NMRPipe seriesTab - Revision history

Bugman: removed Category:Software using HotCat

2020-10-21T16:08:19Z

removed Category:Software using HotCat

Bugman: Formatting improvements.

2015-11-06T15:47:18Z

Formatting improvements.

Tlinnet at 13:16, 27 August 2013

2013-08-27T13:16:49Z

Bugman admin: /* See also */

2013-08-13T09:20:09Z

Troels Emtekær Linnet: /* seriesTab */

2013-06-21T13:38:47Z

seriesTab

Troels Emtekær Linnet: /* See also */

2013-06-21T12:20:43Z

Troels Emtekær Linnet: /* seriesTab */

2013-06-21T12:20:32Z

seriesTab

Troels Emtekær Linnet at 11:51, 20 June 2013

2013-06-20T11:51:54Z

Troels Emtekær Linnet: /* seriesTab */

2013-06-20T11:51:34Z

seriesTab

Troels Emtekær Linnet: Created page with "== seriesTab == [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 N..."

2013-06-20T11:51:02Z

Created page with "== seriesTab == [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 N..."

New page

== seriesTab ==
[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>
http://spin.niddk.nih.gov/NMRPipe/ref/prog/seriestab.html

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
<source lang="text">
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
...
</source>

'''files.list''' contains
<source lang="text">
test.ft2
</source>

For folders [0,1,2..,22] with extracted CPMG interleaved spectra, containing '''test.ft2'''

A call to function could be:
<source lang="bash">
#! /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
</source>

The output is:
<source lang="text">
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
</source>

An input reader is wished, which is auto detected like a SPARKY list. The
format is quite similar to this. <br>
This is an export from CcpNmr Analysis
<source lang="text">
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 --
</source>

@@ Line 76: / Line 76: @@
 == See also ==
 [[Category:NMRPipe]]
 [[Category:Peak_lists]]

← Older revision		Revision as of 13:16, 27 August 2013
Line 77:		Line 77:
	[[Category:NMRPipe]]		[[Category:NMRPipe]]
	[[Category:Software]]		[[Category:Software]]
		+	[[Category:Peak_lists]]

← Older revision		Revision as of 09:20, 13 August 2013
Line 76:		Line 76:
	== See also ==		== See also ==
	[[Category:NMRPipe]]		[[Category:NMRPipe]]
		+	[[Category:Software]]

← Older revision		Revision as of 12:20, 21 June 2013
Line 70:		Line 70:

	== See also ==		== See also ==
−	[Category:NMRPipe]	+	[[Category:NMRPipe]]

← Older revision		Revision as of 12:20, 21 June 2013
Line 68:		Line 68:
	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]

@@ 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.
-See homepage<br>
+== Usage ==
-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
 '''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
 FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s
@@ Line 26: / Line 26: @@
 Or create the files list by:
-<source lang="text">
+<source lang=bash>
 ls -v -d -1 */*.ft2 > files.list
 </source>
@@ Line 33: / Line 33: @@
 A call to function could be:
-<source lang="bash">
+<source lang=bash>
 #! /bin/csh -f
 set x = 0;
@@ Line 45: / Line 45: @@
 The output is:
-<source lang="text">
+<source lang=text>
 REMARK SeriesTab Input: ../peaks.dat Output: ../peaks_0.ser
 REMARK Mode: Summation Dimensions: 2
@@ Line 67: / Line 67: @@
 format is quite similar to this. <br>
 This is an export from CcpNmr Analysis
-<source lang="text">
+<source lang=text>
        Assignment         w1         w2       Height       Volume
      W62NE1-W62HE1    128.374      9.932   0.00E+00   0.00E+00 --

@@ Line 54: / Line 54: @@
 NULLSTRING *
-   246.658    18.268    9.932  128.374 +1.851056e+06 W62NE1-W62HE1
+   246.658    18.268    9.932  128.374 +1.851056e+06 W62NE1-W62HE1 1.0000
    321.698    30.994    9.419  127.066 +3.224387e+05 L10N-L10HN  1.0000
    320.089    55.737    9.430  124.523 +1.479366e+06 V6N-V6HN  1.0000

@@ Line 33: / Line 33: @@
 while ( $x <= 22 )
          cd $x
-         seriesTab -in ../peaks.dat -out ../peaks_${x}.ser -list ../files.list
+         seriesTab -in ../peaks.dat -out ../peaks_${x}.ser -list ../files.list -sum -dx 1 -dy 1
          cd ..
          @ x = $x + 1