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#!/usr/bin/env perl
# works for trinity transcripts or trinity genes, Sept 28 2016 bhaas
# lightweight fasta reader capabilities:
package Fasta_reader;
use strict;
sub new {
my ($packagename, $fastaFile) = @_;
## note: fastaFile can be a filename or an IO::Handle
my $self = { fastaFile => undef,,
fileHandle => undef };
bless ($self, $packagename);
## create filehandle
my $filehandle = undef;
if (ref $fastaFile eq 'IO::Handle') {
$filehandle = $fastaFile;
}
else {
open ($filehandle, $fastaFile) or die "Error: Couldn't open $fastaFile\n";
$self->{fastaFile} = $fastaFile;
}
$self->{fileHandle} = $filehandle;
return ($self);
}
#### next() fetches next Sequence object.
sub next {
my $self = shift;
my $orig_record_sep = $/;
$/="\n>";
my $filehandle = $self->{fileHandle};
my $next_text_input = <$filehandle>;
if (defined($next_text_input) && $next_text_input !~ /\w/) {
## must have been some whitespace at start of fasta file, before first entry.
## try again:
$next_text_input = <$filehandle>;
}
my $seqobj = undef;
if ($next_text_input) {
$next_text_input =~ s/^>|>$//g; #remove trailing > char.
$next_text_input =~ tr/\t\n\000-\037\177-\377/\t\n/d; #remove cntrl chars
my ($header, @seqlines) = split (/\n/, $next_text_input);
my $sequence = join ("", @seqlines);
$sequence =~ s/\s//g;
$seqobj = Sequence->new($header, $sequence);
}
$/ = $orig_record_sep; #reset the record separator to original setting.
return ($seqobj); #returns null if not instantiated.
}
#### finish() closes the open filehandle to the query database.
sub finish {
my $self = shift;
my $filehandle = $self->{fileHandle};
close $filehandle;
$self->{fileHandle} = undef;
}
####
sub retrieve_all_seqs_hash {
my $self = shift;
my %acc_to_seq;
while (my $seq_obj = $self->next()) {
my $acc = $seq_obj->get_accession();
my $sequence = $seq_obj->get_sequence();
$acc_to_seq{$acc} = $sequence;
}
return(%acc_to_seq);
}
##############################################
package Sequence;
use strict;
sub new {
my ($packagename, $header, $sequence) = @_;
## extract an accession from the header:
my ($acc, $rest) = split (/\s+/, $header, 2);
my $self = { accession => $acc,
header => $header,
sequence => $sequence,
filename => undef };
bless ($self, $packagename);
return ($self);
}
####
sub get_accession {
my $self = shift;
return ($self->{accession});
}
####
sub get_header {
my $self = shift;
return ($self->{header});
}
####
sub get_sequence {
my $self = shift;
return ($self->{sequence});
}
####
sub get_FASTA_format {
my $self = shift;
my $header = $self->get_header();
my $sequence = $self->get_sequence();
$sequence =~ s/(\S{60})/$1\n/g;
my $fasta_entry = ">$header\n$sequence\n";
return ($fasta_entry);
}
####
sub write_fasta_file {
my $self = shift;
my $filename = shift;
my ($accession, $header, $sequence) = ($self->{accession}, $self->{header}, $self->{sequence});
my $fasta_entry = $self->get_FASTA_format();
my $tempfile;
if ($filename) {
$tempfile = $filename;
} else {
my $acc = $accession;
$acc =~ s/\W/_/g;
$tempfile = "$acc.fasta";
}
open (TMP, ">$tempfile") or die "ERROR! Couldn't write a temporary file in current directory.\n";
print TMP $fasta_entry;
close TMP;
return ($tempfile);
}
package main;
my $usage = "usage: $0 acc.list.txt file.fasta\n\n";
my $acc_list = $ARGV[0] or die $usage;
my $pep = $ARGV[1] or die $usage;
main: {
my $fasta_reader = new Fasta_reader($pep);
my $acc_text = `cat $acc_list`;
my %accs;
while ($acc_text =~ /(\S+)/g) {
my $acc = $1;
$accs{$acc} = 1;
}
my %seen;
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession();
my $gene_id = $acc;
$gene_id =~ s/_i\d+$//;
if ($accs{$acc} || $accs{$gene_id}) {
print $seq_obj->get_FASTA_format();
$seen{$acc} = 1 if $accs{$acc};
$seen{$gene_id} = 1 if $accs{$gene_id};
}
}
# remove seen entries
foreach my $seen_acc (keys %seen) {
delete $accs{$seen_acc} if exists $accs{$seen_acc};
}
if (%accs) {
print STDERR "Error, could not locate entries for: " . join(", ", keys %accs) . "\n";
exit(1);
}
exit(0);
}
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