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

This script will #extract the intron feature #gff3 and sequence from gene_exon gff3 and fasta file. Extract-intron-from-gff3

Extract sequence by ids $ xargs samtools faidx Adineta_vaga.v2.pep.fa < AlienIds > allAlienSeq.fa #Extract #Ids #Sequences

https://scrapy.org/ #extract #data #from #websites #webscraping

Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

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

Get the sequences using coordinates in bed file. $ bedtools getfasta -fi input_file.fa -bed regions_file.bed #Bed #Extract #Sequence #bedtools

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

#Extract a #sequence from #multi-fasta file: $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file

Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

Extract sequence by using Ids file (assuming one ids in a line): perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' ids.file fasta.file #PerlTricks #PerlOneliner #Perl #Extract #Ids #

Extract fasta sequence by Ids: perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #Perl #PerlOneliner #PerlTrick #Extract #Ids #Fasta

#Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

#Extract all #Reads from #BAM file for a #region Chr10:18000-45500 using #samtools: samtools view input.bam "Chr10:18000-45500" > output.bam

#Extract #tabbed info from #BAM file with samtools: samtools view test.bam|awk '{print $1 "\t" $2 "\t" $3 "\t" $4 "\t" $4+length($10)-1}' > file.xls