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Full Discussion: Extract lines from text files
Top Forums Shell Programming and Scripting Extract lines from text files Post 302885386 by Don Cragun on Saturday 25th of January 2014 03:37:21 PM
Old 01-25-2014
Quote:
Originally Posted by edweena
I have some files containing the following data

Code:
 #  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA 
    1  196 A M              0   0  230      0, 0.0     2,-0.2     0, 0.0     0, 0.0   0.000 360.0 360.0 360.0  76.4   21.7   -6.8   11.3
    2  197 A D        +     0   0  175      1,-0.1     2,-0.1     0, 0.0     0, 0.0  -0.193 360.0 151.5 -46.2  99.1   23.2   -9.3   13.8
    3  198 A E        -     0   0  170     -2,-0.2    -1,-0.1     0, 0.0     0, 0.0  -0.622  29.3-158.9-134.6  66.9   26.9   -9.0   13.0
    4  199 A K        -     0   0  161      1,-0.1     0, 0.0    -2,-0.1     0, 0.0   0.037  18.7-134.6 -43.9 157.1   28.8   -9.8   16.3
    5  200 A R        +     0   0  174      3,-0.0     2,-1.6     2,-0.0    -1,-0.1   0.294  60.4 134.1 -97.8   0.9   32.4   -8.5   16.6
    6  201 A R        +     0   0  178      1,-0.1    -2,-0.1     2,-0.1     0, 0.0  -0.429  24.5 143.8 -54.0  86.9   33.5  -11.9   17.9
    7  202 A A        +     0   0   76     -2,-1.6    -1,-0.1     2,-0.1    -2,-0.0  -0.471  24.7 108.8-134.5  48.7   36.5  -11.8   15.5
    8  203 A Q  S    S+     0   0  149      3,-0.0     2,-0.1     4,-0.0    -2,-0.1  -0.694  77.8  88.8-115.4  54.1   39.3  -13.4   17.4
    9  204 A H  S >> S-     0   0  121      4,-0.0     3,-2.1     0, 0.0     4,-0.7  -0.341  88.3  -9.7-128.0-146.1   38.5  -16.0   14.8
   10  205 A N  H 3> S+     0   0  145      1,-0.3     4,-0.8     2,-0.2     5,-0.2   0.673 125.2  50.8 -27.9 -50.8   39.4  -17.0   11.2
   11  206 A E  H 34 S+     0   0  159      1,-0.2     4,-0.3     2,-0.1    -1,-0.3   0.843 106.1  59.4 -64.2 -34.5   41.5  -13.9   10.2
   12  207 A V  H X4 S+     0   0   60     -3,-2.1     3,-0.5     2,-0.1     4,-0.4   0.982 107.8  32.9 -62.8 -61.2   43.7  -14.0   13.3
   13  208 A E  H >X S+     0   0   78     -4,-0.7     3,-4.0     1,-0.2     4,-0.9   0.950 109.6  53.5 -70.0 -62.3   45.4  -17.4   13.2

I want to extract the lines only if the values in the phi and psi column must between -67<=phi<=-99 and 100<=psi<=165
I would like to save the outputs in to another folder having the input file names. I highly appreciate your valuable suggestions.

Thanks a lot.
There are several problems here. First, and most importantly, your specification requiring a value for PHI that is greater than -67 and simultaneously less than -99 (-67<=phi<= -99) always yields the empty set.

If we assume that you meant -99 <= PHI <= -67, your sample data still produces no output (except for the heading) because only the fifth line of your input file has a PSI value between 100 and 165, and the PHI value on that line is -43.9 (which is out of range). These values are marked in red above.

When Akshay provided his suggested code, he apparently didn't notice that the data under the heading "STRUCTURE" looks like 0, 1, 2, or 3 fields to awk (when using the default field delimiter). Yoda compensated for that problem, but apparently didn't notice that sometimes there are no field delimiters between values under the headings KAPPA, ALPHA, PHI, and PSI. Some samples of this problem are marked in green above. So, rather than using field delimiters, any code processing these lines will have to be based on column positions in the input file; not field counts.

Are there ever any <tab> characters in your input files? Or, are all of the spaces between fields just sequences of <space> characters?

Please provide us with a specification that doesn't always produce an empty set, and provide us some sample input that includes some lines that will be selected as well as some lines that will be rejected. And, show us the sample output you expect to be produced for that sample input.

And, please tell us how the name of the directory to contain the new files will be passed to your script.
Last edited by Don Cragun; 01-25-2014 at 04:39 PM.. Reason: fix typo
These 2 Users Gave Thanks to Don Cragun For This Post:
Akshay Hegde Yoda
 

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