如何将文本文件读入matlab并将其作为列表？

Question

我有一个格式为

的文本文件

 gene            complement(22995..24539)
                 /gene="ppp"
                 /locus_tag="MRA_0020"
 CDS             complement(22995..24539)
                 /gene="ppp"
                 /locus_tag="MRA_0020"
                 /codon_start=1
                 /transl_table=11
                 /product="putative serine/threonine phosphatase Ppp"
                 /protein_id="ABQ71738.1"
                 /db_xref="GI:148503929"
 gene            complement(24628..25095)
                 /locus_tag="MRA_0021"
 CDS             complement(24628..25095)
                 /locus_tag="MRA_0021"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /protein_id="ABQ71739.1"
                 /db_xref="GI:148503930"
 gene            complement(25219..26802)
                 /locus_tag="MRA_0022"
 CDS             complement(25219..26802)
                 /locus_tag="MRA_0022"
                 /codon_start=1
                 /transl_table=11
                 /product="hypothetical protein"
                 /protein_id="ABQ71740.1"
                 /db_xref="GI:148503931"

我想将文本文件读入Matlab并制作一个列表，其中包含来自line gene的信息作为列表中每个项目的起点。因此，对于此示例，列表中将有3个项目。我尝试了一些东西，但是无法让它发挥作用。任何人对我能做什么有任何想法？

Answer 1

以下是算法的快速建议：

1. 使用fopen
打开文件
2. 开始阅读fgetl行，直至找到以'CDS'开头的行。
3. 保持阅读行，直到您获得以'gene'开头的另一行。
4. 对于（2）和（3）中的行之间的所有行
   • 找到'/'和'='之间的字符串。这是fieldname
   • 找到引号之间的字符串。这是字段的值
5. 将计数器加1，从＃2开始，直到您完成阅读文件

这些命令可能会有所帮助：

• 查找特定包含的字符串 字符，例如使用 regexp(lineThatHasBeenRead,'/(.+)=','tokens','once')
• 创建 输出结构，使用动态 字段名称，例如 output(ct).(fieldname) = value;

---

修改

这是一些代码。我将你的例子保存为'test.txt'。

% open file
fid = fopen('test.txt');

% parse the file
eof = false;
geneCt = 1;
clear output % you cannot reassign output if it exists with different fieldnames already
output(1:1000) = struct; % you may want to initialize fields here
while ~eof
    % read lines till we find one with CDS
    foundCDS = false;
    while ~foundCDS
        currentLine = fgetl(fid);
        % check for eof, then CDS. Allow whitespace at the beginning
        if currentLine == -1
            % end of file
            eof = true;
        elseif ~isempty(regexp(currentLine,'^\s+CDS','match','once'))
            foundCDS = true;
        end
    end % looking for CDS

    if ~eof

        % read (and remember) lines till we find 'gene'
        collectedLines = cell(1,20); % assume no more than 20 lines pere gene. Row vector for looping below
        foundGene = false;
        lineCt = 1;
        while ~foundGene
            currentLine = fgetl(fid);
            % check for eof, then gene. Allow whitespace at the beginning
            if currentLine == -1;
                % end of file - consider all data has been read
                eof = true;
                foundGene = true;
            elseif ~isempty(regexp(currentLine,'^\s+gene','match','once'))
                foundGene = true;
            else
                collectedLines{lineCt} = currentLine;
                lineCt = lineCt + 1;
            end
        end

        % loop through collectedLines and assign. Do not loop through the
        % gene line
        for line = collectedLines(1:lineCt-1)
            fieldname = regexp(line{1},'/(.+)=','tokens','once');
            value = regexp(line{1},'="?([^"]+)"?$','tokens','once');
            % try converting value to number
            numValue = str2double(value);
            if isfinite(numValue)
                value = numValue;
            else
                value = value{1};
            end
            output(geneCt).(fieldname{1}) = value;
        end
        geneCt = geneCt + 1;
    end
end % while eof

% cleanup
fclose(fid);
output(geneCt:end) = [];