spctools-discuss Google Group

Re: [spctools-discuss] Setting up TPP - unable to access /tpp/html files?

brian.pr...@insilicos.com (Brian Pratt) — Sat, 21 Nov 2009 18:54:33 UT

Sounds like you may also need to set the path for whatever user is running
the apache process.

Brian

(or maybe you already figured that out - this got to my inbox just today but
you posted 4 days ago?)

Setting up TPP - unable to access /tpp/html files?

aakpitc...@gmail.com (Austin) — Tue, 17 Nov 2009 20:47:45 UT

Hi Everyone,

I started setting up the TPP on Ubuntu 9.04 / Apache2 over the weekend
following the instructions found at
[link],
and have had a few minor issues (so far). The setup seems to have gone
fine, and I can log into /tpp/cgi-bin/tpp_gui.pl and all that jazz.

Re: [spctools-discuss] Re: "base_name" constraint in pepXML

bowers...@gmail.com (Greg Bowersock) — Fri, 20 Nov 2009 19:34:08 UT

David, just a quick reply to part of your message. Normally, I make a
directory for an experiment and I will process the mascot, sequest,
and possibly X!Tandem data from each mzXML file in the same directory. I do
append the name of the search to the TPP files, so I can determine which
search engine the data came from. These data sometimes are combined (not

Re: [spctools-discuss] Re: "base_name" constraint in pepXML

dshteynb...@systemsbiology.org (David Shteynberg) — Fri, 20 Nov 2009 18:51:10 UT

I will try to reason this through using trying to think from the
original authors point of view. The idea is that different searches
of the same data would happen in separate directories and the
base_name (full path to the data file) would identify one search of an
mzXML file representing one msms_run, and more than one search would

Re: [spctools-discuss] Re: "base_name" constraint in pepXML

dshteynb...@systemsbiology.org (David Shteynberg) — Fri, 20 Nov 2009 18:30:10 UT

OK I take that back. I see where the unique constraint is listed. I
will have to consider your questions further.

-David

On Fri, Nov 20, 2009 at 10:27 AM, David Shteynberg

Re: [spctools-discuss] Re: "base_name" constraint in pepXML

dshteynb...@systemsbiology.org (David Shteynberg) — Fri, 20 Nov 2009 18:27:32 UT

Hi Hendrik,

The element msms_pipeline_analysis/msms_ru n_summary has an attribute
base_name to specify the path to the datafile. In case the searched
file specified is different from the original data file there is
another entry in the element
msms_pipeline_analysis/msms_ru n_summary/search_summary for base_name.

Export result data for blast?

malm.e...@gmail.com (ChargedPeptide) — Tue, 10 Nov 2009 13:11:45 UT

Hi guys, I'm running a couple of searches with an un-annotated
datbase.
As such I would like to take the results from the prot.xml file and
run a blastP search with the sequences against an annotated related
databases.
Is there any easy way to export fasta sequences of a search together
with their protein ID? I've only come up with a very roundabout way

X!Tandem Output vs PepXML

eddi...@gmail.com (Edwin Mulwa) — Mon, 09 Nov 2009 16:36:47 UT

Hi,

I have recently converted an X!Tandem output file to PepXML format using
Tandem2XML utility. The X!Tandem output file was generated from an MGF file.
After the conversion, I compared the contents of the X!Tandem output and
PepXML files to try to determine which attributes in the PepXML file

Re: [spctools-discuss] re: patch: Sqt2XML fixes

jke...@gmail.com (Jimmy Eng) — Wed, 18 Nov 2009 19:50:16 UT

The patch was added as revision 4777. Works for the sqt file I have
access to but someone should still test with whatever sqt files were
causing the problem in the first place. Note I felt obligated to also
change the output extension from .pepXML to .pep.xml to conform with
all of our other pep.xml converter tools.

Re: [spctools-discuss] re: patch: Sqt2XML fixes

brian.pr...@insilicos.com (Brian Pratt) — Wed, 18 Nov 2009 18:15:31 UT

Hi Mike,

I'll have a go at it. It might be easiest if you just emailed me your
modified code directly.

Brian Pratt

re: patch: Sqt2XML fixes

tutu...@gmail.com (Mike Coleman) — Wed, 18 Nov 2009 00:20:02 UT

It doesn't look like this patch ever made it into the SVN tree. Could
someone look at adding it? I think someone here's going to mention
this program in a paper, but without this patch this program doesn't
function correctly. Thanks!

[link]

Re: [spctools-discuss] Re: building on windows

brian.pr...@insilicos.com (Brian Pratt) — Tue, 17 Nov 2009 22:14:39 UT

Oops, I wasn't up to date after all, sorry.

Just add an (int) cast in front of that strlen call and drive on...

Re: building on windows

nelson...@gmail.com (Bill Nelson) — Tue, 17 Nov 2009 20:56:16 UT

Must be the time difference. Does Seattle observe daylight savings
time?

My SVN root is :[link]
trunk/trans_proteomic_pipeline /src/Parsers/Algorithm2XML/Seq uest2XML
I'm at version 4775

At line 752 in out2xml.cxx I have: for (i=2; i <strlen(szPep)-2; i++)

Re: [spctools-discuss] Re: building on windows

brian.pr...@insilicos.com (Brian Pratt) — Tue, 17 Nov 2009 19:42:18 UT

Glad it's coming along.

There is some weirdness here, though - my copy of out2xml.cxx doesn't have a
comparison operator at line 752, and it's current with SVN.

Brian

Re: [spctools-discuss] Re: MzXML2Search problem (Agilent msconvert-ed data)

brian.pr...@insilicos.com (Brian Pratt) — Tue, 17 Nov 2009 18:52:10 UT

Actually it will write 6 digit scan numbers as is. The formatting just
specifies that it won't write any fewer than 5 digits.

I think the only code change I would want to make is to set that default
upper limit to the largest possible integer value, but as there's a
workaround I don't think we need to worry about it.