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Top Forums UNIX for Dummies Questions & Answers awk code to reconstruct sequence from alignment Post 302835591 by Scrutinizer on Monday 22nd of July 2013 05:02:21 PM
Old 07-22-2013
With regular awk, try:
Code:
awk '
  NR==FNR{
    if(/Sbjct/)A[$2 "-" $4]=$3
    next
  }
  { 
    for(i=2; i<=NF; i+=2) $i=A[$i]
  }
  1
' file2 FS='\\(Sbjct:|\\)' OFS= file1

Code:
$ cat file1
(Sbjct:26325115-26325094)NNNN(Sbjct:33716368-33716347)NNNN(Sbjct:33769033-33769073)NNNN(Sbjct:34869860-34869889)

Output:
Code:
ttagggtttagagttaaggggtNNNNaaaatgaccaaaatatttcattNNNNccctaggattaactaatctaaac-ttagggtttagagttaagNNNNatcaaaatgaacaaaatgtttcattaaaaa

 

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NEATEN(1)						      General Commands Manual							 NEATEN(1)

NAME
neaten - neaten up output columns SYNOPSIS
neaten [ format ] DESCRIPTION
Neaten reads from its standard input and neatens up columns separated by white space using the specified format. The format is a string consisting of a positive integer followed by an alignment character and another integer. The alignment character is usually a decimal point ('.'), but it can be any non-digit. The alignment character is used as the central point of each column. The total column field width will be the number to the left of the alignment character plus one for the alignment character itself plus the number to the right of the alignment character. If a field does not contain the alignment character, it will be printed to the left of where the alignment character would have appeared. If a field is too long to print within the specified format, the entire field will be printed and that row will not be aligned with the rest. The default format is "8.8". EXAMPLE
To examine a file with columns of numbers: neaten 10.8 < input | more BUGS
Columns wider than the total width of the format specification will be printed without any separating white space. The program does not do anything special with tabs on the input. AUTHOR
Greg Ward SEE ALSO
cnt(1), rcalc(1), rlam(1), total(1) RADIANCE
11/15/93 NEATEN(1)
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