Hi,
Such a feature can go directly into the relax trunk. Its development
does not belong to the relax_disp branch. I suggest the following
steps:
- Create the directory 'test_suite/shared_data/peak_lists/seriesTab',
for example. Though I'll let you choose the directory name.
- Add the necessary files from the support request
(http://gna.org/support/?3043). You'll have to tell me which ones.
- Create a system test for reading this file format. In the
test_suite/system_tests/peak_lists.py, this can be done by copying and
modifying the test_read_peak_list_nmrview() test, for example.
- Implement the backend for the spectrum.read user function. Again
this would be by copying and modifying the code of one of the other
formats.
Once the test passes, then relax will be able to read this file format
forever. I'll let you tell me what to do ;) By copying what is done
for the other peak list formats, this should not be too much work.
Regards,
Edward
On 18 June 2013 13:16, Troels E. Linnet
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/support/?3043>
Summary: Support for NMRPipe seriesTab format *.ser
Project: relax
Submitted by: tlinnet
Submitted on: Tue 18 Jun 2013 11:16:58 AM GMT
Category: None
Priority: 5 - Normal
Severity: 4 - Important
Status: None
Privacy: Public
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: Microsoft Windows
_______________________________________________________
Details:
seriesTab can extract Max Values or Sum of regions in an NMRPipe-format
Spectral Series, using an NMRPipe-format Peak Table as Input.
A call to the function could be:
seriesTab -in peaks.dat -out peaks_0.ser -list files.list -sum -dx 1 -dy 1
peaks.dat contains the peak list with information of spectral position
VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s
1 246.658 18.268 9.932 128.374 +7.000000e+05 W62NE1-W62HE1
2 321.698 30.994 9.419 127.066 +7.000000e+05 L10N-L10HN
3 320.089 55.737 9.430 124.523 +7.000000e+05 V6N-V6HN
...
files.list contains
test.ft2
For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing
test.ft2
A call to function could be:
#! /bin/csh -f
set x = 0;
while ( $x <= 22 )
cd $x
seriesTab -in ../peaks.dat -out ../peaks_${x}.ser -list
../files.list
-sum -dx 1 -dy 1
cd ..
@ x = $x + 1
end
The output is:
REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser
REMARK Mode: Summation Dimensions: 2
REMARK Input Region: X +/- 1 X-ZF: 3
REMARK Analysis Region: X +/- 1
REMARK Input Region: Y +/- 1 Y-ZF: 3
REMARK Analysis Region: Y +/- 1
VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f
NULLVALUE -666
NULLSTRING *
1 246.658 18.268 9.932 128.374 +1.851056e+06 W62NE1-W62HE1
1.0000
2 321.698 30.994 9.419 127.066 +3.224387e+05 L10N-L10HN 1.0000
3 320.089 55.737 9.430 124.523 +1.479366e+06 V6N-V6HN 1.0000
----------------------------
An input reader is wished, which is auto detected like a SPARKY list. The
format is quite similar to this. This is an export from
CcpNmr Analysis
Assignment w1 w2 Height Volume
W62NE1-W62HE1 128.374 9.932 0.00E+00 0.00E+00 --
L10N-L10HN 127.066 9.419 0.00E+00 0.00E+00 --
V6N-V6HN 124.523 9.430 0.00E+00 0.00E+00 --
Test files are provided.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Tue 18 Jun 2013 11:16:58 AM GMT Name: peaks.dat Size: 297B By:
tlinnet
<http://gna.org/support/download.php?file_id=18108>
-------------------------------------------------------
Date: Tue 18 Jun 2013 11:16:58 AM GMT Name: peaks_0.ser Size: 603B By:
tlinnet
<http://gna.org/support/download.php?file_id=18109>
-------------------------------------------------------
Date: Tue 18 Jun 2013 11:16:58 AM GMT Name: files.list Size: 9B By:
tlinnet
<http://gna.org/support/download.php?file_id=18110>
_______________________________________________________
Reply to this item at:
<http://gna.org/support/?3043>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-devel
Re: [sr #3043] Support for NMRPipe seriesTab format *.ser