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The Wire
#OneLiner
Wire posts tagged with 'OneLiner'
LEGE
@lege
Thread
By
LEGE
1176 days ago
Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa
#count
#fasta
#oneliner
Jit
@jit.aber
Thread
By
Jit
1858 days ago
https:/
/
github.com/
stephenturner/
oneliners
#Bash
#Tutorial
#OneLiner
BioJoker
@biojoker
Thread
By
BioJoker
2028 days ago
Genome Mapping
#OneLiner
https:/
/
bioinformaticsonline.com/
snippets/
view/
39310/
one-liner-for-reads-mapping
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
2723 days ago
Unmasking the lower case values in genome. $ perl -pe '/^[^>]/ and $_=uc' genomic.fna > genomic.unmasked.fna
#Genome
#Unmask
#Perl
#Oneliner
Jit
@jit.aber
Thread
By
Jit
2739 days ago
Rename/number the multi-fasta file in ascending order. $ awk '/^>/{print ">" ++i; next}{print}' < Mix_assembly.fasta > Mix_assembly2.fasta
#awk
#oneliner
Jit
@jit.aber
Thread
By
Jit
2760 days ago
Perl OneLiner
http:/
/
userweb.eng.gla.ac.uk/
umer.ijaz/
bioinformatics/
oneliners.html
#Perl
#Oneliner
#NGS
#Script
Jit
@jit.aber
Thread
By
Jit
2760 days ago
NGS onliner
http:/
/
userweb.eng.gla.ac.uk/
umer.ijaz/
bioinformatics/
subsetFASTAFASTAQ.html
#OneLiner
#NGS
Shruti Paniwala
@shruti
Thread
By
Shruti Paniwala
2859 days ago
Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa
#Length
#Linux
#OneLiner
Jit
@jit.aber
Thread
By
Jit
3175 days ago
Print all text after a matching string perl -ne "print unless 1 .. m(String)"
#Perl
#OneLiner
#String
#Perl
#Trick
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3361 days ago
Count the number of sequences in fastaq file. grep -c '^@' sample1.fq
#Fastaq
#Count
#Number
#Grep
#Dirty
#Oneliner
#NGS
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3361 days ago
Remove the fasta description and just keep the identifier. perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa
#Perl
#Oneliner
#Trick
#Tips
#Fasta
#Identifier
#Remove
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3361 days ago
Extract sequences by their ID from a fasta file. perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if
@ARGV
' ids.txt sample1.fa
#Extract
#Sequences
#IDs
#Fasta
#Perl
#Trick
#Oneliner
Rahul Nayak
@rahul
Thread
By
Rahul Nayak
3429 days ago
Fancy One-Liner
http:/
/
userweb.eng.gla.ac.uk/
umer.ijaz/
bioinformatics/
oneliners.html
#Perl
#OneLiner
#Bioinformatics
#Quick
#Common
#Tricks
#CommandLine
#Terminal
Abhimanyu Singh
@abhimanyu
Thread
By
Abhimanyu Singh
3785 days ago
Linux one-liner.
https:/
/
wikis.utexas.edu/
display/
bioiteam/
Scott%27s+list+of+linux+one-liners
#Linux
#Oneliner
#NGS
Jit
@jit.aber
Thread
By
Jit
3821 days ago
Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName
#Delete
#Space
#Fasta
#Perl
#Oneliner
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