结果并没有给我正确的答案

Question

所以我给我的班级布置了这个作业，它是这样的：

创建一个能够读取 FASTQ 格式文件的程序。存储每个读数的碱基和各自的质量值（作为整数）。
计算并存储每次阅读的平均质量。
计算并存储每个读数的长度。
此外，程序应该能够将读取数据写回 FASTQ 格式。
丢弃平均质量低于确定阈值的所有读取。
丢弃所有长度低于确定阈值的读取。
写一份报告，说明有多少读数由于质量低和长度短而被丢弃。以下是名为
```
my_test.fastq
```
.

FilteringReport:
  Filename: my_test.fastq
  TotalReads: 4000
  DiscardLowQual: 89
  DiscardLen: 11
  ReadsAfterFilter: 3900

规则

程序必须用Python 3编写。
程序不能是线性的 -> 大部分代码（超过 90%）必须位于函数和类内部。
所有函数都必须至少接受一个参数，但并非所有函数都必须返回某些内容。
您可以从 Python 的标准库（Python 中包含的库）导入模块，但不能从第三方包（如
```
BioPython
```
）导入模块。
输入和输出文件必须作为命令行参数提供给程序。
输入fastq文件
输出fastq文件
输出报告文件
质量和长度阈值也必须作为命令行参数传递。
最小长度阈值
最低平均质量阈值
即使只传递这两个参数之一，程序也需要工作
从输入文件读取的内容必须读入“中间表示”：名为 Read 的类的实例。
FASTQ 格式有两种变体 - BASE33 和 BASE64。对于此作业，您始终可以假设 BASE33（特别是 Illumina 1.8+）。
假设永远不能重复读取名称。您的脚本必须记录在 README.md 文件中

Description
Usage
Hints

强烈建议您使用像
```
argparse
```
这样的参数解析器。你也可以使用简单的
```
sys.argv
```
，但是它会让你的程序更难编写和使用。
这是一个大问题。不要忘记将其分解为更小的任务，以便它们易于管理。
将长度和平均质量计算器实现为类方法可以简化您的工作（但请随意按照您认为合适的方式进行操作！）

下面是按顺序列出 ASCII 质量值的表格（第一个字符的质量值是 0，最后一个字符是 50）”

我的代码的最终版本是这样的：

import argparse
import os 

class Entry:
    def __init__(self, header, content, quality):
        self.header = header
        self.content = content
        self.quality = quality
        self.average_quality = 0
        self.content_length = 0

class DataProcessor:
    def __init__(self, data_file, output_file, quality_threshold, length_threshold):
        self.data_file = data_file
        self.output_file = output_file
        self.quality_threshold = quality_threshold
        self.length_threshold = length_threshold
        self.entries = []
        self.discard_low_qual = 0
        self.discard_len = 0

    def validate_input(self):
        if not os.path.exists(self.data_file):
            raise FileNotFoundError(f"Input file '{self.data_file}' not found.")
        if self.quality_threshold < 0 or self.quality_threshold > 50:
            raise ValueError("Quality threshold must be between 0 and 50.")
        if self.length_threshold < 0:
            raise ValueError("Length threshold must be a non-negative integer.")

    def read_entries(self):
        if not os.path.exists(self.data_file):
            raise FileNotFoundError(f"Input file '{self.data_file}' not found.")
        with open(self.data_file, 'r') as file:
            lines = file.readlines()
        for line_index in range(0, len(lines), 4):
            header = lines[line_index].strip()
            content = lines[line_index + 1].strip()
            quality = lines[line_index + 3].strip()
            entry = Entry(header, content, quality)
            self.entries.append(entry)

    def validate_thresholds(self):
        # Check if quality_threshold and length_threshold are positive integers
        if not isinstance(self.quality_threshold, int) or not isinstance(self.length_threshold, int):
            raise ValueError("Thresholds must be positive integers.")
        if self.quality_threshold < 0 or self.length_threshold < 0:
            raise ValueError("Thresholds must be non-negative integers.")

    def calculate_and_store_averages(self):
        for entry in self.entries:
            total_quality = 0
            for q in entry.quality:
                total_quality += ord(q) - 33
            avg_quality = total_quality / len(entry.quality) if entry.quality else 0
            entry.average_quality = avg_quality

    def calculate_and_store_lengths(self):
        for entry in self.entries:
            entry.content_length = len(entry.content)

    def filter_entries(self):
        initial_entry_count = len(self.entries)   
        filtered_entries_quality = [entry for entry in self.entries if entry.average_quality >= self.quality_threshold]
        self.discard_low_qual = initial_entry_count - len(filtered_entries_quality)
        filtered_entries_length = [entry for entry in filtered_entries_quality if entry.content_length >= self.length_threshold]
        self.discard_len = len(filtered_entries_quality) - len(filtered_entries_length)
        self.entries = filtered_entries_length


    def write_filtered_entries(self):
        with open(self.output_file, 'w') as file:
            for entry in self.entries:
                file.write(f"{entry.header}\n{entry.content}\n+\n{entry.quality}\n")

    def generate_filtering_report(self):
        total_entries = len(self.entries) + self.discard_low_qual + self.discard_len
        print(f"FilteringReport:")
        print(f"  TotalEntries: {total_entries}")
        print(f"  DiscardLowQual: {self.discard_low_qual}")
        print(f"  DiscardLen: {self.discard_len}")
        print(f"  EntriesAfterFilter: {len(self.entries)}")


def process_data_entries():
    parser = argparse.ArgumentParser(description="Process a data file, filter entries, and generate a filtering report.")
    parser.add_argument('data_file', help="Path to the data file")
    parser.add_argument('--output_file', help="Path to the output data file", default='filtered_data.txt')
    parser.add_argument('--quality_threshold', type=int, help="Quality threshold for filtering entries")
    parser.add_argument('--length_threshold', type=int, help="Length threshold for filtering entries")

    args = parser.parse_args()

    data_processor = DataProcessor(args.data_file, args.output_file, args.quality_threshold, args.length_threshold)
    data_processor.validate_input()
    data_processor.validate_thresholds()
    data_processor.read_entries()
    data_processor.calculate_and_store_averages()
    data_processor.calculate_and_store_lengths()
    data_processor.filter_entries()
    data_processor.write_filtered_entries()
    data_processor.generate_filtering_report()

if __name__ == "__main__":
    process_data_entries()

真正的问题是结果 DiscardLen，它始终为 0，而且不应该，有时它等于我的另一个值 DiscardLowQual。

我现在真的迷失了，因为尽管我试图理解错误在哪里，但我就是找不到它，并且我使用这个 stackoverflow 作为尝试找到错误的最后希望，我不'不想要正确的答案，我只想了解错误以及为什么它不起作用。还是谢谢啦

真正的问题是结果 DiscardLen，它始终为 0，而且不应该，有时它等于我的另一个值 DiscardLowQual。

Answer 1

ok尝试重现你的错误，我的输入

test_2.fastq

：

@2fa9ee19-5c51-4281-abdd-eac8663f9b49 runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=109831 ch=33 start_time=2019-09-12T12:05:03Z
CGGTAGCCAGCTGCGTTCAGTATGGAAGATTTGATTTGTTTAGCGATCGCCATACTACCGTGACAAGAAAGTTGTCAGTCTTTGTGACTTGCCTGTCGCTCTATCTTCCAGACTCCTTGGTCCGTGTTCAATCCCGGTAGTAGCGACGGGCGGTGTATGTATTATCAGCGCAACAGAAACAAAGACACC
+
+&&-&%$%%$$$#)33&0$&%$''*''%$#%$%#+-5/---*&&%$%&())(&$#&,'))5769*+..*&(+28./#&1228956:7674';:;80.8>;91;>?B=%.**==?(/'($$$$*'&'**%&/));807;3A=;88>=?9498++0%"%%%%'#&5/($0.$2%&0'))*'%**&)(.%&&
@1f9ca490-2f25-484a-8972-d60922b41f6f runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=106343 ch=28 start_time=2019-09-12T12:05:07Z
GATGCATACTTCGTTCGATTTCGTTTCAACTGGACAACCTACCGTGACAAAGAAAGTTGTCGATGCTTTGTGACTTGCTGTCCTCTATCTTCAGACTCCTTGGTCCATTTCAAGACCAAACAATCAGTAGTAGCGACGGGCGGTGTGGCAATATCGCTTTCAACGAAACACAAAGAAT
+
&%&%''&'+,005<./'%*-)%(#$'$#$%&&'('$$..74483=.0412$*/,)9/194/+('%%(+1+'')+,-&,>;%%.*@@D>>?)3%%296070717%%16;<'<236800%(,734(0$7769879@;?8)09:+/4'1+**7<<4.4,%%(.)##%&'(&&%*++'&#%$
@06936a64-6c08-40e9-8a10-0fbc74812c89 runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=83531 ch=23 start_time=2019-09-12T12:03:50Z
GTTTTGTCGCTGCGTTCAGTTTATGGGTGCGGGTGTTATGATGCTTCGCTTTACGTGACAAGAAAGTTAGTAGATTGTCTTTATGTTTCTGTGGTGCTGATATTGCCACACCGCCCGATAGCTCTACCGATTGAAACACGGACCAAGGAATCGGAAATGTAGGCGAGCAGGCCGTCCTGAACACCCATTAACTTTCTTGTC
+
$&'((&%$$$.$2/=-*#'.2'&&##$$#$#&&(&+-%'(%&#"###""$$%#)%,+)+&'(,&%*((%%&%$%'+),,+,,&%$')1+*$.&+6*+(*%(&'*(''&%*+,*)('%#$$$%,$&&'&)))12)*&/*,364$%$%))$'')#%%&%$#$%$$#('$(%$%$%%$$*$&$%)''%%$$&'&$)+2++,)&%
@d6a555a1-d8dd-4e55-936f-ade7c78d9d38 runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=112978 ch=97 start_time=2019-09-12T12:03:49Z
CGTATGCTTTGAGATTCATTCAGGAGGCGGGTATTTGCTCGATCATACCATACGTGGCAAGAAAGTTGTCAGTGTCTTTGTGTTTCTCTGTGGTGCGCGATATTGCCACGCCCGTCGCTACACCGATTGAAACACGGACCGAAGTCTGAAGATAGAGCGACGAGCGAAGTCACAAAGGAACTAGAGCAACTTTTTATC
+
#$%%%%''(($$%$*-&%$%)%*'%(+($)(%$,.)##$&$$#$$&('(%&%%%%#$$%(&*('('+18/(6?65510+))'--*&&$$$,*+;/+%%&&''13&%&%(133<;9=/.2*$*657,0*&(237'85;A1/$$%'7:;;:<2:..%$)0,*.)(1)1&&1+-$$,-&(-&&####%%98:AHFEB4(%,
@91ca9c6c-12fe-4255-83cc-96ba4d39ac4b runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=110811 ch=113 start_time=2019-09-12T12:04:28Z
CGGTGTACTT
+
%$&'$&'&&'0,42%*$&&%$%$#$)$*+,'($&))(*$%$%'-8644(()-&'%&*'')%*('579:?.*,9:+)1-9.'(7491:7,(52.11'7;:<===E@;>448,,(%*.''*,%&$-.;<:;66138/**,2?8<:**'%&)%&#$&&,,'&
@4dbe5037-abe2-4176-88db-32cc336a67fb runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=113290 ch=97 start_time=2019-09-12T12:05:31Z
GCAGGTGATGCTTTGGTTCAGTTTCAGATTTGGGTGTTTTATGATTTATACTATACGTGACAAGAAAGTTGTCATTGTGTATCTTTGTACTTTTGCCTGTGTCGCTCTATCTTCCAGACTCCCGGTCCGTGTTTCAATCGGTAGCTAGCGACGGGCGGTGTGGCAATATCCAGCACCAACAAACGCAAGACACCGACAACAT
+
#$%'(('#%'###$#&&(%$'.+%+&'##%%%'%4.4570'%%##%$('%##%&$',:8;7--0/**.6:6,,%#$%$##%''))$#$$#%&&&#))+&()/.(,0+-4;;FE(-/38@B/7+$,01=8?>:;/@54.(-/(%$#%+.+849.5;=35;6>62277;;%%>734298&'5$'%(%'()*,1/..-<3'''#$
@df3de4e9-48ca-45fc-83f4-02d7f066a41a runid=f53ee40429765e7817081d4bcdee6c1199c2f91d sampleid=18S_amplicon read=109639 ch=69 start_time=2019-09-12T12:05:16Z
CATGCTTCGT
+
&&&%(((*./)%(&,%$%'+#%(,+*-1+,/,%$$&%&)-.1422/29+,)&,1-,5'2=;<==<9).'7:>B?;91%+A988(*,,,,05356455395='&)###"(219;9262%+%,18+,#$''%$499999111,-/6:987-099-.048'%-.0)%-0*)*)),+121.5;<;;7.&'

你的代码

question-003.py

：

import argparse
import os 

class Entry:
    def __init__(self, header, content, quality):
        self.header = header
        self.content = content
        self.quality = quality
        self.average_quality = 0
        self.content_length = 0
        print(self.header[:20] , len(self.content))

class DataProcessor:
    def __init__(self, data_file, output_file, quality_threshold, length_threshold):
        self.data_file = data_file
        self.output_file = output_file
        self.quality_threshold = quality_threshold
        self.length_threshold = length_threshold
        self.entries = []
        self.discard_low_qual = 0
        self.discard_len = 0

    def validate_input(self):
        if not os.path.exists(self.data_file):
            raise FileNotFoundError(f"Input file '{self.data_file}' not found.")
        if self.quality_threshold < 0 or self.quality_threshold > 50:
            raise ValueError("Quality threshold must be between 0 and 50.")
        if self.length_threshold < 0:
            raise ValueError("Length threshold must be a non-negative integer.")

    def read_entries(self):
        if not os.path.exists(self.data_file):
            raise FileNotFoundError(f"Input file '{self.data_file}' not found.")
        with open(self.data_file, 'r') as file:
            lines = file.readlines()
        for line_index in range(0, len(lines), 4):
            header = lines[line_index].strip()
            content = lines[line_index + 1].strip()
            quality = lines[line_index + 3].strip()
            entry = Entry(header, content, quality)
            self.entries.append(entry)

    def validate_thresholds(self):
        # Check if quality_threshold and length_threshold are positive integers
        if not isinstance(self.quality_threshold, int) or not isinstance(self.length_threshold, int):
            raise ValueError("Thresholds must be positive integers.")
        if self.quality_threshold < 0 or self.length_threshold < 0:
            raise ValueError("Thresholds must be non-negative integers.")

    def calculate_and_store_averages(self):
        for entry in self.entries:
            total_quality = 0
            for q in entry.quality:
                total_quality += ord(q) - 33
            avg_quality = total_quality / len(entry.quality) if entry.quality else 0
            entry.average_quality = avg_quality

    def calculate_and_store_lengths(self):
        for entry in self.entries:
            entry.content_length = len(entry.content)
        
        
        for i in self.entries :
        
                print(i ,i.content_length) 

    def filter_entries(self):
        initial_entry_count = len(self.entries)   
        filtered_entries_quality = [entry for entry in self.entries if entry.average_quality >= self.quality_threshold]
        self.discard_low_qual = initial_entry_count - len(filtered_entries_quality)
        filtered_entries_length = [entry for entry in filtered_entries_quality if entry.content_length >= self.length_threshold]
        self.discard_len = len(filtered_entries_quality) - len(filtered_entries_length)
        self.entries = filtered_entries_length


    def write_filtered_entries(self):
        with open(self.output_file, 'w') as file:
            for entry in self.entries:
                file.write(f"{entry.header}\n{entry.content}\n+\n{entry.quality}\n")

    def generate_filtering_report(self):
        total_entries = len(self.entries) + self.discard_low_qual + self.discard_len
        print(f"FilteringReport:")
        print(f"  TotalEntries: {total_entries}")
        print(f"  DiscardLowQual: {self.discard_low_qual}")
        print(f"  DiscardLen: {self.discard_len}")
        print(f"  EntriesAfterFilter: {len(self.entries)}")


def process_data_entries():
    parser = argparse.ArgumentParser(description="Process a data file, filter entries, and generate a filtering report.")
    parser.add_argument('data_file', help="Path to the data file")
    parser.add_argument('-o' , '--output_file', help="Path to the output data file", default='filtered_data.txt')
    parser.add_argument('-q' , '--quality_threshold', type=int, help="Quality threshold for filtering entries")
    parser.add_argument('-l' , '--length_threshold', type=int, help="Length threshold for filtering entries")

    args = parser.parse_args()

    data_processor = DataProcessor(args.data_file, args.output_file, args.quality_threshold, args.length_threshold)
    data_processor.validate_input()
    data_processor.validate_thresholds()
    data_processor.read_entries()
    data_processor.calculate_and_store_averages()
    data_processor.calculate_and_store_lengths()
    data_processor.filter_entries()
    data_processor.write_filtered_entries()
    data_processor.generate_filtering_report()

if __name__ == "__main__":
    
    process_data_entries()

使用

> python3 ./question-003.py test_2.fastaq -q 1 -l 50

输出：

@2fa9ee19-5c51-4281- 189
@1f9ca490-2f25-484a- 178
@06936a64-6c08-40e9- 201
@d6a555a1-d8dd-4e55- 198
@91ca9c6c-12fe-4255- 10
@4dbe5037-abe2-4176- 202
@df3de4e9-48ca-45fc- 10
<__main__.Entry object at 0x7f282a744f70> 189
<__main__.Entry object at 0x7f282a692040> 178
<__main__.Entry object at 0x7f282a6920a0> 201
<__main__.Entry object at 0x7f282a692100> 198
<__main__.Entry object at 0x7f282a692160> 10
<__main__.Entry object at 0x7f282a6921c0> 202
<__main__.Entry object at 0x7f282a692220> 10
FilteringReport:
  TotalEntries: 7
  DiscardLowQual: 0
  DiscardLen: 2
  EntriesAfterFilter: 5

所以我没有收到你的错误

结果并没有给我正确的答案

问题描述投票：0回答：1

规则

1个回答

最新问题

结果并没有给我正确的答案

问题描述 投票：0回答：1

规则

1个回答

最新问题

问题描述投票：0回答：1