perl script to preprocess eland output

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tim

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Dec 14, 2011, 11:11:41 AM12/14/11
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Hi,
line 42 of the perl script you provide :" my ($t1, $seq, $map, $t3,
$t4, $t5, $chrt, $pos, $str, @rest) = split /\s+/, $_;" and line
73 :" my ($t1, $seq, $map, $t3, $t4, $t5, $chrt, $pos, $str, @rest) =
split /\s+/, $_;". Should I replace split /\s+/ with split /\t/?


Thanks,
tim

Dongjun Chung

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Dec 17, 2011, 1:10:26 AM12/17/11
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Hi Tim,

Sorry for the late response. Because /\s+/ includes /\t/ implicitly, /
\s+/ should usually work. I did not face problems regarding this so
far. However, of course, if you have problems regarding /\s+/, you are
free to modify it. If you have any problem with /\s+/, please let me
know more details about the problem.

Thanks,
Dongjun

Yingtao Bi

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Dec 20, 2011, 5:27:54 PM12/20/11
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Hi Dongjun,
Thanks so much for your response. Could you please send me a sample of  "eland_results.out" file?  I am trying to convert my bowtie output to eland format.

Best,
tim

Dongjun Chung

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Dec 20, 2011, 6:28:49 PM12/20/11
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HI Tim,

I am now actually preparing new version of mosaics package with significant improvents. I also have updated the perl script so that it can process popular aligned read file formats. You can download this new perl script ("process_readfiles.pl") here:

http://www.stat.wisc.edu/~chungdon/mosaics/

This new perl script can process following file formats:
- eland result
- eland extended
- eland export
- bowtie default
- SAM
- BED

This perl script will be incorporated into the new version of mosaics package. In the new version of mosaics package, you will be able to process aligned read files within the R environment.

Command line:

> perl process_readfiles.pl [file_format] [frag_len] [bin_size] [collapse] [infile_location] [output_location] [infile_name] [generate_by_chr]

You don't need to specify the chromosome to process with this new perl script and chromosomes will be automatically extracted from the aligned read file. For example, if you want to construct bin-level files (bin size = 50; will be exported to the current directory) from "bowtie_results.out" (bowtie file format; located in the current directory), where average fragment length is 200, the command line will be:

> perl process_readfiles.pl bowtie 200 50 3 ./ ./ bowtie_results.out Y

Please try this new perl script for your bowtie file and let me know whether it works for you.

Thanks,
Dongjun

Yingtao Bi

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Dec 21, 2011, 12:26:43 PM12/21/11
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Hi,

The link is not working.

Thanks,
tim



This is a broken CGI. It is probably maintained by the same people that maintain:

http://www.cs.wisc.edu/
Please refer to that page to determine the correct contact address to report an error to.

If you're trying to write a CGI and keep you getting this message, read the instructions.
If you think that this was actually a server error, send mail to w...@cs.wisc.edu.
To help with debugging, the last ten lines of the error log are:

[Wed Dec 21 11:24:40 2011] [error] [client 146.151.110.68] (13)Permission denied: access to /~baumgard/index.html denied
[Wed Dec 21 11:24:40 2011] [error] [client 206.41.39.34] File does not exist: /s/www/html-pages/styles, referer: http://pages.cs.wisc.edu/~athula/temp/viewBoardingPass.htm
[Wed Dec 21 11:24:45 2011] [error] [client 66.249.71.9] Request exceeded the limit of 10 internal redirects due to probable configuration error. Use 'LimitInternalRecursion' to increase the limit if necessary. Use 'LogLevel debug' to get a backtrace.
[Wed Dec 21 11:24:45 2011] [error] [client 66.249.71.9] Request exceeded the limit of 10 internal redirects due to probable configuration error. Use 'LimitInternalRecursion' to increase the limit if necessary. Use 'LogLevel debug' to get a backtrace.
[Wed Dec 21 11:24:56 2011] [crit] [client 146.151.110.68] (13)Permission denied: /u/t/i/timc/public/html/food/.htaccess pcfg_openfile: unable to check htaccess file, ensure it is readable
[Wed Dec 21 11:24:57 2011] [crit] [client 146.151.110.68] (13)Permission denied: /u/t/i/timc/public/html/Carrie/.htaccess pcfg_openfile: unable to check htaccess file, ensure it is readable
[Wed Dec 21 11:24:57 2011] [error] [client 24.183.40.128] File does not exist: /u/h/o/hopman/public/html/cs679/dungeon/CS679-Project3/sceneassets/models/monsterWeak.FBX, referer: http://pages.cs.wisc.edu/~hopman/cs679/dungeon/CS679-Project3/game.html
[Wed Dec 21 11:24:58 2011] [error] [client 24.183.40.128] File does not exist: /u/h/o/hopman/public/html/cs679/dungeon/CS679-Project3/sceneassets/models/monsterWeak.FBX, referer: http://pages.cs.wisc.edu/~hopman/cs679/dungeon/CS679-Project3/game.html
[Wed Dec 21 11:24:58 2011] [error] [client 128.105.7.45] (13)Permission denied: exec of '/u/c/h/chungdon/public/html/mosaics/process_readfiles.pl' failed, referer: http://www.stat.wisc.edu/~chungdon/mosaics/
[Wed Dec 21 11:24:58 2011] [error] [client 128.105.7.45] Premature end of script headers: process_readfiles.pl, referer: http://www.stat.wisc.edu/~chungdon/mosaics/

Dongjun Chung

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Dec 21, 2011, 4:15:40 PM12/21/11
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Hi Tim,

Based on the error messages you attached below, I guess that you clicked the link to "process_readfiles.pl" after you opened the page "http://pages.stat.wisc.edu/~chungdon/mosaics/" (correct me if it is not the case). It you click the link to the perl script in your web browser, your web browser tries to "run" it instead of saving it. So please don't click the link to the perl script but instead save the perl script to your local drive using "Save Link As..." in the menu. If you still have the problem with downloading the perl script, I'll send it to you through e-mail instead.

Thanks,
Dongjun

Yingtao Bi

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Dec 21, 2011, 8:18:42 PM12/21/11
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Hi Dongjun,

  I downloaded the "process_readfiles.pl" according to what you said, however that file contains nothing but the error message. Please send the perl script to me by email.

Thanks so much!
tim 

dongju...@gmail.com

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Dec 21, 2011, 9:39:12 PM12/21/11
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Hi Tim,

It seems that the web browser recognized the extension of the perl script (*.pl). So I changed the file name to "process_readfiles.txt". It should work now. Please try to download the file and let me know whether it works.

Thanks,
Dongjun

Akshar Punuganti

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May 30, 2013, 5:07:03 PM5/30/13
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Hi Dongjun,

I tried downloading the 'process_readfiles.txt'. The downloaded file just contains the error message posted above by Tim.
Also, I looked into Version 1.6 of Mosaics, there doesn't seem to be a Perl script to process SAM format yet.

So can you email the general Perl script to me as well?

Thank you!
Sharad

Akshar Punuganti

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May 30, 2013, 5:33:53 PM5/30/13
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I got the script, when I run "perl process_readfiles.pl -filename s70-1.sam", I get the output:
Cannot open

Sharad

Dongjun Chung

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May 31, 2013, 9:38:50 AM5/31/13
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Hi Sharad,

Please use constructBins() function in the mosaics package instead of the perl script process_readfiles.pl mentioned above. For more details, please read the vignette in the recent mosaics packages, e.g.,

http://www.bioconductor.org/packages/2.13/bioc/vignettes/mosaics/inst/doc/mosaics-example.pdf

constructBins() is available since mosaics version 1.2.3 and you can process the aligned read files within the R environment much more conveniently. I have maintained constructBins(), but not process_readfiles.pl in the website, since then.

constructBins() supports various file formats: eland result, eland extended, eland export, bowtie, sam, bed, and csem bed. From mosaics version 1.5.2, constructBins() also supports paired end (PET) tag aligned read files in eland result and sam file formats.

Thanks,
Dongjun


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