Question

我有一个python脚本如下：

<?php 

        $soapClient = new SoapClient("http://168.187.136.18:8090/APIService/PostaWebClient.svc?wsdl"); 

        // Prepare SoapHeader parameters 
        $sh_param = array( 
                    'Username'    =>    'username', 
                    'Password'    =>    'password'); 
        $headers = new SoapHeader('http://soapserver.example.com/webservices', 'UserCredentials', $sh_param); 

        // Prepare Soap Client 
        $soapClient->__setSoapHeaders(array($headers)); 

        // Setup the RemoteFunction parameters 
        $ap_param = array( 
                    'amount'     =>    $irow['total_price']); 

        // Call RemoteFunction () 
        $error = 0; 
        try { 
            $info = $soapClient->__call("RemoteFunction", array($ap_param)); 
        } catch (SoapFault $fault) { 
            $error = 1; 
            print(" 
            alert('Sorry, blah returned the following ERROR: ".$fault->faultcode."-".$fault->faultstring.". We will now take you back to our home page.'); 
            window.location = 'main.php'; 
            "); 
        } 

        if ($error == 0) {        
            $auth_num = $info->RemoteFunctionResult; 

            if ($auth_num < 0) { 
                .... 

                // Setup the OtherRemoteFunction() parameters 
                $at_param = array( 
                            'amount'        => $irow['total_price'], 
                            'description'    => $description); 

                // Call OtherRemoteFunction() 
                $trans = $soapClient->__call("OtherRemoteFunction", array($at_param)); 
                $trans_result = $trans->OtherRemoteFunctionResult; 
            .... 
                } else { 
                    // Record the transaction error in the database 

                // Kill the link to Soap 
                unset($soapClient); 
            } 
        } 
    }    
} 

?>

我想为同一个输入文件运行上面的脚本，但是对于40个不同的wanted_files - 具有不同的名称--A_ids.txt，B_ids.txt等。我想各自不同的产出 - A.fasta，B.fasta等。

我是否需要更改我的python脚本，或者我需要创建一个循环来为所有想要的文件运行它？

感谢

Answer 1

我同意@BlackVegetable。将其设置为使用命令行参数，通过执行以下操作：

#!/usr/bin/python
from Bio import SeqIO

import sys # for sys.argv

fasta_file = sys.argv[1] # This is now going to be name.fa, the fasta file
wanted_file = sys.argv[2] # This is now going to be name_ids.txt, or whatever you passed
# as an argument
result_file = sys.argv[3] # Output fasta file, now passed as arg

wanted = set()
with open(wanted_file) as f:
    for line in f:
        line = line.strip()
        if line != "":
            wanted.add(line)

fasta_sequences = SeqIO.parse(open(fasta_file),'fasta')
with open(result_file, "w") as f:
    for seq in fasta_sequences:
        if seq.id in wanted:
            SeqIO.write([seq], f, "fasta")

然后，您可以使用python input.fa A_ids.txt A.fasta来调用该程序。或者，python inputB.fa B_ids.txt B.fasta。

Answer 2

考虑让这个程序采用命令行选项。这将允许您从命令行中读取wanted_file名称作为参数，您可以通过解析给定的参数并遵循模式（例如用.fasta给出的替换扩展名来推断出相应的输出文件名）或者输出模式是某种形式的另一个命令行参数。

你可以将你的程序称为python my_script.py A_ids.txt并通过bash循环。您还可以选择允许可变数量的参数，每个参数都会调用给定名称的逻辑。

我对处理命令行参数的偏好是https://docs.python.org/3.3/library/argparse.html和https://docs.python.org/2/library/argparse.html，具体取决于你的python版本。

（另外，如果您采用wanted_file使用单个命令行参数的路径，则只需通过stdout或类似函数将内容输出到print并使用命令行中的重定向操作符将输出发送到提供的文件名：python my_script.py A_ids.txt > A.fasta）

Answer 3

我认为更简单的方法是将40个文件名存储在一个文件中（在代码中：wanted_filenames_file），将它们存储在一个数组（wanted_files）中并循环每个文件：< / p>

# !/usr/bin/python
from Bio import SeqIO

fasta_file = "input.fa"  # Input fasta file
wanted_filenames_file = "filenames.txt"
with open(wanted_filenames_file) as f:
    wanted_files = f.readlines()
result_file = []  # Output fasta file
for wanted_file in wanted_files:
    wanted = set()
    with open(wanted_file) as f:
        for line in f:
            line = line.strip()
            if line != "":
                wanted.add(line)

    fasta_sequences = SeqIO.parse(open(fasta_file), 'fasta')
    result_file = wanted_file.replace("_ids.txt", ".fasta")
    with open(result_file, "w") as f:
        for seq in fasta_sequences:
            if seq.id in wanted:
                SeqIO.write([seq], f, "fasta")

如何将python脚本作为不同文件的循环运行？

3 个答案: