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我必须制作一个通用解析器来使用 Python 解析 fasta 文件。

格式如下：

>gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_1, whole genome shotgun sequence  
    TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCA

>gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_2, whole genome shotgun sequence
CAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGA
AGTTTATATATAAATTTCCTTTTTATTGGA

>gi|348686675|gb|JH159151.1| Phytophthora sojae unplaced genomic scaffold PHYSOscaffold_3, whole genome shotgun sequence
GAACTTAACATTTTCTTATGACGTAAATGAAGTTTATATATAAATTTCCTTTTTATTGGA
TAATATGCCTATGCCGCATAATTTTTATATCTTTCTCCTAACAAAACATTCGCTTGTAAA

我必须分别检索每个标题和序列，并将值插入我创建的 MySQL 数据库中。

eg: title1 = PHYSOscaffold_1
    sequence2 = TACGAGAATAATTTCTCATCATCCAGCTTTAACACAAAATTCGCA
    title2 = PHYSOscaffold_2
    sequence1 = CAGTTTTCGTTAAGAGAACTTAACATTTTCTTATGACGTAAATGA AGTTTATATATAAATTTCCTTTTTATTGGA

等等...我将这些值插入到 MySQL 表中。

我的解析输出应该是这样的：

name1 \t sequence1 \t length_of_sequence \t a_count \t t_count \t g_count \t c_count

name2 \t sequence2 \t length_of_sequence \t a_count \t t_count \t g_count \t c_count

到目前为止，我已经编写了一个非常基本的脚本，如下所示：

infile = open("simple.fasta")
line = infile.readline()
if not line.startswith(">"):
raise TypeError("Not a FASTA file: %r" % line)
title = line
sequence_lines = []
while 1:
  line = infile.readline().rstrip()
  if line == "":
    break
  sequence_lines.append(line)

我只得到我的第一个序列和标题。

我是新手，需要专家帮助。

4

1 回答 1

0

您只获得第一个标题和序列的原因是因为每次读取之间的行都是空白的。所以当你这样做时：

if line == "":
    break

它将在第一个序列后中断。使用 readline() 无法检测文件的结尾，因为它只会返回 ''。

这是一个不优雅的问题解决方案：

infile = open("simple.fasta")
# State variable so we can handle the start of the file properly
# There are probably much better ways to do this.
start = True

# Its much better to iterate over the lines than to use a while 1 loop.
for line in infile.readlines():
    if line.startswith(">"):
        if start:
            start = False
        else:
            # Each time we get here we have complete information for a read
            # You can then store that read in your database.
        sequence_lines = []
        title = line
    else:
        if start:
            raise TypeError("Not a FASTA file: %r" % line)
            start = FALSE
        sequence_lines.append(line)
于 2013-05-25T06:55:45.933 回答