[[FASTA]] format.
A sequence in FastaFormat begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence is:
{{{
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK
>my test sequence for 532319
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
LAAVEAQQQMLKLTIWGVK
}}}
BioSequence is expected to be represented in the standard IUB/IUPAC AminoAcid and NucleicAcid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in AminoAcid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown NucleicAcid residue or X for unknown AminoAcid residue).
== BioPython을 써서 FastaFormat다루기 ==
BioPython으로 FastaFormat을 다루는 요령은 다음과 같다.
=== 입력할때 - 주로 FastaFormat의 Parsing ===
{{{#!python
from Bio import Fasta, File
from cStringIO import StringIO
#file = File.UndoHandle(StringIO(fastaStr)) # 만일 스트링으로 갖고있을경우
file = open('file.fasta', 'r')
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(file, parser)
while 1:
curRecord = iterator.next() # 하나의 fasta file내에 여러개의 record를 반복적으로 접근
if curRecord is None: break
title = curRecord.title # 레코드에서 타이틀
seq = curRecord.sequence # 레코드에서 서열
}}}
=== 출력할때 - stdout으로 뿌려준다면 ===
{{{#!python
from Bio import Fasta
title = '>This is test title' # fasta file의 title
seq = 'ATGGGGGTGTGTGTGGGG' # 하나의 긴 문자열
fasta = Fasta.Record() # fasta라는 인스턴스를 만듦
fasta.title = title # 강제로 title속성에 값을 부여
fasta.sequence = seq # 마찬가지
print fasta # 이 명령으로 60자리후의 '\n'입력까지 자동으로 된다.
# if you want to write on file
wfile = open('쓰고자하는파일', 'w')
wfile.write(str(fasta))
}}}
== RelationalDatabase에서 직접만들기 ==
{{{
SELECT CONCAT(">gi|", annot.gi, "|sp|", annot.acc, "|", sp.name, " ", annot.descr, "\n", protein.seq)
FROM protein INNER JOIN annot USING (prot_id) INNER JOIN sp USING (acc)
WHERE annot.current = 1;
$ mysql seqdb -N < swissprot.sql > swissprot.fa
}}}
== 관련코드모음 ==
[[HTML]]로 FastaFormat꾸미기
* DecoratorPattern 이용 : [[FastaDecorator.py]]
* JuneKim씨 코드(2004-06-13) : 파이썬 커뮤니티에 정규식 중에 중간에 개행문자가 들어와도 되는 경우를 물으셨더군요. 다음과 같이 할 수도 있습니다.
{{{#!python
import re
class Enclose:
def __init__(self,d):
self.d=[(v,self.fragmentable(k)) for k,v in d]
self.p=re.compile("(?i)(%s)"%")|(".join([f for _,f in self.d]))
def fragmentable(self,s): return '\s?'.join(list(s))
def __call__(self, m):
opener,closer=self.d[m.lastindex-1][0]
return "%s%s%s"%(opener,m.group(),closer)
def do(self, text):
return self.p.sub(self, text)
if __name__ == "__main__":
sequence = """\
TCTTCTCCTCACCTCGCTCTCGCCGCCTGCTCGCCCCGNCCGCTTTGCTCGGCGCCCCAA
AACACNCTTCCACCATGNGCCACCTCGGCGAGCCCTCCCACTTGAACAAAGGGGTGCTCG
GCGCGTGTACNNATGGCCC\
"""
expected="""TCTTCTCCTCACCTCGCTCTCGCCGCCTGCTCGCCCCGNCCGCTTTGCTCGGCGCCCCAA
AACACNCTTCCACCATGNGCCACCTCGGCGAGCCCTCCCACTTGAACAAAGGGGTGCTCG
GCGCGTGTACNNATGGCCC"""
d=(('CCCCAAAACACN',('','')),
('TCGGCGCGTG',('','')),
('ACCTCGGCGAGCC',('','')),
)
r=Enclose(d).do(sequence)
assert r==expected
}}}
간단한 [[Iterator]]
{{{#!python
class FastaIterator:
def __init__(self, ifile):
self.ifile = ifile
self.g = self.getGenerator()
def getGenerator(self):
lines = [self.ifile.next()]
for line in self.ifile:
if line.startswith('>'):
yield ''.join(lines)
lines = [line]
else:
lines.append(line)
else:
yield ''.join(lines)
def __iter__(self):
return self.g
}}}
프로그래밍 교육용 예제
{{{#!python
#!/usr/bin/env python
import unittest, sys
from cStringIO import StringIO
class DNA:
CompMap = {'A':'T','T':'A','G':'C','C':'G'}
def __init__(self):
self.title = ''
self.sequence = ''
def getRevCompSeq(self):
return ''.join(DNA.CompMap[nucleotide]
for nucleotide in reversed(self.sequence))
def getFasta(self, cols=60):
result = []
result.append('>'+self.title)
seq = self.sequence
while seq:
result.append(seq[:cols])
seq = seq[cols:]
return '\n'.join(result)+'\n'
@staticmethod
def parseFasta(aStr):
dna=DNA()
lines = aStr.splitlines()
dna.title = lines[0][1:]
dna.sequence = ''.join(lines[1:])
return dna
def FastaGenerator(aFile):
lines =[aFile.next()]
for line in aFile:
if line.startswith('>'):
yield ''.join(lines)
lines = []
lines.append(line)
else:
yield ''.join(lines)
class DnaTest(unittest.TestCase):
def setUp(self):
self.dna = DNA()
self.dna.title = 'test'
self.dna.sequence = 'AGTC'
def testRevComp(self):
self.assertEquals('GACT',self.dna.getRevCompSeq())
def testParsing(self):
input='''\
>test
AGTC
CCC'''
self.dna = DNA.parseFasta(input)
self.assertEquals('test',self.dna.title)
self.assertEquals('AGTCCCC', self.dna.sequence)
def testRepr(self):
self.dna.sequence = 'AGTCCCC'
expected='''\
>test
AGT
CCC
C
'''
self.assertEquals(expected, self.dna.getFasta(cols=3))
def testFastaGenerator(self):
input = StringIO("""\
>test1
AGTC
CCC
>test2
GGGG
""")
g = FastaGenerator(input)
expect1 = """\
>test1
AGTC
CCC
"""
self.assertEquals(expect1, g.next())
expect2 = """\
>test2
GGGG
"""
self.assertEquals(expect2, g.next())
#self.assertRaise(StopIteration, g.next)
def main():
g = FastaGenerator(sys.stdin)
for record in g:
dna = DNA.parseFasta(record)
dna.sequence = dna.getRevCompSeq()
sys.stdout.write(dna.getFasta())
if __name__=='__main__':
#main()
unittest.main()
}}}
각종 변환 프로그램(using WxPython) --> YongsLib:wiki/FastaConvertor