Difference between revisions of "NMRPipe seriesTab"

From relax wiki
Jump to navigation Jump to search
m (removed Category:Software using HotCat)
 
(6 intermediate revisions by 4 users not shown)
Line 1: Line 1:
== seriesTab ==
+
[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 Max Values or Sum of regions in an NMRPipe-format
 
Spectral Series, using an NMRPipe-format Peak Table as Input.
 
  
See homepage<br>
+
== Usage ==
http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html
 
  
A call to the function could be:
+
An example program usage is:
seriesTab -in peaks.dat -out peaks_0.ser -list files.list -sum -dx 1 -dy 1
+
 
 +
<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="text">
+
<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="bash">
+
<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="text">
+
<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="text">
+
<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 68: Line 73:
 
         V6N-V6HN    124.523      9.430  0.00E+00  0.00E+00 --
 
         V6N-V6HN    124.523      9.430  0.00E+00  0.00E+00 --
 
</source>
 
</source>
 +
 +
== See also ==
 +
[[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 --

See also