Results for "ids"
Bio-Scripts
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 $fh2,"2888 days ago
Perl script to extract fasta sequence by matching name/ids !!
...use warnings; use Text::Trim qw(trim); #Usage perl extractSeqbyID.pl ids.txt seq.fasta Result.fasta...ie; while () { chomp; next if /^\s*$/; s/>//g; my @ids=split (/\t/, $_); $selec...2888 days ago
Extract ids from file with perl
...$_; my @cells = split /\t/, $_; $idHash{$cells[0]}=$.; push @allIds, $cells[0]; } #Delete the...st id for secutiry -- might does not finish all steps delete $hash{$allIds[-1]}; next if exists $hash{$...2621 days ago
Extract fasta sequence from a multifasta file with coordinates
...zeED = shift; my $db = Bio::DB::Fasta->new( $fastaFile ); my @ids = $db->get_all_primary_ids; foreach my $id (@ids) {...$db = Bio::DB::Fasta->new('/path/to/fasta/files/'); my @ids = $db->get_all_primary_i...2545 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 LIS...2531 days ago
- my @ids =qw (scaffold_4 scaffold_4 scaffold_15 scaffold_40 scaffold_44 scaffold_51...58 scaffold_470 scaffold_480 scaffold_521 scaffold_644); foreach my $i (@ids) { print "Working on $i\n"...
2479 days ago
Extract fasta sequence with Ids with Bash script
#!/bin/bash while IFS='' read -r line || [[ -n "$line" ]]; do echo "Text read from file: $line" samtools faidx ONT.fasta $line > $line.faa done < "$1"2367 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2252 days ago
Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2252 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...pendancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]);...tmpOutfile"; foreach my $chr (@$SeqIds) { my $cnt=0; my $value=s...q}\n>@$SeqIds[$cnt]\n$refSeq->{@$SeqIds[$cnt]}{seq}\n"; close $ofh...{$seqid}{desc} = $2; push @allIds, $seqid; }...2153 days ago
