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Perl to identify specific runs in input and print only lines identified

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Top Forums Shell Programming and Scripting Perl to identify specific runs in input and print only lines identified
# 8  
Old 12-18-2016
Quote:
Originally Posted by cmccabe
In the instance of:

input
Code:
>hg19_refGene_NM_001918_3 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcttttagGTATGTAAAAGAAGGAGATACAGTGTCTCAGTTTGATAGC
ATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACCATCACTAGTCGTTA
TGATGGAGTCATTAAAAAAACTCTATTATAATCTAGACGATATTGCCTATG
TGGGGAAGCCATTAGTAGACATAGAAACGGAAGCTTTAAAAGgtattgta

there is a run of 7A in bold, so if the if I am looking for 6A, there are 6 in that sequence. However,

Code:
perl -076 -nE 's/(.+)//; $h=$1; s/\s//g; if(/a{6}/i){say qq(>$h); say $1 while /(a{6,})/gi}' input

output
Code:
>hg19_refGene_NM_001918_3 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
AAAAAAA

desired output
Code:
>hg19_refGene_NM_001918_3 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
AAAAAA

Is there a way to print the 6A from this run instead of the entire run of 7A if only 6A is being searched for? Thank you Smilie.
Quote:
Originally Posted by Scrutinizer
Hi Aia, that would also match 6 [Aa]'s or more. But OP in #4 is looking for matches of exactly six [Aa]'s. This approach would also match in the header and not just in the payload unlike the earlier suggestions and it does not find consecutive [Aa]'s that are on either side of a line wrap in the payload, nor would it find mixed case matches..
Hi Scrutinizer,
Post #4 shows that the OP still would like to print matches with more than 6 but only show the match amount, this case 6. Please, see highlighted parts of that post.
Also, in fasta you are not going to find six A or a in the header.
My suggestion does not match mixed cases.

I used the following exaggerated examples to test:

cat fasta02.file
Code:
>hg19_refGene_NM_001918_2 range=chr1:100700982-100701077 5'pad=10 3'pad=10 strand=- repeatMasking=none
gtctttgaagCTCTCCGTGGACAGGTTGTTCAGTTCAAGCTCTCAGACAT
TGGAGAAGGGATTAGAGAAGTAACTGTTAAAGAATGgtaagtgaat
>hg19_refGene_NM_001918_3 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcttttagGTATGTAAAAGAAGGAGATACAGTGTCTCAGTTTGATAGC
ATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACCATCACTAGTCGTTA
TGATGGAGTCATTAAAAAACTCTATTATAATCTAGACGATATTGCCTATG
TGGGGAAGCCATTAGTAGACATAGAAACGGAAGCTTTAAAAGgtattgta
ag
>hg19_refGene_NM_001918_10 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
tttcttttagGTATGTAAAAGAAGGAGATACAGTGTCTCAGTTTGATAGC
ATCTGTGAAGTTCAAAGTGATAAAGCTTCTGTTACCATCACTAGTCGTTA
TGATGGAGTCATTAAAAAACTCTATTATAATCTAGACGATATTGCCTATG
TGGGGAAGCCATTAGTAGACATAGAAAAAAaaaaaaCGGAAGCTTTAAAAGgtattgta
ag
>hg19_refGene_NM_001918_4 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
ttgttaccagATTCAGAAGAAGATGTTGTTGAAACTCCTGCAGTGTCTCA
TGATGAACATACACACCAAGAGATAAAGGGCCGAAAAACACTGGCAACTC
CTGCAGTTCGCCGTCTGGCAATGGAAAACAATgtaagttctc
>hg19_refGene_NM_001918_7 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
ttgttaccagATTCAGAAGAAGATGTTGTTGAAACTCCTGCAGTGTCTCA
TGATGAACATACACACCAAGAGATAAAAAAAGGGCCGAAAAACACTGGCAACTCaaaaaa
CTGCAGTTCGCCGTCTGGCAATGGAAAACAATgtaagttctc
>hg19_refGene_NM_001918_5 range=chr1:100681529-100681765 5'pad=10 3'pad=10 strand=- repeatMasking=none
cattttttagATTAAGCTGAGTGAAGTTGTTGGCTCAGGAAAAGATGGCA
GAATACTTAAAGAAGATATCCTCAACTATTTGGAAAAGCAGACAGGAGCT
ATATTGCCTCCTTCACCCAAAGTTGAAATTATGCCACCTCCACCAAAGCC
AAAAGACATGACTGTTCCTATACTAGTATCAAAACCTCCGGTATTCACAG
GCAAAGACAAAACAGAACCCATAAAAGgtaatgataa
>hg19_refGene_NM_001918_8 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
ttgttaccagATTCAGAAGAAGATGTTGTTGAAACTCCTGCAGTGTCTCA
TGATGAACATACACACCAAGAGATAAaaaAAGGGCCGAAAAACACTGGCAACTC
CTGCAGTTCGCCGTCTGGCAATGGAAAACAATgtaagttctc

Here's the result:
Code:
perl -076 -naF'\n' -e '@c=/(A{6}|a{6})/g and print ">$F[0]\n@c\n"' fasta02.file
>hg19_refGene_NM_001918_3 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
AAAAAA
>hg19_refGene_NM_001918_10 range=chr1:100696279-100696480 5'pad=10 3'pad=10 strand=- repeatMasking=none
AAAAAA AAAAAA aaaaaa
>hg19_refGene_NM_001918_7 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
AAAAAA aaaaaa


Let's fix the problem of missing possible matches if found in multiple lines:

Code:
perl -076 -naF'\n' -e 's/\n+//g; @c=/(A{6}|a{6})/g and print ">$F[0]\n@c\n"'

Last edited by Aia; 12-18-2016 at 10:57 PM.. Reason: Adds fix for multiple lines.
This User Gave Thanks to Aia For This Post:
cmccabe
# 9  
Old 12-18-2016
Hi Aia, OK I think you may be right about your interpretation of only printing 6 A's when there would be 7 consecutive A's. That would leave an interesting question of what to do when there are a mutiple of 6 [Aa]'s or more. Should that then also only be printed once?

I am not sure about multiple [Aa]'s under no circumstances present in the FASTA header. Unlikely sure, but impossible? The OP's original approach excludes that from matching..

The mixed case I think could be mitigated by using:
Code:
@c=/a{6}/ig

But this also leaves the line wrap case; this approach does not find consecutive [Aa]'s that are on either side of a line wrap in the payload. So the newlines would need to be removed in the payload before the matching.

Code:
>hg19_refGene_NM_001918_9 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
ttgttaccagATTCAGAAGAAGATGTTGTTGAAACTCCTGCAGTGTCTCA
ATGATGAACATACACACCAAGAGATAAAGGGCCGAAAAACACTGGCAACTCAAAA
AACTGCAGTTCGCCGTCTGGCAATGGAAAACAATgtaagttctc

This User Gave Thanks to Scrutinizer For This Post:
cmccabe
# 10  
Old 12-18-2016
Quote:
Originally Posted by Aia
Hi Scrutinizer,
Post #4 shows that the OP still would like to print matches with more than 6 but only show the match amount, this case 6. Please, see highlighted parts of that post.
Also, in fasta you are not going to find six A or a in the header.
My suggestion does not match mixed cases.

[...]

Let's fix the problem of missing possible matches if found in multiple lines:

Code:
perl -076 -naF'\n' -e 's/\n+//g; @c=/(A{6}|a{6})/g and print ">$F[0]\n@c\n"'

Quote:
Originally Posted by Scrutinizer
Hi Aia, OK I think you may be right about your interpretation of only printing 6 A's when there would be 7 consecutive A's. That would leave an interesting question of what to do when there are a mutiple of 6 [Aa]'s or more. Should that then also only be printed once?

I am not sure about multiple [Aa]'s under no circumstances present in the FASTA header. Unlikely sure, but impossible? The OP's original approach excludes that from matching..

The mixed case I think could be mitigated by using:
Code:
@c=/a{6}/ig

But this also leaves the line wrap case; this approach does not find consecutive [Aa]'s that are on either side of a line wrap in the payload. So the newlines would need to be removed in the payload before the matching.

Code:
>hg19_refGene_NM_001918_9 range=chr1:100684172-100684313 5'pad=10 3'pad=10 strand=- repeatMasking=none
ttgttaccagATTCAGAAGAAGATGTTGTTGAAACTCCTGCAGTGTCTCA
ATGATGAACATACACACCAAGAGATAAAGGGCCGAAAAACACTGGCAACTCAAAA
AACTGCAGTTCGCCGTCTGGCAATGGAAAACAATgtaagttctc

Hi, Scrutinizer,
I did post a fix for the case of multiple lines, previously. Please, see post #8.

On purpose, I did want not this to be that case, by design. If I error in this case, that adaptation might suffices.
Quote:
The mixed case I think could be mitigated by using:
Code:
@c=/a{6}/ig

Last edited by Aia; 12-18-2016 at 11:52 PM..
This User Gave Thanks to Aia For This Post:
cmccabe
# 11  
Old 12-19-2016
Thank you all for your help and explanations, I really appreciate it Smilie.
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