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08-13-2015

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Text replacement with awk or sed?

Hi guys,

I worked for almost a half-day for the replacement of some text automatically with script. But no success.
The problem is I have hundred of files, which need to be replaced with some new text. It's a painful work to work manually and it's so easy to do it wrong.

For example,

I have a main text as follows,

Code:

 <molecule id="a_feco4_s">
...many lines...
   <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">37.95 67.28 74.69 90.71 91.25 345.01 355.62 366.66 422.13 439.40 451.58 467.53 486.57 533.13 584.49 637.10 642.25 2009.41 2032.85 2036.21 2122.57 </array>
   </property>
...many lines...
 </molecule>
 <molecule id="c_feco4_t">
...many lines...
   <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">58.43 72.58 75.35 80.62 87.16 318.76 324.15 324.42 375.24 419.54 444.45 447.44 488.53 505.86 517.68 538.85 543.24 2029.98 2035.26 2040.33 2111.69 </array>
   </property>
...many lines...
 </molecule>
 <molecule id="b_feco4_t-3">
...many lines...
  <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">49.30 75.79 77.16 79.22 84.50 310.74 316.63 342.47 399.25 453.74 464.46 465.14 508.24 521.78 550.22 569.23 572.50 2010.41 2033.03 2034.16 2103.89 </array>
   </property>
...many lines...
 </molecule>

The text need to be replaced is 'all the numbers' inside (<array units="cm-1"> </array>). These new numbers are stored in the three separate files named 'a_feco4_s', 'c_feco4_t', and 'b_feco4_t-3' as shown below,
a_feco4_s

Code:

c_feco4_t

Code:

b_feco4_t-3

Code:

After the replacement, we will get

Code:

 <molecule id="a_feco4_s">
...many lines...
   <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">
37.9521
90.7132
355.6175
439.3995
486.5668
637.1002
2032.8518
67.2767
91.2457
366.6612
451.5826
533.1265
642.2546
2036.2149
74.6883
345.0079
422.1317
467.5309
584.4914
2009.4132
2122.5729
 </array>
   </property>
...many lines...
 </molecule>
 <molecule id="c_feco4_t">
...many lines...
   <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">
58.4306
80.6210
324.1468
419.5376
488.5270
538.8506
2035.2576
72.5771
87.1616
324.4229
444.4529
505.8570
543.2370
2040.3282
75.3460
318.7635
375.2418
447.4447
517.6800
2029.9848
2111.6905
 </array>
   </property>
...many lines...
 </molecule>
 <molecule id="b_feco4_t-3">
...many lines...
  <property title="Vibrational Frequencies" dictRef="me:vibFreqs">
    <array units="cm-1">
61.14
62.67
83.25
85.59
87.24
341.07
342.04
348.23
409.08
416.25
427.89
470.65
550.47
550.78
564.48
590.82
1893.71
2015.17
2032.38
2061.02
 </array>
   </property>
...many lines...
 </molecule>

I thank you very much for your kind help!

Zhen

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08-13-2015

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What operating system and shell are you using?

What have you tried to solve this problem?

Don Cragun

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08-13-2015

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Code:

#! /usr/bin/perl

$/ = undef;
$_ = <>;

sub slurp { open FH, '<', @_ or die @_; return <FH>; }

s{(<molecule\s+id="([^"]*)".*?<array[^>]*>)(.*?)(</array.*?</molecule>)}
 {join $,, $1, slurp($2), $4}gemsx;

print;

This will replace the values in <array>...</array> with the contents of the file specified by the id attribute of <molecule id="name">.

Last edited by derekludwig; 08-15-2015 at 08:25 AM.. Reason: grammar

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