[Tutor] Problem with printing Python output to HTML Correctly

Tue May 10 20:06:14 CEST 2011

A SOLUTION TO THE PROBLEM I POSTED:

align_file_rmode =
open('/Users/spyros/folder1/python/printsmotifs/alignfiles/' + query1, 'r')
align_file_appmode =
open('/Users/spyros/folder1/python/printsmotifs/alignfiles/' + query2, 'a+')

finalmotifs = motif_file.readlines()
seqalign = align_file_rmode.readlines()

for line in seqalign:
    #align_file_appmode.write('<p> \'line\' </p>')
    for item in finalmotifs:
        item = item.strip().upper()
        annotation = "<span style=\"color:red\">"+item+"</span>"
        if item in line:
            newline = line.replace(item, annotation)
            # sys.stdout.write(newline)
            align_file_appmode.write(newline)

motif_file.close()
align_file_rmode.close()
align_file_appmode.close()

the line

annotation = "<span style=\"color:red\">"+item+"</span>"

added a span and set the color in CSS.

On Tue, May 10, 2011 at 6:14 PM, Spyros Charonis <s.charonis at gmail.com>wrote:

> Hi all,
>
> No need to post answers, I figured out where my mistake was.
>
> Spyros
>
>
> On Tue, May 10, 2011 at 5:11 PM, Spyros Charonis <s.charonis at gmail.com>wrote:
>
>> Hello,
>>
>> I know I posted the exact same topic a few hours ago and I do apologize
>> for this, but my script had a careless error, and my real issue is somewhat
>> different.
>>  I have a Python script that extracts some text from a database file and
>> annotates another file, writing the results to a new file. Because the
>> files I am annotating are ASCII,
>> I am very restricted as to how I can annotate the text, and I would like
>> to instead write the results to HTML so that I can annotate my file in more
>> visually effective ways,e.g. by changing text color where appropriate.  My
>> program extracts text from a database, reads a file that is to be annotated,
>> and writes those
>> annotations to a newly created (.htm) file.
>>
>> finalmotifs = motif_file.readlines()
>> seqalign = align_file_rmode.readlines()
>>
>> # These two files have been created in code that I don't show here because
>> it is not relevant to the issue
>>
>> align_file_appmode.write('<html>')
>> align_file_appmode.write('<head>')
>>
>> align_file_appmode.write
>> ('<title>
>> \'query_\' Multiple Sequence Alignment
>>  </title>')
>>
>> align_file_appmode.write('</head>')
>> align_file_appmode.write('<body>')
>>
>> for line in seqalign:
>>     align_file_appmode.write('<p> \'line\' </p>')
>>     for item in finalmotifs:
>>         item = item.strip().upper()
>>         if item in line:
>>
>>             newline = line.replace
>>             (item, '<p> <font color = "red"> \'item\' </font></p>')
>>
>>             align_file_appmode.write(newline)
>>
>> align_file_appmode.write('</body>')
>> align_file_appmode.write('</html>')
>>
>> motif_file.close()
>> align_file_rmode.close()
>> align_file_appmode.close()
>>
>> The .htm file that is created is not what I intend it to be, it has the
>> word "item"
>> printed every couple lines because I assume I'm not passing the string
>>  sequence that I want to output correctly.
>>
>> QUESTION
>> Basically, HTML (or the way I wrote my code) does not understand that with
>> the
>> escape character '\item\' I am trying to print a string and not the word
>> "item".
>> Is there someway to correct that or would I have to use
>> something like XML to create a markup system that specifically describes
>> my data?
>>
>> I am aware Python supports multiline strings (using the format ''' text
>> ''') but I do want my HTML ( or XML?)
>> to be correctly rendered before I consider making this into a CGI program.
>> Built in python 2.6.5
>>
>
>
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