Results for "Grep"
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Most Commonly used Awk by Bioinformatician
...n many practical cases. Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single...he average of column 2: awk '{x+=$2}END{print x/NR}' input.txt regex (egrep): awk '/^test[0-9]+/' input....3916 days ago
Perl one-liner for bioinformatician !!!
...ne 'printf "%-5d %s", $., $_' : for all the lines)perl -le 'print scalar(grep{/./}<>)' #prints the to..., @ascii)'#converts ascii values into character strings.perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "...3632 days ago
- ...esses running on port 1337 Searching grep pattern files — search for pattern in files grep -r pattern dir — search...
2878 days ago
Run miniasm assembler on nanopore reads !
...s_FAH31515//' AONTself10000.eps > AONTself10000final.eps Assemble with miniasm: miniasm -f ONT_A.fasta AONT.paf > AONT.gfa grep '^S' AONT.gfa |awk '{print "&...2334 days ago
PerlOneLiner for Bioinformatician
...ty lines in a fileperl -le 'print scalar(grep{/./}<>)'perl -le 'print ~~grep{/./}<>'perl -le 'print~...r @F; END { print $t }'perl -alne '$t += grep /regex/, @F; END { print $t }...dd numbers from 1 to 100perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "...2306 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
...st — reverse lookup host lsof -i tcp:1337 — list all processes running on port 1337 Searching grep pattern files — search for pattern in files grep -r pattern dir — s...2284 days ago
Installing Bio::SCF perl module
..... /usr/bin/install -cchecking for ranlib... ranlibchecking for main in -lz... yeschecking how to run the C preprocessor... gcc -Echecking for egrep... grep -Echecking for ANSI C header...2222 days ago
- ...fastq To count all sequences in a fasta file: grep "^>" yourfile.fasta -c To...current directory: for a in *.fasta; do ls $a; grep "^>" -c $a; done To keep.... here lenght >= 4000 + coverage >=100): grep "^>" scaffolds.fasta | sed...
2221 days ago
