Skip to content

Instantly share code, notes, and snippets.

View lambdalisue's full-sized avatar
🎮

Λlisue (Ali sue・ありすえ) lambdalisue

🎮
View GitHub Profile
@lambdalisue
lambdalisue / install_pbzip2_centos.sh
Created February 13, 2014 20:01
A script to install pbzip2 (CentOS)
#!/usr/bin/env bash
VERSION="1.1.8"
NAME="pbzip2-$VERSION"
FILENAME="$NAME.tar.gz"
URL="http://compression.ca/pbzip2/$FILENAME"
if [[ ! -f "$FILENAME" ]]; then
echo "Download $NAME..."
curl -o $FILENAME $URL
fi
@lambdalisue
lambdalisue / rsync_pull_pwd.sh
Created February 14, 2014 01:59
A script to pull remote changes to local via rsync
#!/usr/bin/env bash
BASE=$(pwd)
HOST=$1
if [[ "$HOST" = "" ]]; then
echo "usage: rsync_pull HOST_ADDRESS"
exit 1
fi
askYesOrNo() {
@lambdalisue
lambdalisue / rsync_push_pwd.sh
Created February 14, 2014 02:00
A script to push local changes to remote server via rsync
#!/usr/bin/env bash
BASE=$(pwd)
HOST=$1
if [[ "$HOST" = "" ]]; then
echo "usage: rsync_pull HOST_ADDRESS"
exit 1
fi
askYesOrNo() {
@lambdalisue
lambdalisue / main.py
Created February 20, 2014 08:09
An example code to make clickable window on Qt
# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
try:
from PySide import QtCore
from PySide import QtGui
except ImportError:
from PyQt4 import QtCore
from PyQt4 import QtGui
@lambdalisue
lambdalisue / trace_atoms.py
Created March 4, 2014 09:22
A pymol script to trance the atoms movements
# coding: utf-8
#===============================================================================
# Name: track_atoms.py
# Description: draw tracking arrows for atoms trajectory (iterate states)
# Author: Alisue <lambdalisue@hashnote.net>
# License: MIT license
# Required: colour, natsort, pymol, chempy
# (C) 2014, hashnote.net, Alisue
#===============================================================================
import re
@lambdalisue
lambdalisue / colors.py
Created March 13, 2014 16:01
A library of Colors
#!/usr/bin/env python
# coding=utf-8
"""
Colors
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
import collections
Colors = collections.namedtuple('Colors', [
"LIGHT_PINK", "LIGHT_BROWN", "LIGHT_PURPLE", "LIGHT_ORANGE",
"LIGHT_BLUE", "LIGHT_GREEN", "LIGHT_RED", "LIGHT_BLACK",
@lambdalisue
lambdalisue / aminoacids.py
Created April 27, 2014 13:25
A library for handling Amino Acid sequence
# coding=utf-8
"""
Amino acid sequence manupulation library
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
AMINOACIDS = list("ARNDCEQGHILKMFPSTWYV")
AMINOACIDS3 = (
'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY', 'HIS', 'ILE', 'LEU',
'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL',
)
@lambdalisue
lambdalisue / load_fasta.py
Created April 29, 2014 11:05
A library to load fasta format text
# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
def load_fasta(iterator):
"""
Load fasta file and return sequence list
>>> fasta = '''
... >avGFP
@lambdalisue
lambdalisue / hydrophobicity.py
Created April 29, 2014 14:10
A library to define the residual hydrophobicities
# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
# Refence:
# Eisenberg D., Schwarz E., Komarony M., Wall R.
# J. Mol. Biol. 179:125-142(1984).
HYDROPHOBICITIES = {
'A': 0.620, 'R': -2.530, 'N': -0.780, 'D': -0.900, 'C': 0.290,
@lambdalisue
lambdalisue / corresponding_residue.py
Created April 29, 2014 14:11
A library to find a corresponding residues from a fasta alignment
# coding=utf-8
"""
"""
__author__ = 'Alisue <lambdalisue@hashnote.net>'
import re
def find_alignment_offsets(sequence):
"""
Get alignment offset from alignment sequence