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 <[email protected]> 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 > [email protected] > > 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 _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] 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
