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

 
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# 8  
Old 09-15-2013
Try:
Code:
perl -nle 'print $& while /.{20}GG/g' file

# 9  
Old 09-17-2013
@wisecracker - thanks. The code works great, but doesn't get desiredthe results because there are line breaks.
# 10  
Old 09-17-2013
Hi Twinklefingers...

Can you copy and paste what you are getting...

Thanks...
# 11  
Old 09-17-2013
@wisecracker

Input:

Code:
TCAAATTTTATGGCATAGTAAAGATAACAAAAGAAGTGATCGAATTTATTCTTTAGATAT
TCAACCATATCCAAATTATTATAGTGTTAAAAAATTAAATAGGAAATATGAATTGTTTAT
CAAATATTTAAAAGAAAAAGGAAAAATAGAATGTAATAAATTCGACACTTTAGAAGAAAA
ACAAAAAATTATAAATGATTCAACATTGCCCTCAAATAATAATTATAATAATAGTAGTAA
TAATAATAATAATAATAATAAATATGAAACATTAAAATTAGATAAAGAACTGAATCAAGG
AAATGAGGATAACATTATAAAGACGGTAATTGGGAATAACACGGAAGTTAGTAATAATAA
CTTATTAGATGATACAAACAATAAATTAAACGAAATAAAAACAAATACATCTACGGAAGA
TCACCAAGAACACAATTTAGTAAATAAAAAAAACGAAACGAATAGTTCATCTAATGACAA
TATTTCACATAATAAAACACCAATGCAATCAAATAAATTACTTACATCATTACAAGATGA
TAAAACAAAAAAAAAACCTATCAAATTTAATATAGCTACATGTGGTGCTGACGAATTCGT
ACATTTGTGGAGAATATTTATAAAAGATGATATTTCAATTAAATGCTTAGGTAGATTTAT
AGGTCATAGTGGTGAAATAAATTGTGTTCGTTTTAACAAAAATGGTAGATATATAGCAAG
TGGGGGAGAAGATAAATTTTTATATATATGGGAAAAAAGTAAAAAACCAAAAAATATACC
ATTAGGTTATGATATAAGCTTTTTAGATTATAAAGAATGGTGGAATGTCGTAGGGTCTTT
CAGATGTAGTGGTGTAATAAATAGTATTATTTGGTCAAACAATGATACCTTATATGTAGC

Output:

Code:
L01883730:dir$ sh 22mers_17Sept13.sh 

TCAAATTTTATGGCATAGTAAAGATAACAAAAGAAGTGATCGAATTTATTCTTTAGATAT

TTTAGATAT

Thank you!
# 12  
Old 09-17-2013
Try GNU awk:
Code:
awk 'NR>1{print p} {gsub(/\n/,x); p=substr($0,length-19,20) RS}' RS=GG file

Or can there also be strings that also have GG among the 20 characters?
# 13  
Old 09-17-2013
@Scrutinizer

Thank you very much. I think this is getting into the right ballpark. However,

for the input:
Code:
TCAAATTTTATGGCATAGTAAAGATAACAAAAGAAGTGATCGAATTTATTCTTTAGATAT
TCAACCATATCCAAATTATTATAGTGTTAAAAAATTAAATAGGAAATATGAATTGTTTAT
CAAATATTTAAAAGAAAAAGGAAAAATAGAATGTAATAAATTCGACACTTTAGAAGAAAA
ACAAAAAATTATAAATGATTCAACATTGCCCTCAAATAATAATTATAATAATAGTAGTAA

the desired output is:
Code:
TAGTGTTAAAAAATTAAATAGG
TCAAATATTTAAAAGAAAAAGG

the script returns:
Code:
TCAAATTTTATGG
GG
CATAGG
TAAAGG
ATAACAAAAGG
AAGG
TGG
ATCGG
AATTTATTCTTTAGG
ACCATATCCAAATTATTATAGG
TGG
TTAAAAAATTAAATAGG
GG
AAATATGG
AATTGG
TTTATCAAATATTTAAAAGG
AAAAAGG
GG
AAAAATAGG
AATGG
TAATAAATTCGG
ACACTTTAGG
AAGG
AAAAACAAAAAATTATAAATGG
ATTCAACATTGG
AAATAATAATTATAATAATAGG
TAGG

# 14  
Old 09-17-2013
Would something like this work then (GNU awk or mawk):
Code:
awk 'length(p)==22{print p} {$0=p $0; gsub(/\n/,x); p=substr($0,length-19,20) RS}' RS=GG file

Is should also find strings that have been part of a previous match, except the first GG in the previous example on line 1 because it does not have 20 chars before.

--
edit, this should also find the first short one:
Code:
awk 'NR>1{print p; $0=p $0} {gsub(/\n/,x); p=substr($0,length-19,20) RS}' RS=GG file

Code:
GGTCAAATTTTATGG
TAGTGTTAAAAAATTAAATAGG
TCAAATATTTAAAAGAAAAAGG
TAGATAAAGAACTGAATCAAGG
ACTGAATCAAGGGGAAATGAGG
GGGGATAACATTATAAAGACGG
ATTATAAAGACGGGGTAATTGG
GGTAATTGGGGGAATAACACGG
ATAAAAACAAATACATCTACGG
AATTTAATATAGCTACATGTGG
TGACGAATTCGTACATTTGTGG
ATATTTCAATTAAATGCTTAGG
TGCTTAGGGGTAGATTTATAGG
AGATTTATAGGGGTCATAGTGG
GTGTTCGTTTTAACAAAAATGG
GGGGTAGATATATAGCAAGTGG
TAGATATATAGCAAGTGGGGGG
AGATAAATTTTTATATATATGG
AACCAAAAAATATACCATTAGG
CTTTTTAGATTATAAAGAATGG
TAGATTATAAAGAATGGGGTGG
ATGGGGTGGGGAATGTCGTAGG
GGGGGTCTTTCAGATGTAGTGG
TGTAATAAATAGTATTATTTGG

Last edited by Scrutinizer; 09-17-2013 at 05:57 PM.. Reason: change > 19 to ==22
 
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