BOL: Wire posts tagged with 'pattern'

Wire post by Jit

Jit — Mon, 11 Feb 2019 18:01:41 -0600

Extract fasta with pattern $ perl -n -e '$on=(/^>(A)/) if (/^>/); print $_ if ($on);' pilonCor_round1.fasta > A_set.fa
#Pattern #Extract #Fasta

Rahul Nayak — Wed, 28 Mar 2018 17:14:25 -0500

#Extract all the files from a #directory and #sub-dir with #pattern. $ find TrimmedDir -type f | grep "L_" | xargs -i cp {} .

Jit — Wed, 21 Mar 2018 06:48:18 -0500

Find matching file names with pattern in a directory. $ ls -dq *_name2search_* | wc -l #file #search #hits #pattern #names #directory

Jit — Fri, 30 Jun 2017 07:16:30 -0500

Find a pattern in first 7 characters of reads. bioawk -c fastx 'substr($seq,0,7) == $TAG { print }' reads.fq.gz #Reads #NGS #Extract #Pattern

Jit — Mon, 08 Feb 2016 12:50:01 -0600

Print all the values beetween a pattern "abc" > awk '/abc/{flag=1;next}/mno/{flag=0}flag' file #awk #print #range #pattern

John Parker — Sun, 21 Sep 2014 16:19:13 -0500

Search a PATTERN in a file and print the line. perl -ne '/PATTERN/ && print' fileName #Perl #Pattern #Print #Search #Line

Rahul Agarwal — Fri, 13 Jun 2014 13:38:22 -0500

Suffix Trees ! http://www.cs.cmu.edu/~ckingsf/bioinfo-lectures/suffixtrees.pdf #SuffixTree #Pattern