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Extracting 22-character strings from text using sed/awk?

 
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# 15  
Old 09-17-2013
But this was not your original post...

You said it was a flat file of aplha(-numeric) characters only "without line breaks".

Also the first pair of "GG"s does not have 20 characters before it...
Is this also required?
# 16  
Old 09-17-2013
Quote:
Originally Posted by wisecracker
But this was not your original post...

You said it was a flat file of aplha(-numeric) characters only "without line breaks".
You're 100% right. The long reason is that, just in the two days from when I posted and when I grabbed your code to use it, this aspect of the project changed and I was negligent in remembering the details of the original post. The short answer is that I am an idiot, apologies

Quote:
Also the first pair of "GG"s does not have 20 characters before it...
Is this also required?
Yes, but I can remedy this on my own if need be.

Thanks again.
# 17  
Old 09-17-2013
This has its flaws as you will see but it is a starter...

Code:
#!/bin/bash --posix
textfile=$(tr -d '\n' < ~/flatfile.dat)
echo ""
echo "$textfile"
echo ""
for n in $( seq 19 1 ${#textfile} )
do
	if [ "${textfile:$n:2}" == "GG" ]
	then
		echo "${textfile:$[ ( $n - 20 ) ]:22}"
	fi
done
echo ""

Results. NOTE, that there are "GGG"s at least once in the file...
Code:
Last login: Tue Sep 17 21:28:08 on ttys000
AMIGA:barrywalker~> ./flatfile.sh

TCAAATTTTATGGCATAGTAAAGATAACAAAAGAAGTGATCGAATTTATTCTTTAGATATTCAACCATATCCAAATTATTATAGTGTTAAAAAATTAAATAGGAAATATGAATTGTTTATCAAATATTTAAAAGAAAAAGGAAAAATAGAATGTAATAAATTCGACACTTTAGAAGAAAAACAAAAAATTATAAATGATTCAACATTGCCCTCAAATAATAATTATAATAATAGTAGTAATAATAATAATAATAATAATAAATATGAAACATTAAAATTAGATAAAGAACTGAATCAAGGAAATGAGGATAACATTATAAAGACGGTAATTGGGAATAACACGGAAGTTAGTAATAATAACTTATTAGATGATACAAACAATAAATTAAACGAAATAAAAACAAATACATCTACGGAAGATCACCAAGAACACAATTTAGTAAATAAAAAAAACGAAACGAATAGTTCATCTAATGACAATATTTCACATAATAAAACACCAATGCAATCAAATAAATTACTTACATCATTACAAGATGATAAAACAAAAAAAAAACCTATCAAATTTAATATAGCTACATGTGGTGCTGACGAATTCGTACATTTGTGGAGAATATTTATAAAAGATGATATTTCAATTAAATGCTTAGGTAGATTTATAGGTCATAGTGGTGAAATAAATTGTGTTCGTTTTAACAAAAATGGTAGATATATAGCAAGTGGGGGAGAAGATAAATTTTTATATATATGGGAAAAAAGTAAAAAACCAAAAAATATACCATTAGGTTATGATATAAGCTTTTTAGATTATAAAGAATGGTGGAATGTCGTAGGGTCTTTCAGATGTAGTGGTGTAATAAATAGTATTATTTGGTCAAACAATGATACCTTATATGTAGC

TAGTGTTAAAAAATTAAATAGG
TCAAATATTTAAAAGAAAAAGG
TAGATAAAGAACTGAATCAAGG
GAACTGAATCAAGGAAATGAGG
GAGGATAACATTATAAAGACGG
ACATTATAAAGACGGTAATTGG
CATTATAAAGACGGTAATTGGG
ACGGTAATTGGGAATAACACGG
ATAAAAACAAATACATCTACGG
AATTTAATATAGCTACATGTGG
TGACGAATTCGTACATTTGTGG
ATATTTCAATTAAATGCTTAGG
AATGCTTAGGTAGATTTATAGG
GTAGATTTATAGGTCATAGTGG
GTGTTCGTTTTAACAAAAATGG
ATGGTAGATATATAGCAAGTGG
TGGTAGATATATAGCAAGTGGG
GGTAGATATATAGCAAGTGGGG
GTAGATATATAGCAAGTGGGGG
AGATAAATTTTTATATATATGG
GATAAATTTTTATATATATGGG
AACCAAAAAATATACCATTAGG
CTTTTTAGATTATAAAGAATGG
TTTAGATTATAAAGAATGGTGG
AAGAATGGTGGAATGTCGTAGG
AGAATGGTGGAATGTCGTAGGG
TAGGGTCTTTCAGATGTAGTGG
TGTAATAAATAGTATTATTTGG

AMIGA:barrywalker~>

This User Gave Thanks to wisecracker For This Post:
Twinklefingers
# 18  
Old 09-17-2013
Indeed there are GGG's, so the G's should shift per 1 therefore GG kan not be used a record separator. So then this should do, which should work with any awk:

Code:
awk 'p~/GG$/{print p} {$0=p $0; gsub(/\n/,x); p=substr($0,length-20,21) RS}' RS=G file

This User Gave Thanks to Scrutinizer For This Post:
Twinklefingers
 
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