Results for "Symbol IDs Convert"
Bio-Scripts
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqIO-...2910 days ago
Perl script to extract lines with matching ids !!
#!/usr/bin/perl use strict; use warnings; my %patterns; #USAGE: perl extactByIds.pl Idsfile1 file2 > Result # Open file and get patterns to search for open(my $fh2,"2869 days ago
Perl script to extract fasta sequence by matching name/ids !!
#!/usr/bin/perl use strict; use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta...chomp; next if /^\s*$/; s/>//g; my @ids=spl...2869 days ago
Extract ids from file with perl
#!/usr/bin/perl use strict; use warnings; my $fh=read_fh("fin.txt"); my %idHash...lit /\t/, $_; $idHash{$cells[0]}=$.; push @allIds, $cells[0]; } #Delete the...might does not finish all steps delete $hash{$allIds[-1]...2602 days ago
Extract fasta sequence from a multifasta file with coordinates
#!/usr/bin/perl use Bio::DB::Fasta; #USAGE perl extractFASTAwithSIZE.pl fi...y $db = Bio::DB::Fasta->new( $fastaFile ); my @ids = $db->get_all_primary_ids; foreach my $id (@ids) {...DB::Fasta->new('/path/to/fasta/files/'); my @ids...2526 days ago
Extract fasta sequence from a multifasta file with fasta header Ids
#!/usr/bin/perl use strict; use warnings; #Usage: perl my $list = shift @ARGV; my $fasta = shift @ARGV; my $out = shift @ARGV; my %select; open LIST,...2512 days ago
- my @ids =qw (scaffold_4 scaffold_4 scaffold_15 scaffold_40 scaffold_44 scaffold_51 scaffold_54 scaffold_12...58 scaffold_470 scaffold_480 scaffold_521 scaffold_644); foreach my $i (@ids) {...
2460 days ago
Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2364 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2348 days ago
Convert fastq to fasta in Perl
use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq');...2324 days ago
