生物信息数据格式：fasta格式

格式说明

Fasta格式首先以大于号>开头，接着是序列的标识符，然后是序列的描述信息。换行后是序列信息，序列中允许空格，换行，空行，直到下一个大于号，表示该序列的结束。

查看fasta

!cat ./data/AY810830.fasta

实例演练

读取fasta文件，并打印

def cat(file):
    """
    读入FASTA格式的文件
    :param file: FASTA格式的文件
    :return: None
    """
    for line in open(file):
        print(line.strip())

cat("./data/test1.fa")

>NM_001011874 gene=Xkr4 CDS=151-2091
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg
>NM_001195662 gene=Rp1 CDS=55-909
AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA
>NM_011283 gene=Rp1 CDS=128-6412
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
>NM_0112835 gene=Rp15 CDS=128-6412
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
>NM_001011874 gene=Xkr4 CDS=151-2091
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg
aggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTG
CCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACC
CCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG

把每条FASTA序列连成一行然后输出

def formatFasta(filename):
    """
    把每条FASTA序列连成一行然后输出
    :param filename: 文件名
    :return: None
    """
    alist = []
    for line in open(filename):
        if line[0] == '>':
            lineL = line.split(' ')
            if alist:
                print(''.join(alist))
                alist = []
            name = lineL[0]
            print(name)
        else:
            alist.append(line.strip())
    #不要忘了最后一个序列
    print(''.join(alist))

filename = "./data/test2.fa"
formatFasta(filename)

>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA

把每条FASTA序列按一定长度输出

def formatFasta(filename,length):
    """
    把每条FASTA序列按一定长度输出
    :param filename: 文件名
    :param length: 长度
    :return: None
    """
    alist = []
    for line in open(filename):
        if line[0] == '>':
            lineL = line.split(' ')
            if alist:
                seq = ''.join(alist)
                len_seq = len(seq)
                for i in range(0,len_seq,length):
                    print(seq[i:i+length])
                alist = []
            name = lineL[0]
            print(name)
        else:
            alist.append(line.strip())
    #不要忘了最后一个序列
    seq = ''.join(alist)
    len_seq = len(seq)
    for i in range(0,len_seq,length):
        print(seq[i:i+length] )
length = 60
filename = "./data/test2.fa"
formatFasta(filename,length)

>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTA
TACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTC
ACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGG
TCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG
TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTC
CTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGG
GGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA
GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA
GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCT
CTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAG
GCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTT
GAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATT
CATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTA
GTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTG
GTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAG
GTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACC
AGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTA
TACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTC
ACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGG
TCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG
TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTC
CTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGG
GGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA
GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA
GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCT
CTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAG
GCTCGTGGTCTTCCGGAATGGTGACCCGAA

提取fasta.name中名字对应的test2.fa的序列，并输出到屏幕。

fasta.name文件内容如下：

!cat "./data/fasta.name"

NM_011283

aDict = {}
seqFile = "data/test2.fa"
nameFile = "data/fasta.name"

for line in open(seqFile):
    if line[0] == '>':
        key = line.split()[0][1:] 
        aDict[key] = []  
    else:
        aDict[key].append(line.strip())

for line in open(nameFile):
    name = line.strip()
    print(">%s\n%s" % (name, ''.join(aDict[name])))
    print(">%s\n%s" % (name, aDict[name]))

>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_011283
['AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC', 'ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC', 'CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT', 'CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG', 'GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC', 'TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA', 'GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG', 'CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA', 'TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA', '']