Question

我有一个像这样的fastq文件（文件的一部分）：

@A80HNBABXX:4:1:1344:2224#0/1
AAAACATCAGTATCCATCAGGATCAGTTTGGAAAGGGAGAGGCAATTTTTCCTAAACATGTGTTCAAATGGTCTGAGACAGACGTTAAAATGAAAAGGGG  
+
\\YYWX\PX^YT[TVYaTY]^\^H\`^`a`\UZU__TTbSbb^\a^^^`[GOVVXLXMV[Y_^a^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB  
@A80HNBABXX:4:1:1515:2211#0/1
TTAGAAACTATGGGATTATTCACTCCCTAGGTACTGAGAATGGAAACTTTCTTTGCCTTAATCGTTGACATCCCCTCTTTTAGGTTCTTGCTTCCTAACA  
+  
ee^e^\`ad`eeee\dd\ddddYeebdd\ddaYbdcYc`\bac^YX[V^\Ybb]]^bdbaZ]ZZ\^K\^]VPNME][`_``Ubb_bYddZbbbYbbYT^_  
@A80HNBABXX:4:1:1538:2220#0/1
CTGAGTAAATCATATACTCAATGATTTTTTTATGTGTGTGCATGTGTGCTGTTGATATTCTTCAGTACCAAAACCCATCATCTTATTTGCATAGGGAAGT  
+
fff^fd\c^d^Ycac`dcdcded`effdfedb]beeeeecd^ddccdddddfff`eaeeeffdTecacaLV[QRPa\\a\`]aY]ZZ[XYcccYcZ\\]Y  
@A80HNBABXX:4:1:1666:2222#0/1
CTGCCAGCACGCTGTCACCTCTCAATAACAGTGAGTGTAATGGCCATACTCTTGATTTGGTTTTTGCCTTATGAATCAGTGGCTAAAAATATTATTTAAT  
+
deeee`bbcddddad\bbbbeee\ecYZcc^dd^ddd\\`]``L`ccabaVJ`MZ^aaYMbbb__PYWY]RWNUUab`Y`BBBBBBBBBBBBBBBBBBBB

FASTQ文件每个序列使用四行。第1行以＆＃39; @＆＃39;开头。字符，后跟序列标识符。第2行是DNA序列字母。第3行以＆＃39; +＆＃39;开头。字符。第4行编码第2行中序列的质量值（＆＃34; +＆＃34;以及下一个＆＃34; @＆＃34;之前的部分，并且必须包含与字母中相同数量的符号顺序。

我想将fastq文件读入这样的字典中（关键是DNA序列，值是质量值，以＆＃34开头; @＆＃34;＆＃34; + ＆＃34;可以丢弃）：

{'AAAACATCAGTATCCATCAGGATCAGTTTGGAAAGGGAGAGGCAATTTTTCCTAAACATGTGTTCAAATGGTCTGAGACAGACGTTAAAATGAAAAGGGG':'\YYWX\PX^YT[TVYaTY]^\^H`^a\UZU__TTbSbb^\a^^^[GOVVXLXMV[Y_^a^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB',
 'CTGAGTAAATCATATACTCAATGATTTTTTTATGTGTGTGCATGTGTGCTGTTGATATTCTTCAGTACCAAAACCCATCATCTTATTTGCATAGGGAAGT':'fff^fd\c^d^Ycacdcdcdedeffdfedb]beeeeecd^ddccdddddfffeaeeeffdTecacaLV[QRPa\a`]aY]ZZ[XYcccYcZ\]Y ',
    ....}

我写下面的代码，但它没有给我我想要的东西。任何人都可以帮我修改/改进我的代码吗？

class fastq(object):
def __init__(self,filename):
    self.filename = filename
    self.__sequences = {}

def parse_file(self):
    symbol=['@','+']
    """Stores both the sequence and the quality values for the sequence"""
    f = open(self.filename,'rU')
    for lines in self.filename:
        if symbol not in lines.startwith()
        data = f.readlines()
return data

Answer 1

这是一种非常快速有效的方法：

def parse_file(self):
    with open(self.filename, 'r') as f:
        content = f.readlines()

        # Recreate content without lines that start with @ and +
        content = [line for line in content if not line[0] in '@+']

        # Now the lines you want are alternating, so you can make a dict
        # from key/value pairs of lists content[0::2] and content[1::2]
        data = dict(zip(content[0::2], content[1::2]))

    return data

Answer 2

我不认为使用读取作为关键是好主意，如果你有完全相同的读取怎么办。但无论如何你想要这样做：

In [9]:
with open('temp.fastq') as f:
    lines=f.readlines()
head=[item[:-1] for item in lines[::4]] #get rid of '\n'
read=[item[:-1] for item in lines[1::4]]
qual=[item[:-1] for item in lines[3::4]]
dict(zip(read, qual))

Out[9]:

{'AAAACATCAGTATCCATCAGGATCAGTTTGGAAAGGGAGAGGCAATTTTTCCTAAACATGTGTTCAAATGGTCTGAGACAGACGTTAAAATGAAAAGGGG': '\\\\YYWX\\PX^YT[TVYaTY]^\\^H\\`^`a`\\UZU__TTbSbb^\\a^^^`[GOVVXLXMV[Y_^a^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB',
 'CTGAGTAAATCATATACTCAATGATTTTTTTATGTGTGTGCATGTGTGCTGTTGATATTCTTCAGTACCAAAACCCATCATCTTATTTGCATAGGGAAGT': 'fff^fd\\c^d^Ycac`dcdcded`effdfedb]beeeeecd^ddccdddddfff`eaeeeffdTecacaLV[QRPa\\\\a\\`]aY]ZZ[XYcccYcZ\\\\]Y',
 'CTGCCAGCACGCTGTCACCTCTCAATAACAGTGAGTGTAATGGCCATACTCTTGATTTGGTTTTTGCCTTATGAATCAGTGGCTAAAAATATTATTTAAT': 'deeee`bbcddddad\\bbbbeee\\ecYZcc^dd^ddd\\\\`]``L`ccabaVJ`MZ^aaYMbbb__PYWY]RWNUUab`Y`BBBBBBBBBBBBBBBBBBBB',
 'TTAGAAACTATGGGATTATTCACTCCCTAGGTACTGAGAATGGAAACTTTCTTTGCCTTAATCGTTGACATCCCCTCTTTTAGGTTCTTGCTTCCTAACA': 'ee^e^\\`ad`eeee\\dd\\ddddYeebdd\\ddaYbdcYc`\\bac^YX[V^\\Ybb]]^bdbaZ]ZZ\\^K\\^]VPNME][`_``Ubb_bYddZbbbYbbYT^_'}

Answer 3

您可以像这样使用Bio的功能：

    from Bio import SeqIO

    myf=mydir+myfile
    startlist=[]
    for record in SeqIO.parse(myf, "fastq"):
       startlist.append(str(record.seq)) #or without 'str'

将fastq文件读入字典

3 个答案: