Difference between revisions of "NMRPipe seriesTab"
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| − | + | [http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html seriesTab] can extract maximum values or the sum of regions in an NMRPipe-format spectral series, using an NMRPipe-format peak tables as input. | |
| − | [http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html seriesTab] can extract | ||
| − | |||
| − | + | == Usage == | |
| − | |||
| − | + | An example program usage is: | |
| − | + | ||
| + | <source lang=bash> | ||
| + | seriesTab -in peaks.dat -out peaks_0.ser -list files.list -sum -dx 1 -dy 1 | ||
| + | </source> | ||
'''peaks.dat''' contains the peak list with information of spectral position | '''peaks.dat''' contains the peak list with information of spectral position | ||
| − | <source lang= | + | <source lang=text> |
VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS | VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS | ||
FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s | FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s | ||
| Line 23: | Line 23: | ||
<source lang="text"> | <source lang="text"> | ||
test.ft2 | test.ft2 | ||
| + | </source> | ||
| + | |||
| + | Or create the files list by: | ||
| + | <source lang=bash> | ||
| + | ls -v -d -1 */*.ft2 > files.list | ||
</source> | </source> | ||
| Line 28: | Line 33: | ||
A call to function could be: | A call to function could be: | ||
| − | <source lang= | + | <source lang=bash> |
#! /bin/csh -f | #! /bin/csh -f | ||
set x = 0; | set x = 0; | ||
| Line 40: | Line 45: | ||
The output is: | The output is: | ||
| − | <source lang= | + | <source lang=text> |
REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser | REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser | ||
REMARK Mode: Summation Dimensions: 2 | REMARK Mode: Summation Dimensions: 2 | ||
| Line 62: | Line 67: | ||
format is quite similar to this. <br> | format is quite similar to this. <br> | ||
This is an export from CcpNmr Analysis | This is an export from CcpNmr Analysis | ||
| − | <source lang= | + | <source lang=text> |
Assignment w1 w2 Height Volume | Assignment w1 w2 Height Volume | ||
W62NE1-W62HE1 128.374 9.932 0.00E+00 0.00E+00 -- | W62NE1-W62HE1 128.374 9.932 0.00E+00 0.00E+00 -- | ||
| Line 71: | Line 76: | ||
== See also == | == See also == | ||
[[Category:NMRPipe]] | [[Category:NMRPipe]] | ||
| + | [[Category:Peak_lists]] | ||
Latest revision as of 16:08, 21 October 2020
seriesTab can extract maximum values or the sum of regions in an NMRPipe-format spectral series, using an NMRPipe-format peak tables as input.
Usage
An example program usage is:
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
Or create the files list by:
ls -v -d -1 */*.ft2 > files.list
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 --
