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POregexp find and replace: bash variables inside sed
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2013-10-16T19:32:11.280
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2013-10-17T03:37:53.910
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I would like to remove this sequence when present at the beginning of the line: ATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG followed by at least 3 A characters. Both, sequence and multiple A should be removed and the rest of the file should be preserved. My input files look like this: <pre><code>@M00946:3:000000000-A2WF2:1:1101:18115:1962 1:N:0:2 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACATTTTCTTTCTTACTTCGTTCACTTTCCACTTCTTTCTCCCTATCTTCCCCCTTCTGTCTGCCCCAGCTGTCTATCCCACTTATTGTCTCCCCCCACTGCCCCACACTCCTACCTTCTTCATCTTCACCTAACACCTCCCGCTCCCTCCTTATCGTCTCTTATCCTTTCCTTGTTCC + ????????DDDDDDDDGGGGGGHHIIIIHHHIIIIFHIIIH/CGFHHIIIIHEDHHIIIIHI=5EEGFEHHEC+5,,4@,@,,....--..+77,,.6..6.....7.4..7.76=..-5.>.4-)134-.5....-3*))0***1*********10*0**01*1*)''..0***.)0'))*****00*11******01***0****0*)**0)'''...*0)0*11********1****1*0******** @M00946:3:000000000-A2WF2:1:1101:19888:2900 1:N:0:2 GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAACACAAATACCGTTCCAATATCTTTTTGTTTCATGTCTAATAAC + <<??????BB?BBBBBCAFFFCFHF;>EFCDFGFFHFBGHCA=FHA>EFGEE7CF>F?FFHB=?EEGF>>DH5<)++,++,4,,4+=:,,,,5,,,,,,,,),33?,3,3,3,,,,33 </code></pre> I was trying to use script replace.sh which looks like this <pre><code>file=$1; adapter_sequence=$2; sed -r "s/${adapter_sequence}A{3}//" $file </code></pre> from the command line: ./replace.sh file.fastq GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG It did not work. Any help in any script language will be appreciated.
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<regex><bash><sed>
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regexp find and replace: bash variables inside sed
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