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Full Discussion: Matching string and assembling
Top Forums UNIX for Dummies Questions & Answers Matching string and assembling Post 302969911 by RudiC on Wednesday 30th of March 2016 01:57:44 AM
Old 03-30-2016
T'was too late last night - sorry. Try
Code:
awk '
BEGIN           {for (i = split ("A C G T", Y); i>0; i--) R[Y[i]] = Y[5-i]
                }

function MM(CR) {for (i=0; i<length (CR); i++)  {X = substr (CR, 1, i) "." substr (CR, i+2)
                                                 for (j=i; j<length (CR); j++)  {T = substr (X,  1, j) "." substr (X,  j+2)
                                                                                 if (match (REF, T))  return 1
                                                                                }
                                                }
                 return 0
                }
/^>/            {SN = $0
                 next
                }
                {RV = ""
                 for (i = split ($0, A, ""); i>0; i--) RV = RV R[A[i]]
                 }
match (REF, $0) ||
MM($0)          {print SN ORS $0
                }
match (REF, RV) ||
MM(RV)          {print SN ORS RV
                }
' REF="AGAGAGACCTGGAGAGAGAGTGACGATGAGCAGTGACGATGACGTACGATAGCAGTAGACGCA" file
>read1 ori 498
AGAGAGACCTGGAGAGAGAGT
>read2 ori-rep 500
AGAGAGACCTGGAGAGAGAGT
>read3 1-misma 456
GGAGAGACCTGGAGAGAGAGT
>read4 2-misma 456
TGAGAGACCTGGAGAGAGAGA
>read5 ori-rev 532
AGAGAGACCTGGAGAGAGAGT
>read6 ori-rev-1-misma 499
GGAGAGACCTGGAGAGAGAGT
>read7 medium 512
AGAGAGAGTGACGATGAGCAG
>read8 last 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read9 last rep 488
AGTGACGATGACGTACGATAGCAGTAGACGCA
>read10 last gap 488
AGTGACGATGACGTACGATAGCAGTAGACGA

This User Gave Thanks to RudiC For This Post:
Xterra
 

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LEARN ABOUT DEBIAN

replaygain

REPLAYGAIN(1)							       rgain							     REPLAYGAIN(1)

NAME

       replaygain - single file Replay Gain editor

SYNOPSIS

       replaygain [options] AUDIO_FILE [AUDIO_FILE ...]
       replaygain --help
       replaygain --version

DESCRIPTION

       replaygain applies or displays Replay Gain information for audio files.

OPTIONS

       --version
	      Display the version of the software.

       -h, --help
	      Display a short documentation.

       -f, --force
	      Recalculate Replay Gain even if the file already contains gain information.

       -d, --dry-run
	      Don't actually modify any files.

       -r REF, --reference-loudness=REF
	      Set the reference loudness to REF dB (default: 89 dB)

       --mp3-format=MP3_FORMAT
		 Choose the Replay Gain data format for MP3 files.  Since there is no commonly accepted standard for Replay Gain in MP3 files, you
		 need to choose.  Possible formats are :

	      o ql (used by Quod Libet). This is the default value.

	      o fb2k (read and written by foobar2000, also understood by Quod Libet)

	      o mp3gain (tags as written by the mp3gain program; this doesn't modify the MP3 audio data as said program does).

       --no-album
	      Don't write any album gain information.

       --show Don't calculate anything, simply show Replay Gain information for the  specified	files.	In  this  mode,  all  options  other  than
	      --mp3-format are ignored.

SEE ALSO

       collectiongain(1)

1.0								    2011-11-26							     REPLAYGAIN(1)
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