Problems In Viewing Alignment File...
Hello all,
What i want to do is view my alignment file on web. However when i do so using PHP the entire alignment file is read but the text aligns itself to left and leaves the alignment hard to interpret. this is my PHP code
$file = fopen("res.aln", "r") or exit("Select sequences to align!");
while(!feof($file))
{
echo fgets($file). "<br />";
}
fclose($file);
Is there a way to read alignment files without incorporating any viewer. Also is it possible to directly open the alignment file like we do by double-clicking it???
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Jorge Amigo
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Nikita •
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Nikita •
1 answer
the .aln extension is typically from an alignment file, a result from a program like Clustal for instance. assuming that what you want is to display it as it is I see 2 simple options:
- you may directly put a link to the file. since it is a plain text file the user should see it perfectly displayed on the email browser.
- if you need to read it and display its results on a formatted web page of yours I would definitely go for Michael's suggestion of enclosing its contents into "pre" tags.
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what kind of alignment file? why don't you use this: http://biostar.stackexchange.com/questions/6134/blast-output-into-jsp-html. or simply:
Yes, sounds like you just need pre tags...
@michael Dondrup: Its a multiple sequence alignment file..
that shouldn't matter. keep in mind that it surely is a plain text file, so in terms of web serving it's like dealing with any other text. just echo a "
" just after it and it should do. I would though think carefully about how exactly I would want the users to interact with that file, as serving it as described may not be optimal.@Michael Dondrup, Jorge Amigo : thankss for it!! it worked!!