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Top Forums Shell Programming and Scripting Perl to identify specific runs in input and print only lines identified Post 302987921 by cmccabe on Sunday 18th of December 2016 08:38:23 AM
Old 12-18-2016
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.
 

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PERLCC(1)						 Perl Programmers Reference Guide						 PERLCC(1)

NAME
perlcc - generate executables from Perl programs SYNOPSIS
$ perlcc hello # Compiles into executable 'a.out' $ perlcc -o hello hello.pl # Compiles into executable 'hello' $ perlcc -O file # Compiles using the optimised C backend $ perlcc -B file # Compiles using the bytecode backend $ perlcc -c file # Creates a C file, 'file.c' $ perlcc -S -o hello file # Creates a C file, 'file.c', # then compiles it to executable 'hello' $ perlcc -c out.c file # Creates a C file, 'out.c' from 'file' $ perlcc -e 'print q//' # Compiles a one-liner into 'a.out' $ perlcc -c -e 'print q//' # Creates a C file 'a.out.c' $ perlcc -I /foo hello # extra headers (notice the space after -I) $ perlcc -L /foo hello # extra libraries (notice the space after -L) $ perlcc -r hello # compiles 'hello' into 'a.out', runs 'a.out'. $ perlcc -r hello a b c # compiles 'hello' into 'a.out', runs 'a.out'. # with arguments 'a b c' $ perlcc hello -log c # compiles 'hello' into 'a.out' logs compile # log into 'c'. DESCRIPTION
perlcc creates standalone executables from Perl programs, using the code generators provided by the B module. At present, you may either create executable Perl bytecode, using the "-B" option, or generate and compile C files using the standard and 'optimised' C backends. The code generated in this way is not guaranteed to work. The whole codegen suite ("perlcc" included) should be considered very experimen- tal. Use for production purposes is strongly discouraged. OPTIONS
-Llibrary directories Adds the given directories to the library search path when C code is passed to your C compiler. -Iinclude directories Adds the given directories to the include file search path when C code is passed to your C compiler; when using the Perl bytecode option, adds the given directories to Perl's include path. -o output file name Specifies the file name for the final compiled executable. -c C file name Create C code only; do not compile to a standalone binary. -e perl code Compile a one-liner, much the same as "perl -e '...'" -S Do not delete generated C code after compilation. -B Use the Perl bytecode code generator. -O Use the 'optimised' C code generator. This is more experimental than everything else put together, and the code created is not guaran- teed to compile in finite time and memory, or indeed, at all. -v Increase verbosity of output; can be repeated for more verbose output. -r Run the resulting compiled script after compiling it. -log Log the output of compiling to a file rather than to stdout. perl v5.8.9 2009-06-25 PERLCC(1)
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