BOL: Results for "Replace"

Results for "Replace"

- BioJoker@biojoker
AWK for beginners !
...many of which rely heavily on regular expressions. # Search and replace, first instance (sub) or all instances (gsub) # Both return number of matches replaced localvar = "fooooobar";...
1845 days ago
- BioStar@biostar
Perl one-liner for beginners !
...s//\n/' all.sent.classOnly > all.sent.classOnly.sep Replace all occurrences of pattern1 (...delete every character that is not a letter, white space or line end (replace with nothing) perl -pne&...
1391 days ago
+1 more Blogs

- Jit@jit.aber
Tetra-Nucleotide Analysis
...it weak, phylogenetic signals. Even though tetra-nucleotide analysis (TNA) utilizes the information of whole genome, it is evident that it cannot replace other alignment-based phyloge...
2568 days ago

- Jit@jit.aber
Clean the FASTA file
Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3876 days ago

- Jit@jit.aber
Genome Assembly Tools and Software - PART2 !!
...e AssemblyD is a software which performed the local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines requi...
2695 days ago
- Neelam Jha@neelam
Awesome perl frameworks, libraries and software - PART 4
...h can load FLEX dynamiclly punchdrunker/iOSEmoji - information about unicode6 emoji used in iOS5 openresty/replace-filter-nginx-module - Streaming regular expression replacement in response bodies djabb...
2504 days ago

- Neelam Jha@neelam
Most Commonly used Awk by Bioinformatician
...y with Perl, awk is simpler in many practical cases. Why awk? You can replace a pipeline of 'stuff | grep |...calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column: awk '{prin...
3922 days ago
- Jit@jit.aber
BBMap/BBTools package: Multipurpose tool designed for converting reads or other nucleotide data between different formats.
...may need to type "bash reformat.sh" instead of just "reformat.sh". For users of Windows or other platforms that do not support bash shellscripts, replace "reformat.sh" with "java -ea...
2724 days ago
+9 more Top-level pages

- Jit@jit.aber
Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter. #Vim #vi #N #Replace #Fasta
3631 days ago
- Jitendra Narayan@admin
Creates 100 random DNA sequences with 20 residues. sapply(1:100, function(x) paste(sample(c("A","T","G","C"), 20, replace=T), collapse="")) #R #Random #Sequence #DNA #Script
3635 days ago
+7 more Wire posts

- Radha Agarkar@radhaagarkar
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...DERR $s->id(), "\t$ambig\n"; if (defined($opt_m)) { $thisSeq = ReplaceAmbiguousChar($thisSeq, $opt_m...[ATGC-]//g; $string =~ s/\s+//g; return $string; } sub ReplaceAmbiguousChar { my ($stri...
2924 days ago
- Abhinav@abhinav
String matching with Perl
...atch in dna1 $pos = index($dna1, $pattern); print “The match position of ATG in dna1 is : $pos \n”; # replace the ATG sites with CCC $dna3 =~ s/ATG/CCC/g; print “Replaced dna3 with CCC is : $dna3 \n”...
2919 days ago
+6 more Bio-Scripts

- BioStar@biostar
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
...will also print the folder perl is installing the package into. If you want to be extra-sure, you can also install most Perl packages via conda. Replace the ':' by '-', lower-case ev...
426 days ago
- LEGE@lege
Comment on "Short-read assembly using Spades !"
...input data is stored. Then, enter the following command: spades.py -1 <read1.fastq> -2 <read2.fastq> -o <output_dir> Replace read1.fastq and read2.fastq w...
430 days ago
+2 more Comments