convert an Illumina manifest file (ex. - Human1M-Duov3_C.bpm) to a standard .csv file or tab-delimited file

[vdesb...@immport.org]

Hi All,

I am a new glu-user and was wondering if it is possible to use the glu
programs or utilities to convert an Illumina manifest file (ex. -
Human1M-Duov3_C.bpm) to a standard .csv file or tab-delimited file.

fyi - The manifest files I am trying to convert are the latest
versions, and my o/s info etc .is:

bisc_data@devdb1 glu-1.0b1-Linux_Intel_EM64T>$ ./glu --version
glu 1.0b1
bisc_data@devdb1 glu-1.0b1-Linux_Intel_EM64T>$ uname -a
Linux devdb1.immport.net 2.6.18-8.1.14.el5 #1 SMP Tue Sep 25 11:45:55
EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
bisc_data@devdb1 glu-1.0b1-Linux_Intel_EM64T>$ python -V
Python 2.4.3
bisc_data@devdb1 glu-1.0b1-Linux_Intel_EM64T>$ ./glu --version
glu 1.0b1
bisc_data@devdb1 glu-1.0b1-Linux_Intel_EM64T>$


Thank you, - Vince Desborough

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Vince,

Yes, GLU can parse and export Illumina manifest files, even their newest.  Unfortunately, you'll need a more recent version than GLU 1.0b1, which is actually quite old by now.  I need to generate a new binary installer, though others have had success installing from the source code.

-Kevin

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[vdesb...@immport.org]

Hi Kevin,

Thank you very much for the quick reply. That's great news in that it
handles the newest manifest files too!
So if I were to build from source code, what would be the new GLU
version that I will need?

Thanks again, - Vince Desborough


On Feb 8, 7:40 am, "Kevin Jacobs <jac...@bioinformed.com>"

<bioinfor...@gmail.com> wrote:
> Hi Vince,
>
> Yes, GLU can parse and export Illumina manifest files, even their newest.
>  Unfortunately, you'll need a more recent version than GLU 1.0b1, which is
> actually quite old by now.  I need to generate a new binary installer,
> though others have had success installing from the source code.
>
> -Kevin
>

> On Tue, Feb 8, 2011 at 1:56 AM, vdesboro...@immport.org <

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Vince,

See my reply earlier today to Nick Orr on the list. The best version for the newest manifests is for you is the most recent snapshot from the Google Mercurial repository. However your current b1 version may be sufficient if you're working with pre-Omni manifests like the Human1M-Duo.

Try:

glu convert.dump_bpm Human1M-Duov3_C.bpm -o Human1M-Duov3_C.txt

or

glu convert.dump_bpm Human1M-Duov3_C.bpm -o Human1M-Duov3_C.csv

If in doubt, I suggest exporting via GenomeStudio, since my code is not endorsed by Illumina, although it works well in practice.

-Kevin

[vdesb...@immport.org]

Hi Kevin,

Thanks for your timely reply. Sounds good. I've just downloaded the
latest source code
from Mercurial and after installing some necessary pre-requisites, I
plan to do the install
from the source code. The GLU version I will be compiling now is 1.0b2-
dev.

Thanks again for your help, and I will keep you posted on my
progress.

Have a good one, - Vince D.

(

On Feb 8, 11:46 am, "Jacobs, Kevin (NIH/NCI) [C]"

[vdesb...@immport.org]

Hi Kevin,

Thank you very much for your assistance! I was able to successfully
convert my Illumina *.bpm files to *.txt files (and also to *.csv).

I thought I was going to need to upgrade my Python 2.4.3 to Python
2.5.2 in order to compile the latest GLU code so that I could run the
conversion. However, I found that this Python upgrade would impact
too many other things beyond my control. So, I thought that may be I
would just try only copying the affected GLU code (that uses
illumina.py) to the proper locations, and see if it would run. And
voila, it ran just fine!

The GLU parts I copied were:
=====================
- the glu/modules/convert/* directory and all files.
- the glu/lib/* directory and all files and directories under that.

Then I just ran the file conversion using the command line (just like
you told me) shown below:

bisc_data@devdb1 bpm_files>$ glu convert.dump_bpm Human1M-Duov3_C.bpm -
o Human1M-Duov3_C.txt
WARNING: Using slow binary string reader.
GLU 1.0b1 module: convert.dump_bpm
Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of
Health & Human Services. Funded by NCI under Contract N01-CO-12400.

bisc_data@devdb1 bpm_files>$ ll Human1M-Duov3_C.bpm
-rw-r--r-- 1 bisc_data oinstall 198759625 Oct 15 15:12 Human1M-
Duov3_C.bpm
bisc_data@devdb1 bpm_files>$ ll Human1M-Duov3_C.txt
-rw-r--r-- 1 bisc_data oinstall 154041783 Feb 11 12:21 Human1M-
Duov3_C.txt
bisc_data@devdb1 bpm_files>$

Once again, thanks for all of your help!

- Vince Desborough



On Feb 8, 1:06 pm, "vdesboro...@immport.org" <vdesboro...@immport.org>
wrote:

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Vince,

There are a few places where the difference in Python versions will matter, but it seems that none of them are involved in the code you needed. The alternative is that it is fairly simple to install multiple versions of Python (e.g. in /usr/local) using the 'altinstall' option that does not replace the "default" python executable or affect other users.

-Kevin

________________________________________
From: vdesb...@immport.org [vdesb...@immport.org]
Sent: Friday, February 11, 2011 12:32 PM

[Vince Desborough]

Hi Kevin,

Wow, that's great. Thanks for the information on the "altinstall" option.  So then, for the long-term, I will definitely install that way, so as not to affect the other users etc.  I have a feeling that we will be using GLU for several other things...
Thanks!  

- Vince.

 

---

From: Jacobs, Kevin (NIH/NCI) [C] [mailto:jaco...@mail.nih.gov]
To: glu-...@googlegroups.com [mailto:glu-...@googlegroups.com]
Sent: Fri, 11 Feb 2011 12:32:49 -0500
Subject: RE: [glu-users] Re: convert an Illumina manifest file (ex. - Human1M-Duov3_C.bpm) to a standard .csv file or tab-delimited file