20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
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+package main;
+our $SEE;
+
+=head1 NAME
+
+CDNA::Gene_obj_alignment_assembler;
+
+=cut
+
+=head1 DESCRIPTION
+
+This package assembles multiple gene objs by assembling compatible sets of coordinates.  This module inherits from the CDNA::Genome_based_cDNA_assembler module.  Please see this inherited module for additional methods available.
+
+=cut
+
+package CDNA::Gene_obj_alignment_assembler;
+use strict;
+use base qw (CDNA::PASA_alignment_assembler);
+use CDNA::CDNA_alignment;
+
+
+=item new()
+
+=over 4
+
+B<Description:> Instantiate a new CDNA::Gene_obj_alignment_assembler object.
+
+B<Parameters:> $seq_ref
+
+$seq_ref is a scalar reference to the genomic sequence string.
+
+B<Returns:> obj_ref 
+
+=back
+
+=cut
+
+
+sub new {
+    my $packagename = shift;
+    my $seqref = shift;
+    my $self = $packagename->SUPER::new();
+    $self->{sequence_ref} = $seqref;
+    bless ($self, $packagename);
+   
+    return ($self);
+}
+    
+
+
+=item assemble_genes()
+
+=over 4
+
+B<Description:> assembles a list of Gene_obj(s).  Each of the Gene_objs
+
+B<Parameters:> @Gene_obj
+
+@Gene_obj is an array of gene objects created via the Gene_obj.pm module.
+
+B<Returns:> @CDNA_alignments
+
+The @CDNA_alignments array contains the list of CDNA::CDNA_alignment objects created based on the gene objects.
+
+The CDNA_alignment accession is set to the Model_feat_name of the gene_obj.  Retrieving the cDNA acc using the get_acc() method will allow a mapping back to the gene object.  Also, the newly created CDNA_alignment objects that are returned should be in the same order as the inputed gene objects, so indexing should provide mapping info as well.
+
+use the get_assemblies() function to fetch the merged genes.
+
+=back
+
+=cut
+
+
+
+
+
+sub assemble_genes {
+    my $self = shift;
+    my @gene_objs = @_;
+    my @cDNA_alignments;
+    foreach my $gene_obj (@gene_objs) {
+	my $alignment_obj = $self->gene_obj_to_cdna_alignment($gene_obj);
+	push (@cDNA_alignments, $alignment_obj);
+    }
+    $self->assemble_alignments(@cDNA_alignments);
+    return (@cDNA_alignments);
+}
+
+
+
+=item gene_obj_to_cdna_alignment()
+
+=over 4
+
+B<Description:> method converts a Gene_obj to a CDNA::CDNA_alignment obj.
+
+B<Parameters:> Gene_obj
+
+B<Returns:> CDNA::CDNA_alignment
+
+=back
+
+=cut
+
+sub gene_obj_to_cdna_alignment {
+    my $self = shift;
+    my $gene_obj = shift;
+    my @exons = $gene_obj->get_exons();
+    my %coords;
+    my @alignment_segments;
+    my $cdna_length = 0;
+    foreach my $exon (@exons) {
+	my ($end5, $end3) = $exon->get_coords();
+	my $alignment_seg = new CDNA::Alignment_segment($end5, $end3);
+	push (@alignment_segments, $alignment_seg);
+	$cdna_length += abs ($end3 - $end5) + 1;
+    }
+    my $alignment_obj = new CDNA::CDNA_alignment($cdna_length, \@alignment_segments, $self->{sequence_ref});
+    my $feat_name = $gene_obj->{Model_feat_name};
+    print "Gene has the following model feat_name: $feat_name\n" if $SEE;
+    $alignment_obj->set_acc($feat_name);
+    $alignment_obj->set_title($gene_obj->{com_name});
+    $alignment_obj->set_fli_status(1); #treat like a fli cdna
+    my $align_orient = $alignment_obj->get_spliced_orientation();
+    ## Make sure strand is set correctly (should only matter for single exon genes).
+    if ($align_orient ne $gene_obj->{strand}) {
+	$alignment_obj->set_orientation($gene_obj->{strand});
+	$alignment_obj->set_spliced_orientation($gene_obj->{strand});
+    }
+    $alignment_obj->remap_cdna_segment_coords();
+    print $alignment_obj->toToken() ." " . $alignment_obj->get_acc() .  "\n" if $SEE;
+    return ($alignment_obj);
+}
+
+
+1; #EOM
+
+
+
+