melpa" . "http://melpa.org/packages/") t)

(package-initialize)

azalea

# Say I have such classes A, B, C, ..., Y, and Z that do different things,
# and classes AComment, BComment, CComment, ..., YComment and ZComment 
# that record comments on instances of class A, B, ..., Y and Z respectively.
# All XComment classes share the same attributes except one property 
# that is is dependent on the class the comment is for.
# e.g. AComment has a property 'a' and BComment has a property 'b'.
        
class A():
    def __init__(self):
        print 'init an instance of class A'

azalea

Find the length of each line in the file

while read line; do echo -n "$line" | wc -c; done< f1

azalea

#!/bin/sh

# Replace more than one consecutive spaces with tab in files on both Linux and Mac OS X. 
# You need to install gnu-sed on Mac OS X for this to work. 
# Usage: spaces2tab.sh [file ...]
# See also: http://azaleasays.com/2014/03/07/os-x-sed-does-not-recognize-tab-character/


if [ "$(uname -s)" == "Darwin" ] # If the system is Mac OS X
then

azalea

#!/bin/sh

oldext=".md"
newext=".markdown"

for file in $(git ls-files | grep ${oldext}\$); do
    echo processing $file...
    filename="${file%.*}"
    git mv $file ${filename}$newext
done

azalea

# only ask for my SSH key passphrase once!
# use existing ssh-agent if possible

if [ -f ${HOME}/.ssh-agent ]; then
   . ${HOME}/.ssh-agent > /dev/null
fi
if [ -z "$SSH_AGENT_PID" -o -z "`/usr/bin/ps -a|/usr/bin/egrep \"^[ ]+$SSH_AGENT_PID\"`" ]; then
   /usr/bin/ssh-agent > ${HOME}/.ssh-agent
   . ${HOME}/.ssh-agent > /dev/null
fi

azalea

'''This code tried to do things the hard way to solve: http://www.biostars.org/p/92205/ by
first, the function split_fasta() splits the original fasta file into files containing individual sequence records;
second, blast_seq_the_hard_way() iterates over these individual files and feeds their filenames to BLAST.
Please note that BLAST can handle multiple sequences in -query and -subject at the same time, so there is no need
to split the files. This code is just for demonstration purposes.
'''
import os
import re

from Bio.Blast.Applications import NcbiblastpCommandline