destine/2005-05 - BioHackersNet

MonthCalendar2(destine,2005,5) CategoryWebLogDestine 페이지 고치기

2005-05-29

으아.. 학기말이 되니 밀려오는 진도의 압박. 사실 눈앞의 일보다는 앞으로의 스케쥴을 보고 미리 좌절하는 것은 아닐까.

2005-05-27

BioPython의 PDB classes 에는 2차 구조 정보가 없는 것 같아서 끼워 넣고 있음. (혹시 있나요?--;) PDB Format Description Version 2.2 HELIX Record Format SHEET Record Format TURN Record Fromat

2005-05-25

[BioPythonTutorial/Appendix] Clustalw Download Information Theory Primer [PDBAnalyzer.py] 1C3W.pdb - Sample Data : PDB에서 CA의 좌표만 갖고 오는 Script

2005-05-18

Membrane Protein Explorer (MPEx), a tool for exploring the topology and other features of membrane proteins by means of hydropathy plots using thermodynamic principles.

Membrane Proteins of Known 3D Structure

Several Membrane Proteins Libraries - the WARD Lab at the University of Minnesota

Arabidopsis, Oriza Sativa membrane protein database

MembraneProtein 페이지에 정리하면 좋을듯하여, 조금 편집함 --[yong27], 2005-05-18

논문

Membrane protein folding and oligomerization: the two-stage model (Abstract)

Prediction of the mutation-induced change in thermodynamic stabilities of membrane proteins from free energy simulations - SNU

Determination of peptide oligomerization in lipid bilayers using 19F spin diffusion NMR.

Role of the Degree of Oligomerization in the Structure and Function of Human Surfactant Protein A

Application

Membrane Protein Secondary Structure Prediction Server

2005-05-16

Helix Packing and Helix Packing Moments in Membrane Proteins

Gerstein Lab - Bioinformatics

Engelman Lab - Membrane

TMSTAT

FlyBase

2005-05-13

http://www.genomesonline.org/ GenomesOnLineDatabase [GOLD]

Biopython Examples

Swiss-PDB Viewer

Compare Two Sequences with FASTA

2005-05-11

[Phenocopy]

2005-05-08

IE Automation 관련 사이트(정리 할 것)

http://vsbabu.org/mt/archives/2003/06/13/ie_automation.html http://sourceforge.net/projects/samie

http://www.unix.org.ua/orelly/perl/learn32/appa_18.htm http://www.codecomments.com/archive300-2004-11-317585.html

http://www.mozilla.org/projects/xpcom/ http://aspn.activestate.com/ASPN/Downloads/Komodo/PyXPCOM/

IE Automation Tool http://spaces.msn.com/members/grazilee/Blog/cns!1pWrYYHYycw0kHJlB7ROFqcA!604.entry http://www.rubycentral.com/book/win32.html

PythonChallenge

http://www.pythonchallenge.com 6번 푸는 중.

2005-05-06

http://www.pythonchallenge.com 시작

urllib.urlopen 한 70개 정도 open 하면 항상 에러가 발생함. 우연인가? 아님 무슨 문제 일까?

os.walk 사용 예제

This example displays the number of bytes taken by non-directory files in each directory under the starting directory, except that it doesn't look under any CVS subdirectory:

import os
from os.path import join, getsize
for root, dirs, files in os.walk('python/Lib/email'):
    print root, "consumes",
    print sum([getsize(join(root, name)) for name in files]),
    print "bytes in", len(files), "non-directory files"
    if 'CVS' in dirs:
        dirs.remove('CVS')  # don't visit CVS directories

In the next example, walking the tree bottom up is essential: rmdir() doesn't allow deleting a directory before the directory is empty:

import os
from os.path import join
# Delete everything reachable from the directory named in 'top'.
# CAUTION:  This is dangerous!  For example, if top == '/', it
# could delete all your disk files.
for root, dirs, files in os.walk(top, topdown=False):
    for name in files:
        os.remove(join(root, name))
    for name in dirs:
        os.rmdir(join(root, name))

특정 Directory 아래의 모든 파일 방문(?) 하기( os.walk 이용 )

import os
from os.path import join 

def visitfile(file):
        print 'visiting',file
        
def walktree(dir, callback):
        for root, dirs, files in os.walk(dir):
                for name in files:
                        callback(join(root,name))

if __name__ == '__main__':
    walktree(sys.argv[1], visitfile)

SwissProt database

(for 문 사용)

from Bio.SwissProt import SProt

fh = open(argv[1])                       
sp = SProt.Iterator(fh, SProt.RecordParser())

for record in sp:
    print record.accessions
    print record.annotation_update
    print record.comments
    print record.created
    print record.cross_references
    print record.data_class
    print record.description
    print record.entry_name
    print record.features
    print record.gene_name
    print record.keywords
    print record.molecule_type
    print record.organelle
    print record.organism
    print record.organism_classification
    print record.references
    print record.seqinfo
    print record.sequence
    print record.sequence_length
    print record.sequence_update
    print record.taxonomy_id

    print "============================================================="
    print "============================================================="
fh.close()

2005-05-05

The Biopython-dev Archives

BioPython Tutorial에 있는 코드가 제대로 실행되지 않는다. 왜 그럴까. http://www.expasy.ch/cgi-bin/get-sprot-raw.pl 가 동작 하지 않는걸까. 영어 'O'를 써야 되는데 숫자'0'을 쓰는 바람에 잘못된 id가 입력되었던 문제였음. --;

from Bio.WWW import ExPASy
ids = ['O23729', 'O23730', 'O23731']
all_results = ''
for id in ids:
     results = ExPASy.get_sprot_raw(id)
     all_results = all_results + results.read()

BioPython Parsers 설명

SwissProt data file 읽기

from Bio.SwissProt import SProt
from sys import *

fh = open(argv[1])                       
sp = SProt.Iterator(fh, SProt.RecordParser())

while 1:
    record = sp.next()
    if record is None:
        break
    print record.accessions
    print record.annotation_update
    print record.comments
    print record.created
    print record.cross_references
    print record.data_class
    print record.description
    print record.entry_name
    print record.features
    print record.gene_name
    print record.keywords
    print record.molecule_type
    print record.organelle
    print record.organism
    print record.organism_classification
    print record.references
    print record.seqinfo
    print record.sequence
    print record.sequence_length
    print record.sequence_update
    print record.taxonomy_id

    print "============================================================="
    print "============================================================="
fh.close()

참고로, 최근의 [Iterator]들은 굳이 while문을 안써도 됨. for문으로 다 해결가능.--[yong27], 2005-05-06
- ㅎㅎ 그렇네요.

특정 Directory 아래의 모든 파일 방문(?) 하기

import os, sys
from stat import *

def walktree(dir, callback):
    '''recursively descend the directory rooted at dir,
       calling the callback function for each regular file'''

    for f in os.listdir(dir):
        pathname = '%s/%s' % (dir, f)
        mode = os.stat(pathname)[ST_MODE]
        if S_ISDIR(mode):
            # It's a directory, recurse into it
            walktree(pathname, callback)
        elif S_ISREG(mode):
            # It's a file, call the callback function
            callback(pathname)
        else:
            # Unknown file type, print a message
            print 'Skipping %s' % pathname

def visitfile(file):
    print 'visiting', file

if __name__ == '__main__':
    walktree(sys.argv[1], visitfile)

os.walk를 쓰면 단방에 --[yong27], 2005-05-06
- 그렇네요. os.walk를 쓰면 코드 이해하기도 쉽고 쓰기도 편하네요.

2005-05-04

내일은 박찬호 경기 하는 날이구나. BiologicalDatabase YeastTwoHybrid

2005-05-02

StandAloneBlast -- DB 다운 받는데 넘 오래 걸리네. Valdar Programs 설명 Thornton software 모음 RealWorldRuby - Ruby로 할 수 있는 여러가지 일들

2005-05-01

The Scorecons Server (tool) Scoring residue conservation (pdf)