Question

I do have text manipulation problem that I need to solve in awk, sed & shell.
My text looks like this:

>Sample_1
    100                                                            101
    aaattattacaaaaataattacaaattattacaaaaagaattattacaaaaagaattacaaaa
-1.60   .(((((((.....)))))))...........................................  []
>Sample_2
    1                                35
    aattattacaaaaagaattattacaaaaagaatta
0.00    ...................................  _
>Sample_3
    1                                     123
    gctcacacctgtaatcccagcactttgggaggctgagg
-27.80  ((((.....))))......((((((.(((...))))))).)[][][[][]]
-26.40  (((((.((...(((((..((((((....)).........  [[][]][]
-25.80  ((((.....)))).....((((((...............  [][][][[][]]
    123                                  145
    ctgaggcaggcagatcacgaggtcacgagatcaa
-26.20  (((.....))))))  [][][[][]]
-25.90  ....((((..((....))  [][[][]]
-25.70  ..(((..((....))..(())  [[][]][[][]]
    145                                 256
    gtaatcccagcactttgggaggctgaggcaggcaga
0.00    ...........................................  _
    256                                 342
-25.00  ..((....((((.....((((((...)))....))...  [[][]]
-24.00  ..((.((((.((((())...  [[][][]]
-23.70  .((((((...(((((..((..  [[][]][]

I want to:

1. Extract Sample name (>Sample_1);
2. Extract numeric value that goes after the sample name (it’s either 0 or negative value);
3. From the negative value group (e.g. -27.80;-26.40;-25.80) extract number that goes first (it’s the most negative value).

Perfect output would look like this:

>Sample_1  
-1.60  
>Sample_2  
0.00  
>Sample_3  
-27.80  
-26.20  
0.00  
-25.00

I tried to do this in awk printing $1, grepping ‘>’, 0 & negative values, but wasn’t able to diverge column into groups & and to extract the most negative value.

awk '{print $1}' file | egrep -i '>|0.00|-'

Answer 1

You tagged your question with sed and awk, but if you’re O.K. with Perl instead, you could write:

#!/usr/bin/perl -w

use warnings;
use strict;

my $min = undef;

while(<>)
{
  if(m/^(-?\d+\.\d+)/)
  {
    if(! defined($min) || $1 < $min)
      { $min = $1; }
  }
  else
  {
    if(defined $min)
    {
      print "$min\n";
      $min = undef;
    }
    if(m/^>/)
      { print; }
  }
}

if(defined $min)
  { print "$min\n"; }