SRF conversion help

[Parthiban]

Hi John,

May I request your assistance as well for SRF conversion? I had been
trying for a while now. I managed to install ms-sequest 0.0.4 and all
its dependencies. I get the error below: (I read your reply to Gabe in
the forum, but no use in my case)

=============================================================
C:\rubyrepository\gems\ms-sequest-0.0.4\bin>ruby -rubygems -S
srf_to_sqt.rb Tio2-dhb_2008NovDec04-G4.srf
C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/params.rb:
121:in `parse_io': private method `sub' called for nil:NilCl
ass (NoMethodError)
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf.rb:58:in `get_sequest_params'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf.rb:51:in `open'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf.rb:51:in `get_sequest_params'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf.rb:150:in `from_file'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf.rb:94:in `initialize'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf/sqt.rb:183:in `new'
from C:/rubyrepository/gems/ms-sequest-0.0.4/lib/ms/sequest/
srf/sqt.rb:183:in `process'
from C:/rubyrepository/gems/tap-0.18.0/lib/tap/task.rb:346:in
`call'
from C:/rubyrepository/gems/tap-0.18.0/lib/tap/app/stack.rb:
20:in `call'
from C:/rubyrepository/gems/tap-0.18.0/lib/tap/app.rb:247:in
`dispatch'
from C:/rubyrepository/gems/tap-0.18.0/lib/tap/task.rb:342:in
`execute'
from srf_to_sqt.rb:36
from srf_to_sqt.rb:35:in `each'
from srf_to_sqt.rb:35

=============================================================

When I run srf_to_search, it looks fine:

=============================================================
C:\rubyrepository\gems\ms-sequest-0.0.4\bin>ls
Tio2-dhb_2008NovDec04-G4.srf sequest.params srf_sqt.log
srf_to_search.rb srf_to_sqt.rb

C:\rubyrepository\gems\ms-sequest-0.0.4\bin>ruby -rubygems -S
srf_to_search.rb
usage: srf_to_search.rb <file>.srf ...

configurations
-f, --format FORMAT mgf|dta (default: mgf)
--help Print this help
=============================================================

Can you please tell me where the issue is?

I have the following gems installed in windows 2003 server:

===================================================
C:\rubyrepository\gems>dir
Volume in drive C has no label.
Volume Serial Number is A427-D31C

Directory of C:\rubyrepository\gems

19/06/2009 13:16 <DIR> .
19/06/2009 13:16 <DIR> ..
19/06/2009 13:16 <DIR> arrayclass-0.1.1
19/06/2009 13:16 <DIR> configurable-0.5.0
19/06/2009 13:16 <DIR> external-0.3.0
19/06/2009 13:16 <DIR> lazydoc-0.9.0
19/06/2009 13:16 <DIR> ms-core-0.0.1
19/06/2009 13:16 <DIR> ms-fasta-0.2.3
19/06/2009 13:16 <DIR> ms-sequest-0.0.4
19/06/2009 13:11 <DIR> mspire-0.5.0
19/06/2009 13:12 <DIR> rake-0.8.7
19/06/2009 13:13 <DIR> rspec-1.2.6
19/06/2009 13:16 <DIR> tap-0.18.0
0 File(s) 0 bytes
13 Dir(s) 2,517,422,080 bytes free

===================================================

Many thanks
Parthiban.

[John Prince]

Parthiban,

I hadn't finished support for files with the sequest.params parameter 'print_duplicate_references = 0'.  It is complete now and the conversion of your file appears to be happening properly now.  When you run the conversion, the program will operate correctly and give a helpful warning explaining the situation and how to change it (if desired).

*****************************************************************************
WARNING: This srf file lists only 1 protein per peptide! (based on the
print_duplicate_references parameter in the sequest.params file used in its
creation)  So, downstream output will likewise only contain a single protein
for each peptide hit.  In many instances this is OK since downstream programs
will recalculate protein-to-peptide linkages from the database file anyway.
For complete protein lists per peptide hit, .srf files must be created with
print_duplicate_references > 0. HINT: to capture all duplicate references,
set the sequest parameter 'print_duplicate_references' to 100 or greater.
*****************************************************************************

Please let me know if you have any other troubles with it.
--John

[John Prince]

I should mention that you should be able to install the new version with:

gem install ms-sequest

After installing, to ensure that it is version 0.0.5:

gem list --local ms-sequest

--John

[Vijaya Parthiban]

Thanks for the new version, it was rather quick! I'll try this and get back to you!

Cheers,
Parthiban.

2009/6/22 John Prince <jtpr...@gmail.com>

[Vijaya Parthiban]

Hi John,

It still gives an error, as you see below. I installed 0.0.5 without any issue.

Thanks,
Parthiban.


C:\rubyrepository\gems\ms-sequest-0.0.5\bin>ruby srf_to_sqt.rb Tio2-dhb_2008NovDec04-G4.srf
C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/params.rb:121:in `parse_io': private method `sub' called for nil:NilCl
ass (NoMethodError)
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf.rb:58:in `get_sequest_params'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf.rb:51:in `open'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf.rb:51:in `get_sequest_params'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf.rb:150:in `from_file'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf.rb:94:in `initialize'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf/sqt.rb:181:in `new'
        from C:/rubyrepository/gems/ms-sequest-0.0.5/lib/ms/sequest/srf/sqt.rb:181:in `process'

        from C:/rubyrepository/gems/tap-0.18.0/lib/tap/task.rb:346:in `call'
        from C:/rubyrepository/gems/tap-0.18.0/lib/tap/app/stack.rb:20:in `call'
        from C:/rubyrepository/gems/tap-0.18.0/lib/tap/app.rb:247:in `dispatch'
        from C:/rubyrepository/gems/tap-0.18.0/lib/tap/task.rb:342:in `execute'
        from srf_to_sqt.rb:36
        from srf_to_sqt.rb:35:in `each'
        from srf_to_sqt.rb:35
 

C:\rubyrepository\gems\ms-sequest-0.0.5\bin>

2009/6/23 Vijaya Parthiban <vijaya.p...@gmail.com>