blocks|key|647441|text|我可以在你的几点上给你一些提示。|type|unstyled|depth|inlineStyleRanges|entityRanges|data|647442|我认为您的第一个目标应该是逐个解析文件字符，确保每个字符都是有效的，将它们分成三个核苷酸集合，然后再为您的其他目标工作。|647443|我认为你的生物学也有点差，当你将DNA转录成RNA时，你需要考虑股所涉及的内容。在你的转录步骤中，你可能不需要“补充”你的基础。|offset|length|647444|2.，您应该在解析文件字符时检查这一点。|style|CODE|647445|3.您可以使用一个循环和一些if语句或散列来完成这一任务。|647446|当您逐字符读取文件时，4.很可能会用计数器来完成。因为你需要在第三个字符后插入一个空格。|647447|5.，这将是使用基于氨基酸密码子表的散列的好地方。|647448|6.在解析文件时必须查找gap字符。这似乎与你的第二个要求相矛盾，因为程序说你的文本只能包含ATGC。|647449|有很多perl函数可以使这更容易。还有perl模块，如bioperl。但我认为使用其中的一些可能会使你的任务落空。|647450|entityMap|0|LINK|mutability|MUTABLE|url|http://www.web-books.com/MoBio/Free/Ch4B.htm^0|0|0|W|1|0|0|0|2|0|0|2|0|B|2|0|0|2|0|0|2|0|0^^$0|@$1|2|3|4|5|6|7|13|8|@]|9|@]|A|$]]|$1|B|3|C|5|6|7|14|8|@]|9|@]|A|$]]|$1|D|3|E|5|6|7|15|8|@]|9|@$F|16|G|17|1|18]]|A|$]]|$1|H|3|I|5|6|7|19|8|@$F|1A|G|1B|J|K]]|9|@]|A|$]]|$1|L|3|M|5|6|7|1C|8|@$F|1D|G|1E|J|K]]|9|@]|A|$]]|$1|N|3|O|5|6|7|1F|8|@$F|1G|G|1H|J|K]]|9|@]|A|$]]|$1|P|3|Q|5|6|7|1I|8|@$F|1J|G|1K|J|K]]|9|@]|A|$]]|$1|R|3|S|5|6|7|1L|8|@$F|1M|G|1N|J|K]]|9|@]|A|$]]|$1|T|3|U|5|6|7|1O|8|@]|9|@]|A|$]]|$1|V|3|-4|5|6|7|1P|8|@]|9|@]|A|$]]]|W|$X|$5|Y|Z|10|A|$11|12]]]]

I can give you a few hints on a few of your points. 

I think your first goal should be to parse the file character by character, ensuring each one is valid, group them into sets of three nucleotides and then work on your other goals.

I think your biology is a bit off as well, when you transcribe DNA to RNA you need to think about what <a href="http://www.web-books.com/MoBio/Free/Ch4B.htm" rel="nofollow">strands</a> are involved. You may not need to "complement" your bases during your transcription step.

<code>2.</code> You should check this as your parse the file character by character.

<code>3.</code> You could do this with a loop and some if statements or hash

<code>4.</code> This could probably be done with a counter as you read the file character by character. Since you need to insert a space after every 3rd character. 

<code>5.</code> This would be a good place to use a hash that's based on the amino acid codon table. 

<code>6.</code> You'll have to look for the gap character as you parse the file. This seems to contradict your #2 requirement since the program says your text can only contain ATGC. 

There are a lot of perl functions that could make this easier. There are also perl modules such as bioperl. But I think using some of these could defeat the purpose of your assignment.

blocks|key|1846104|text|看看BioPerl和浏览源模块，看看如何解决这个问题的指标。|type|unstyled|depth|inlineStyleRanges|entityRanges|offset|length|data|1846105|entityMap|0|LINK|mutability|MUTABLE|url|http://www.bioperl.org/wiki/Main_Page|1|http://www.bioperl.org/wiki/Category%253aModules^0|2|7|0|A|5|1|0^^$0|@$1|2|3|4|5|6|7|N|8|@]|9|@$A|O|B|P|1|Q]|$A|R|B|S|1|T]]|C|$]]|$1|D|3|-4|5|6|7|U|8|@]|9|@]|C|$]]]|E|$F|$5|G|H|I|C|$J|K]]|L|$5|G|H|I|C|$J|M]]]]

Look at <a href="http://www.bioperl.org/wiki/Main_Page" rel="nofollow">BioPerl</a> and <a href="http://www.bioperl.org/wiki/Category%3aModules" rel="nofollow">browse the source-modules</a> for indicators on how to go about it.

blocks|key|2201357|text|1.+here+I+will+use+the+<>+operator|type|unstyled|depth|inlineStyleRanges|offset|length|style|CODE|entityRanges|data|2201358|好的，您的计划是逐行读取文件。不要忘记在你走的时候chomp每一行，否则你会在你的序列中出现换行符。|2201359|2.+Check+to+make+sure+the+file+only+contains+acgt+or+die|2201360|if+(+<>+ne+[acgt]+)+{+die+"usage:+file+must+only+contain+nucleotides+\n";+}|2201361|在while循环中，<>操作符将读取的行放入特殊变量$_中，除非您显式地分配它(my+$line+=+<>)。|2201362|在上面的代码中，您从文件中读取一行并丢弃它。你得保留这句话。|2201363|此外，ne运算符比较两个字符串，而不是一个字符串和一个正则表达式。您需要这里的!~运算符(或者=~操作符，带有一个否定的字符类[%5Eacgt]+)。如果需要测试不区分大小写，请查看i标志以进行正则表达式匹配。|2201364|3.+Transcribe+the+DNA+to+RNA+(Every+A+replaced+by+U,+T+replaced+by+A,+C+replaced+by+G,+G+replaced+by+C).|2201365|就像GWW说的，检查你的生物学。T->U是转录的唯一步骤.在这里，您会发现tr+(音译)运算符很有用。|2201366|4.+Take+this+transcription+&+break+it+into+3+character+'codons'+starting+at+the+first+occurance+of+"AUG"|2201367|not+sure+but+I'm+thinking+this+is+where+I+will+start+a+%25hash+variables?|2201368|我会在这里用一个缓冲器。在while(<>)循环之外定义一个标量。使用index来匹配“8月”。如果您找不到它，那么将最后两个基放在标量上(可以使用substr+$line,+-2,+2+)。在循环的下一次迭代中，(用.=)将行追加到这两个基上，然后再次测试"AUG“。如果你被击中，你会知道在哪里，所以你可以标记点，并开始翻译。|2201369|5.+Take+the+3+character+"codons"+and+give+them+a+single+letter+Symbol+(an+uppercase+one-letter+amino+acid+name)|2201370|Assign+a+key+a+value+using+(there+are+70+possibilities+here+so+I'm+not+sure+where+to+store+or+how+to+access)|2201371|同样，正如GWW所说，构建一个哈希表：|2201372|%25codons+=+(+AUG+=>+'M',+...)。|2201373|然后，您可以使用(例如)+split来构建当前行的数组，一次生成三个元素，并从哈希表中获取正确的氨基酸代码。|2201374|6.If+a+gap+is+encountered+a+new+line+is+started+and+process+is+repeated|2201375|not+sure+but+we+can+assume+that+gaps+are+multiples+of+threes.|2201376|请参见上面的。您可以用exists+$codons{$current_codon}测试是否存在空白。|2201377|7.+Am+I+approaching+this+the+right+way?+Is+there+a+Perl+function+that+I'm+overlooking+that+can+simplify+the+main+program?|2201378|你知道，从上面看，这似乎太复杂了。我构建了一些构建块；子程序read_codon和translate：我认为它们极大地帮助了程序的逻辑。|2201379|我知道这是一项家庭作业，但我想它可能会帮助你了解其他可能的方法：|2201380|use+warnings;+use+strict;
use+feature+'state';


#+read_codon+works+by+using+the+new+[state][1]+feature+in+Perl+5.10
#+both+@buffer+and+$handle+represent+'state'+on+this+function:
#+Both+permits+abstracting+reading+codons+from+processing+the+file
#+line-by-line.
#+Once+read_colon+is+called+for+the+first+time,+both+are+initialized.
#+Since+$handle+is+a+state+variable,+the+current+file+handle+position
#+is+never+reset.+Similarly,+@buffer+always+holds+whatever+was+left
#+from+the+previous+call.
#+The+base+case+is+that+@buffer+contains+less+than+3bp,+in+which+case
#+we+need+to+read+a+new+line,+remove+the+"\n"+character,
#+split+it+and+push+the+resulting+list+to+the+end+of+the+@buffer.
#+If+we+encounter+EOF+on+the+$handle,+then+we+have+exhausted+the+file,
#+and+the+@buffer+as+well,+so+we+'return'+undef.
#+otherwise+we+pick+the+first+3bp+of+the+@buffer,+join+them+into+a+string,
#+transcribe+it+and+return+it.

sub+read_codon+{
++++my+($file)+=+@_;

++++state+@buffer;
++++open+state+$handle,+'<',+$file+or+die+$!;

++++if+(@buffer+<+3)+{
++++++++my+$new_line+=+scalar+<$handle>+or+return;
++++++++chomp+$new_line;
++++++++push+@buffer,+split+//,+$new_line;
++++}

++++return+transcribe(
+++++++++++++++++++++++join+'',+
+++++++++++++++++++++++shift+@buffer,
+++++++++++++++++++++++shift+@buffer,
+++++++++++++++++++++++shift+@buffer
+++++++++++++++++++++);
}

sub+transcribe+{
++++my+($codon)+=+@_;
++++$codon+=~+tr/T/U/;
++++return+$codon;
}


#+translate+works+by+using+the+new+[state][1]+feature+in+Perl+5.10
#+the+$TRANSLATE+state+is+initialized+to+0
#+as+codons+are+passed+to+it,+
#+the+sub+updates+the+state+according+to+start+and+stop+codons.
#+Since+$TRANSLATE+is+a+state+variable,+it+is+only+initialized+once,
#+(the+first+time+the+sub+is+called)
#+If+the+current+state+is+'translating',
#+then+the+sub+returns+the+appropriate+amino-acid+from+the+%25codes+table,+if+any.
#+Thus+this+provides+a+logical+way+to+the+caller+of+this+sub+to+determine+whether
#+it+should+print+an+amino-acid+or+not:+if+not,+the+sub+will+return+undef.
#+%25codes+could+also+be+a+state+variable,+but+since+it+is+not+actually+a+'state',
#+it+is+initialized+once,+in+a+code+block+visible+form+the+sub,
#+but+separate+from+the+rest+of+the+program,+since+it+is+'private'+to+the+sub

{
++++our+%25codes+=+(
++++++++AUG+=>+'M',
++++++++...
++++);

++++sub+translate+{
++++++++my+($codon)+=+@_+or+return;

++++++++state+$TRANSLATE+=+0;

++++++++$TRANSLATE+=+1+if+$codon+=~+m/AUG/i;
++++++++$TRANSLATE+=+0+if+$codon+=~+m/U(AA%7CGA%7CAG)/i;

++++++++return+$codes{$codon}+if+$TRANSLATE;
++++}
}|code-block|syntax|javascript|2201381|entityMap^0|0|Y|0|P|5|0|0|1K|0|0|23|0|A|2|Q|2|14|D|0|0|3|2|13|2|1B|2|1R|7|2H|1|0|0|2W|0|11|2|0|0|2W|0|0|1Z|0|D|9|Z|5|22|J|31|2|0|0|33|0|0|30|0|0|0|S|0|D|5|0|0|1Z|0|0|1P|0|B|U|0|0|3D|0|U|A|15|9|0|0|0^^$0|@$1|2|3|4|5|6|7|1U|8|@$9|1V|A|1W|B|C]]|D|@]|E|$]]|$1|F|3|G|5|6|7|1X|8|@$9|1Y|A|1Z|B|C]]|D|@]|E|$]]|$1|H|3|I|5|6|7|20|8|@$9|21|A|22|B|C]]|D|@]|E|$]]|$1|J|3|K|5|6|7|23|8|@$9|24|A|25|B|C]]|D|@]|E|$]]|$1|L|3|M|5|6|7|26|8|@$9|27|A|28|B|C]|$9|29|A|2A|B|C]|$9|2B|A|2C|B|C]]|D|@]|E|$]]|$1|N|3|O|5|6|7|2D|8|@]|D|@]|E|$]]|$1|P|3|Q|5|6|7|2E|8|@$9|2F|A|2G|B|C]|$9|2H|A|2I|B|C]|$9|2J|A|2K|B|C]|$9|2L|A|2M|B|C]|$9|2N|A|2O|B|C]]|D|@]|E|$]]|$1|R|3|S|5|6|7|2P|8|@$9|2Q|A|2R|B|C]]|D|@]|E|$]]|$1|T|3|U|5|6|7|2S|8|@$9|2T|A|2U|B|C]]|D|@]|E|$]]|$1|V|3|W|5|6|7|2V|8|@$9|2W|A|2X|B|C]]|D|@]|E|$]]|$1|X|3|Y|5|6|7|2Y|8|@$9|2Z|A|30|B|C]]|D|@]|E|$]]|$1|Z|3|10|5|6|7|31|8|@$9|32|A|33|B|C]|$9|34|A|35|B|C]|$9|36|A|37|B|C]|$9|38|A|39|B|C]]|D|@]|E|$]]|$1|11|3|12|5|6|7|3A|8|@$9|3B|A|3C|B|C]]|D|@]|E|$]]|$1|13|3|14|5|6|7|3D|8|@$9|3E|A|3F|B|C]]|D|@]|E|$]]|$1|15|3|16|5|6|7|3G|8|@]|D|@]|E|$]]|$1|17|3|18|5|6|7|3H|8|@$9|3I|A|3J|B|C]]|D|@]|E|$]]|$1|19|3|1A|5|6|7|3K|8|@$9|3L|A|3M|B|C]]|D|@]|E|$]]|$1|1B|3|1C|5|6|7|3N|8|@$9|3O|A|3P|B|C]]|D|@]|E|$]]|$1|1D|3|1E|5|6|7|3Q|8|@$9|3R|A|3S|B|C]]|D|@]|E|$]]|$1|1F|3|1G|5|6|7|3T|8|@$9|3U|A|3V|B|C]]|D|@]|E|$]]|$1|1H|3|1I|5|6|7|3W|8|@$9|3X|A|3Y|B|C]]|D|@]|E|$]]|$1|1J|3|1K|5|6|7|3Z|8|@$9|40|A|41|B|C]|$9|42|A|43|B|C]]|D|@]|E|$]]|$1|1L|3|1M|5|6|7|44|8|@]|D|@]|E|$]]|$1|1N|3|1O|5|1P|7|45|8|@]|D|@]|E|$1Q|1R]]|$1|1S|3|-4|5|6|7|46|8|@]|D|@]|E|$]]]|1T|$]]

<code>1. here I will use the &lt;&gt; operator</code>

OK, your plan is to read the file line by line. Don't forget to <code>chomp</code> each line as you go, or you'll end up with newline characters in your sequence.

<hr>

<code>2. Check to make sure the file only contains acgt or die</code>

<code>if ( &lt;&gt; ne [acgt] ) { die "usage: file must only contain nucleotides \n"; }</code>

In a while loop, the <code>&lt;&gt;</code> operator puts the line read into the special variable <code>$_</code>, unless you assign it explicitly (<code>my $line = &lt;&gt;</code>).

In the code above, you're reading one line from the file and discarding it. You'll need to save that line.

Also, the <code>ne</code> operator compares two strings, not one string and one regular expression. You'll need the <code>!~</code> operator here (or the <code>=~</code> one, with a negated character class <code>[^acgt]</code>. If you need the test to be case-insensitive, look into the <code>i</code> flag for regular expression matching.

<hr>

<code>3. Transcribe the DNA to RNA (Every A replaced by U, T replaced by A, C replaced by G, G replaced by C).</code>

As GWW said, check your biology. T->U is the only step in transcription. You'll find the <code>tr</code> (transliterate) operator helpful here.

<hr>

<code>4. Take this transcription &amp; break it into 3 character 'codons' starting at the first occurance of "AUG"</code>

<code>not sure but I'm thinking this is where I will start a %hash variables?</code>

I would use a buffer here. Define an scalar outside the <code>while(&lt;&gt;)</code> loop. Use <code>index</code> to match "AUG". If you don't find it, put the last two bases on that scalar (you can use <code>substr $line, -2, 2</code> for that). On the next iteration of the loop append (with <code>.=</code>) the line to those two bases, and then test for "AUG" again. If you get a hit, you'll know where, so you can mark the spot and start translation.

<hr>

<code>5. Take the 3 character "codons" and give them a single letter Symbol (an uppercase one-letter amino acid name)</code>

<code>Assign a key a value using (there are 70 possibilities here so I'm not sure where to store or how to access)</code>

Again, as GWW said, build a hash table:

<code>%codons = ( AUG =&gt; 'M', ...)</code>.

Then you can use (for eg.) <code>split</code> to build an array of the current line you're examining, build codons three elements at a time, and grab the correct aminoacid code from the hash table.

<hr>

<code>6.If a gap is encountered a new line is started and process is repeated</code>

<code>not sure but we can assume that gaps are multiples of threes.</code>

See above. You can test for the existence of a gap with <code>exists $codons{$current_codon}</code>.

<hr>

<code>7. Am I approaching this the right way? Is there a Perl function that I'm overlooking that can simplify the main program?</code>

You know, looking at the above, it seems way too complex. I built a few building blocks; the subroutines <code>read_codon</code> and <code>translate</code>: I think they help the logic of the program immensely.

I know this is a homework assignment, but I figure it might help you get a feel for other possible approaches:

<pre><code>use warnings; use strict;
use feature 'state';


# read_codon works by using the new [state][1] feature in Perl 5.10
# both @buffer and $handle represent 'state' on this function:
# Both permits abstracting reading codons from processing the file
# line-by-line.
# Once read_colon is called for the first time, both are initialized.
# Since $handle is a state variable, the current file handle position
# is never reset. Similarly, @buffer always holds whatever was left
# from the previous call.
# The base case is that @buffer contains less than 3bp, in which case
# we need to read a new line, remove the "\n" character,
# split it and push the resulting list to the end of the @buffer.
# If we encounter EOF on the $handle, then we have exhausted the file,
# and the @buffer as well, so we 'return' undef.
# otherwise we pick the first 3bp of the @buffer, join them into a string,
# transcribe it and return it.

sub read_codon {
 my ($file) = @_;

 state @buffer;
 open state $handle, '&lt;', $file or die $!;

 if (@buffer &lt; 3) {
 my $new_line = scalar &lt;$handle&gt; or return;
 chomp $new_line;
 push @buffer, split //, $new_line;
 }

 return transcribe(
 join '', 
 shift @buffer,
 shift @buffer,
 shift @buffer
 );
}

sub transcribe {
 my ($codon) = @_;
 $codon =~ tr/T/U/;
 return $codon;
}


# translate works by using the new [state][1] feature in Perl 5.10
# the $TRANSLATE state is initialized to 0
# as codons are passed to it, 
# the sub updates the state according to start and stop codons.
# Since $TRANSLATE is a state variable, it is only initialized once,
# (the first time the sub is called)
# If the current state is 'translating',
# then the sub returns the appropriate amino-acid from the %codes table, if any.
# Thus this provides a logical way to the caller of this sub to determine whether
# it should print an amino-acid or not: if not, the sub will return undef.
# %codes could also be a state variable, but since it is not actually a 'state',
# it is initialized once, in a code block visible form the sub,
# but separate from the rest of the program, since it is 'private' to the sub

{
 our %codes = (
 AUG =&gt; 'M',
 ...
 );

 sub translate {
 my ($codon) = @_ or return;

 state $TRANSLATE = 0;

 $TRANSLATE = 1 if $codon =~ m/AUG/i;
 $TRANSLATE = 0 if $codon =~ m/U(AA|GA|AG)/i;

 return $codes{$codon} if $TRANSLATE;
 }
}
</code></pre>

Looking for suggestions on how to approach my Perl programming homework assignment to write an RNA synthesis program. I've summed and outlined the program below. Specifically, I'm looking for feedback on the blocks below (I'll number for easy reference). I've read up to chapter 6 in Elements of Programming with Perl by Andrew Johnson (great book). I've also read the perlfunc and perlop pod-pages with nothing jumping out on where to start. 

Program Description: The program should read an input file from the command line, translate it into RNA, and then transcribe the RNA into a sequence of uppercase one-letter amino acid names. 

<ol>
<li>Accept a file named on the command line

<blockquote>
 here I will use the &lt;> operator 
</blockquote></li>
<li>Check to make sure the file only contains acgt or die 

<pre><code>if ( &lt;&gt; ne [acgt] ) { die "usage: file must only contain nucleotides \n"; } 
</code></pre></li>
<li>Transcribe the DNA to RNA (Every A replaced by U, T replaced by A, C replaced by G, G replaced by C) 

<blockquote>
 not sure how to do this 
</blockquote></li>
<li>Take this transcription &amp; break it into 3 character 'codons' starting at the first occurance of "AUG" 

<blockquote>
 not sure but I'm thinking this is where I will start a %hash variables? 
</blockquote></li>
<li>Take the 3 character "codons" and give them a single letter Symbol (an uppercase one-letter amino acid name) 

<blockquote>
 Assign a key a value using (there are 70 possibilities here so I'm not sure where to store or how to access) 
</blockquote></li>
<li>If a gap is encountered a new line is started and process is repeated 

<blockquote>
 not sure but we can assume that gaps are multiples of threes. 
</blockquote></li>
<li>Am I approaching this the right way? Is there a Perl function that I'm overlooking that can simplify the main program? </li>
</ol>

<h3>Note</h3>

Must be self contained program (stored values for codon names &amp; symbols). 

Whenever the program reads a codon that has no symbol this is a gap in the RNA, it should start a new line of output and begin at the next occurance of "AUG". For simplicity we can assume that gaps are always multiples of threes.

Before I spend any additional hours on research I am hoping to get confirmation that I'm taking the right approach. Thanks for taking time to read and for sharing your expertise!

Perl Program to Mimic RNA Synthesis

翻译质量差，导致语言生硬或混乱。

没有提供实际的解决方法或示例。

解答不清晰，无法理解或解决问题。

页面排版不美观，阅读体验差。

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寻找关于如何接近我的Perl编程作业作业来编写RNA合成程序的建议。我已经总结并概述了下面的计划。具体来说，我正在寻找关于以下块的反馈(我将编号以便于参考)。我读过安德鲁·约翰逊( Andrew )关于用Perl编程的元素的第6章(很棒的一本书)。我还读过perlfunc和perlop页面，没有任何东西可以从哪里开始。...

问模拟RNA合成的Perl程序
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问模拟RNA合成的Perl程序EN