Question

我有像这个小例子的文本文件：

using System;
using System.Collections.Generic;

namespace WpfPermutations
{
    public class PermutationOuelletLexico3<T>
    {
        // ************************************************************************
        private T[] _sortedValues;

        private bool[] _valueUsed;

        public readonly long MaxIndex; // long to support 20! or less 

        // ************************************************************************
        public PermutationOuelletLexico3(T[] sortedValues)
        {
            if (sortedValues.Length <= 0)
            {
                throw new ArgumentException("sortedValues.Lenght should be greater than 0");
            }

            _sortedValues = sortedValues;
            Result = new T[_sortedValues.Length];
            _valueUsed = new bool[_sortedValues.Length];

            MaxIndex = Factorial.GetFactorial(_sortedValues.Length);
        }

        // ************************************************************************
        public T[] Result { get; private set; }

        // ************************************************************************
        /// <summary>
        /// Return the permutation relative to the index received, according to 
        /// _sortedValues.
        /// Sort Index is 0 based and should be less than MaxIndex. Otherwise you get an exception.
        /// </summary>
        /// <param name="sortIndex"></param>
        /// <param name="result">Value is not used as inpu, only as output. Re-use buffer in order to save memory</param>
        /// <returns></returns>
        public void GetValuesForIndex(long sortIndex)
        {
            int size = _sortedValues.Length;

            if (sortIndex < 0)
            {
                throw new ArgumentException("sortIndex should be greater or equal to 0.");
            }

            if (sortIndex >= MaxIndex)
            {
                throw new ArgumentException("sortIndex should be less than factorial(the lenght of items)");
            }

            for (int n = 0; n < _valueUsed.Length; n++)
            {
                _valueUsed[n] = false;
            }

            long factorielLower = MaxIndex;

            for (int index = 0; index < size; index++)
            {
                long factorielBigger = factorielLower;
                factorielLower = Factorial.GetFactorial(size - index - 1);  //  factorielBigger / inverseIndex;

                int resultItemIndex = (int)(sortIndex % factorielBigger / factorielLower);

                int correctedResultItemIndex = 0;
                for(;;)
                {
                    if (! _valueUsed[correctedResultItemIndex])
                    {
                        resultItemIndex--;
                        if (resultItemIndex < 0)
                        {
                            break;
                        }
                    }
                    correctedResultItemIndex++;
                }

                Result[index] = _sortedValues[correctedResultItemIndex];
                _valueUsed[correctedResultItemIndex] = true;
            }
        }

        // ************************************************************************
        /// <summary>
        /// Calc the index, relative to _sortedValues, of the permutation received
        /// as argument. Returned index is 0 based.
        /// </summary>
        /// <param name="values"></param>
        /// <returns></returns>
        public long GetIndexOfValues(T[] values)
        {
            int size = _sortedValues.Length;
            long valuesIndex = 0;

            List<T> valuesLeft = new List<T>(_sortedValues);

            for (int index = 0; index < size; index++)
            {
                long indexFactorial = Factorial.GetFactorial(size - 1 - index);

                T value = values[index];
                int indexCorrected = valuesLeft.IndexOf(value);
                valuesIndex = valuesIndex + (indexCorrected * indexFactorial);
                valuesLeft.Remove(value);
            }
            return valuesIndex;
        }

        // ************************************************************************
    }
}

此文件被拆分为不同的组。每组有2个部分。第一部分以>ENST00000491024.1|ENSG00000187583.6|OTTHUMG00000040756.4|OTTHUMT00000097942.2|PLEKHN1-003|PLEKHN1|176 SLESSPDAPDHTSETSHSPLYADPYTPPATSHRRVTDVRGLEEFLSAMQSARGPTPSSPLPSVPVSVPASDPRSCSSGPAGPYLLSKKGALQSRAAQRHRGSAKDGGPQPPDAPQLVSSAREGSPEPWLPLTDGRSPRRSRDPGYDHLWDETLSSSHQKCPQLGGPEASGGLVQWI >ENST00000433179.2|ENSG00000187642.5|OTTHUMG00000040757.3|-|C1orf170-201|C1orf170|696 MPTQDGQLRRPARPPGPRAWMEPRGGGSSQFSSCPGPASSGDQMQRLLQGPAPRPPGEPPGSPKSPGHSTGSQRPPDSPGAPPRSPSRKKRRAVGAKGGGHTGASASAQTGSPLLPAASPETAKLMAKAGQEELGPGPAGAPEPGPRSPVQEDRPGPGLGLSTPVPVTEQGTDQIRTPRRAKLHTVSTTVWEALPDVSRAKSDMAVSTPASEPQPDRDMAVSTPASEPQSDRDMAVSTPASEPQPDTDMAVSTPASEPQPDRDMAVSIPASKPQSDTAVSTPASEPQSSVALSTPISKPQLDTDVAVSTPASKHGLDVALPTAGPVAKLEVASSPPVSEAVPRMTESSGLVSTPVPRADAAGLAWPPTRRAGPDVVEMEAVVSEPSAGAPGCCSGAPALGLTQVPRKKKVRFSVAGPSPNKPGSGQASARPSAPQTATGAHGGPGAWEAVAVGPRPHQPRILKHLPRPPPSAVTRVGPGSSFAVTLPEAYEFFFCDTIEENEEAEAAAAGQDPAGVQWPDMCEFFFPDVGAQRSRRRGSPEPLPRADPVPAPIPGDPVPISIPEVYEHFFFGEDRLEGVLGPAVPLPLQALEPPRSASEGAGPGTPLKPAVVERLHLALRRAGELRGPVPSFAFSQNDMCLVFVAFATWAVRTSDPHTPDAWKTALLANVGTISAIRYFRRQVGQGRRSHSPSPSS >ENST00000341290.2|ENSG00000187642.5|OTTHUMG00000040757.3|OTTHUMT00000097943.2|C1orf170-001|C1orf170|676 MEPRGGGSSQFSSCPGPASSGDQMQRLLQGPAPRPPGEPPGSPKSPGHSTGSQRPPDSPGAPPRSPSRKKRRAVGAKGGGHTGASASAQTGSPLLPAASPETAKLMAKAGQEELGPGPAGAPEPGPRSPVQEDRPGPGLGLSTPVPVTEQGTDQIRTPRRAKLHTVSTTVWEALPDVSRAKSDMAVSTPASEPQPDRDMAVSTPASEPQSDRDMAVSTPASEPQPDTDMAVSTPASEPQPDRDMAVSIPASKPQSDTAVSTPASEPQSSVALSTPISKPQLDTDVAVSTPASKHGLDVALPTAGPVAKLEVASSPPVSEAVPRMTESSGLVSTPVPRADAAGLAWPPTRRAGPDVVEMEAVVSEPSAGAPGCCSGAPALGLTQVPRKKKVRFSVAGPSPNKPGSGQASARPSAPQTATGAHGGPGAWEAVAVGPRPHQPRILKHLPRPPPSAVTRVGPGSSFAVTLPEAYEFFFCDTIEENEEAEAAAAGQDPAGVQWPDMCEFFFPDVGAQRSRRRGSPEPLPRADPVPAPIPGDPVPISIPEVYEHFFFGEDRLEGVLGPAVPLPLQALEPPRSASEGAGPGTPLKPAVVERLHLALRRAGELRGPVPSFAFSQNDMCLVFVAFATWAVRTSDPHTPDAWKTALLANVGTISAIRYFRRQVGQGRRSHSPSPSS >ENST00000428771.2|ENSG00000188290.6|OTTHUMG00000040758.2|OTTHUMT00000097945.2|HES4-002|HES4|247 MAADTPGKPSASPMAGAPASASRTPDKPRSAAEHRKVGSRPGVRGATGGREGRGTQPVPDPQSSKPVMEKRRRARINESLAQLKTLILDALRKESSRHSKLEKADILEMTVRHLRSLRRVQVTAALSADPAVLGKYRAGFHECLAEVNRFLAGCEGVPADVRSRLLGHLAACLRQLGPSRRPASLSPAAPAEAPAPEVYAGRPLLPSLGGPFPLLAPPLLPGLTRALPAAPRAGPQGPGGPWRPWLR开头，此部分中的元素由">"分割，之后的行是第二部分。我试图从我的文件中创建一个Python列表，其中包含每个组ID部分的第6个元素。以下是小例子的预期输出：

"|"

我试图首先导入字典，然后使用以下方式创建一个类似于预期输出的列表：

list = ["PLEKHN1", "C1orf170", "C1orf170", "HES4"]

但它不会返回我想要的东西。你知道怎么解决吗？

Answer 1

由于这些显然是FASTA格式的蛋白质序列，我建议您使用Biopython，它可以节省您的时间并且比构建您自己的解析器更健壮：

from Bio import SeqIO

lst = [record.description.split('|')[5] for record in SeqIO.parse('in_file.fasta', 'fasta')]

print(lst)
# ['PLEKHN1', 'C1orf170', 'C1orf170', 'HES4']

Answer 2

试试这个： res = [s[5] for s in [el.split('|') for el in k]]

输出： ['HES4', 'C1orf170', 'PLEKHN1', 'C1orf170']

Answer 3

您可以通过阅读文件中的每一行并仅选择以＆＃39;＆gt;＆＃39;开头的行来获取所需的代币。然后根据＆＃39; |＆＃39;分割结果。角色并采取第6个元素。此代码在一行中执行此操作

  with open('infile.txt') as f:
        tokens =[line.split('|')[5] for line in f.readlines() if line[0] == '>']
  print(tokens)

从FASTA文本文件在python中创建一个列表

3 个答案: