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|
#
# BioPerl module for Bio::Assembly::IO::tigr
#
# Copyright by Florent Angly
#
# You may distribute this module under the same terms as Perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Assembly::IO::tigr - Driver to read and write assembly files in the TIGR
Assembler v2 default format.
=head1 SYNOPSIS
# Building an input stream
use Bio::Assembly::IO;
# Assembly loading methods
my $asmio = Bio::Assembly::IO->new( -file => 'SGC0-424.tasm',
-format => 'tigr' );
my $scaffold = $asmio->next_assembly;
# Do some things on contigs...
# Assembly writing methods
my $outasm = Bio::Assembly::IO->new( -file => ">SGC0-modified.tasm",
-format => 'tigr' );
$outasm->write_assembly( -scaffold => $assembly,
-singlets => 1 );
=head1 DESCRIPTION
This package loads and writes assembly information in/from files in the default
TIGR Assembler v2 format. The files are lassie-formatted and often have the
.tasm extension. This module was written to be used as a driver module for
Bio::Assembly::IO input/output.
=head2 Implementation
Assemblies are loaded into Bio::Assembly::Scaffold objects composed of
Bio::Assembly::Contig and Bio::Assembly::Singlet objects. Since aligned reads
and contig gapped consensus can be obtained in the tasm files, only
aligned/gapped sequences are added to the different BioPerl objects.
Additional assembly information is stored as features. Contig objects have
SeqFeature information associated with the primary_tag:
_main_contig_feature:$contig_id -> misc contig information
_quality_clipping:$read_id -> quality clipping position
Read objects have sub_seqFeature information associated with the
primary_tag:
_main_read_feature:$read_id -> misc read information
Singlets are considered by TIGR Assembler as contigs of one sequence. Contigs
are represented here with features having these primary_tag:
_main_contig_feature:$contig_id
_quality_clipping:$read_primary_id
_main_read_feature:$read_primary_id
_aligned_coord:$read_primary_id
=head1 THE TIGR TASM LASSIE FORMAT
=head2 Description
In the TIGR tasm lassie format, contigs are separated by a line containing a single
pipe character "|", whereas the reads in a contig are separated by a blank line.
Singlets can be present in the file and are represented as a contig
composed of a single sequence.
Other than the two above-mentioned separators, each line has an attribute name,
followed a tab and then an attribute value.
The tasm format is used by more TIGR applications than just TIGR Assembler.
Some of the attributes are not used by TIGR Assembler or have constant values.
They are indicated by an asterisk *
Contigs have the following attributes:
asmbl_id -> contig ID
sequence -> contig ungapped consensus sequence (ambiguities are lowercase)
lsequence -> gapped consensus sequence (lowercase ambiguities)
quality -> gapped consensus quality score (in hexadecimal)
seq_id -> *
com_name -> *
type -> *
method -> always 'asmg' *
ed_status -> *
redundancy -> fold coverage of the contig consensus
perc_N -> percent of ambiguities in the contig consensus
seq# -> number of sequences in the contig
full_cds -> *
cds_start -> start of coding sequence *
cds_end -> end of coding sequence *
ed_pn -> name of editor (always 'GRA') *
ed_date -> date and time of edition
comment -> some comments *
frameshift -> *
Each read has the following attributes:
seq_name -> read name
asm_lend -> position of first base on contig ungapped consensus sequence
asm_rend -> position of last base on contig ungapped consensus sequence
seq_lend -> start of quality-trimmed sequence (aligned read coordinates)
seq_rend -> end of quality-trimmed sequence (aligned read coordinates)
best -> always '0' *
comment -> some comments *
db -> database name associated with the sequence (e.g. >my_db|seq1234)
offset -> offset of the sequence (gapped consensus coordinates)
lsequence -> aligned read sequence (ambiguities are uppercase)
When asm_rend E<lt> asm_lend, the sequence was on the complementary DNA strand but
its reverse complement is shown in the aligned sequence of the assembly file,
not the original read.
Ambiguities are reflected in the contig consensus sequence as
lowercase IUPAC characters: a c g t u m r w s y k x n . In the read
sequences, however, ambiguities are uppercase: M R W S Y K X N
=head2 Example
Example of a contig containing three sequences:
sequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCGCAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
lsequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAsCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCyGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAaGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
quality 0x0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0505050505050505050E0505160505050505050505050505050505050505050505050505050505050303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303030303090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0404040404040404041604040404040404040404040404040404040404040404040404040404040404040404040404040404040E0404040404040404040B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090909090B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B0B
asmbl_id 93
seq_id
com_name
type
method asmg
ed_status
redundancy 1.11
perc_N 0.20
seq# 3
full_cds
cds_start
cds_end
ed_pn GRA
ed_date 08/16/07 17:10:12
comment
frameshift
seq_name SDSU_RFPERU_010_C09.x01.phd.1
asm_lend 1
asm_rend 4423
seq_lend 1
seq_rend 442
best 0
comment
db
offset 0
lsequence CGATGCTGTACGGCTGTTGCGACAGATTGCGCTGGGTCGATACCGCGTTGGTGATCGGCTTGTTCAGCGGGCTCTGGTTCGGCGACAGCGCGGCGATCTTGGCGGCTGCGAAGGTTGCCGGCGCAATCATGCGCTGCTGACCGTTGACCTGGTCCTGCCAGTACACCCAGTCGCCCACCATGACCTTCAGCGCGTAGCTGTCACAGCCGGCTGTGGTCAGCGCAGTGGCGACGGTGGTGTAGGAGGCGCCAGCAACACCTTGGGTGATCATGTAGCAGCCTTCTGACAGGCCGTAGGTCAGCATGGTCGGCCACTGGGTACCAGTCAGTCGGGTCAACCGAGATTCG-CAGCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGG
seq_name SDSU_RFPERU_002_H12.x01.phd.1
asm_lend 339
asm_rend 940
seq_lend 1
seq_rend 602
best 0
comment
db
offset 338
lsequence CGAGATTCGCCACCTGAGCGCCACTGCCGCGCAGAGCGTACATGCCCTTGCGGGTCGCGCCGGTAACACCATCCACGCCGATCAGAACTGCGTCGGTGATGGTGGTGTTACCCGAGGTGCCAGTGGTGAAGGCGACGGTCTGGGTGCTGGCCACAGGCGCCAGAGTGGTCGCGCCAACGGTGGCGATGACCAGTTGCGATGGGCCACGGATACCTGACTGCCCGTTGTTCACGGCGCTGACGATGTTCTGCCACAGCGCCAGGCCAGAGCCGGTGATGTTGTCGAACACTTCGGGCGCAACGCCAGGGAGCGAGACGGTCAGCTTCCAGCTCGAAGCAGCGGAGCCAGTAGCCAGGGCGGCGCTGAGCGAGTTGCCGAGCGTGCCGGTGTAGAACGCGGTCAGCGTGGCGCCGGTGGCGGCGGCAGTGTCCTTCAGCGCACTGGTCGCGGCGGTGTCGGTGCCGTCAGTGACGCGCACGGCGCGGATGTTCGAGGCGCCGCCCTGGATTGATACCGCCAGCGCGGTGCACAGGTCGTACTTGCGCACGGTCCGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATA-GCGTGGCGC
seq_name SDSU_RFPERU_009_E07.x01.phd.1
asm_lend 880
asm_rend 1520
seq_lend 641
seq_rend 1
best 0
comment
db
offset 8803
lsequence CGCACGGTCTGAGTGCCGAACTTCTGCGATGCGTCACCTGGCGAGCCGATAAGCGTGGCGCTGTTCACCGGCCCCCAGTCAGCAATGCCGACGATGCCGAGAATGTCAGTCGGGACGCCATTGATGTAGCGGGTCTTGGGCGCCACTATTTGTATGTACAAATCTGGCGCAGATAAAGCCGCCGTATTCAAATAACCAGCAGGATAGATAGGCATCACGCCTCCAGAATGAAAAAGGCCACCGATTAGGTGGCCTTTGTTGTGTTCGGCTGGCTGTTAGAGCAGCAGCCCGTTTTCCCGCGCAAACGCGAATGGGTCCTTGTCATGCTTCCTGCAATTGCAGGTAGGACAAAGAATTTGCAGGTTGGATTTGTCGTTCGATCCGCCCTTTGCAAGCGGGAACACGTGGTCAACGTGATACCCATCCCTTATGGATATAGTGCACATGGCGCATTTCCAGCGCTGAGCAGCCAGCAAAAATTTTATGTCGTCGCCGGTGTGTGAGCCGACAGCATTTTTCTTGCGAGCCTTGTATGTCCGCGAGAGTGAACGAACTTGCTCCTTGTTGGCTGTCTTCCAGAGCTTTTGAGTAAGCGCACAGAGATCCTTGTTTCTTGATCTCCACTCTCTGGTTGCGGAAAT
|
...
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the BioPerl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Florent E Angly
Email florent dot angly at gmail dot com
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
package Bio::Assembly::IO::tigr;
use strict;
use Bio::Seq::PrimaryQual;
use Bio::LocatableSeq;
use Bio::Seq::Quality;
use Bio::Assembly::IO;
use Bio::Assembly::Scaffold;
use Bio::Assembly::Contig;
use Bio::Assembly::Singlet;
use base qw(Bio::Assembly::IO);
our $progname = 'TIGR_Assembler';
=head2 next_assembly
Title : next_assembly
Usage : my $scaffold = $asmio->next_assembly();
Function: return the next assembly in the tasm-formatted stream
Returns : Bio::Assembly::Scaffold object
Args : none
=cut
sub next_assembly {
my $self = shift;
my $assembly = Bio::Assembly::Scaffold->new( -source => $progname );
# Load contigs and singlets in the scaffold
while ( my $obj = $self->next_contig()) {
# Add contig /singlet to assembly
if ($obj->isa('Bio::Assembly::Singlet')) { # a singlet
$assembly->add_singlet($obj);
} else { # a contig
$assembly->add_contig($obj);
}
}
return $assembly;
}
=head2 next_contig
Title : next_contig
Usage : my $contig = $asmio->next_contig();
Function: return the next contig or singlet TIGR-formatted stream
Returns : Bio::Assembly::Contig or Bio::Assembly::Singlet
Args : none
=cut
sub next_contig {
my $self = shift;
# Contig and read related
my $contigobj;
my $iscontig = 1;
my %contiginfo;
my %readinfo;
# Loop over all assembly file lines
while ($_ = $self->_readline) {
chomp;
if ( /^\|/ ) { # a line with a single pipe |
# The end of a read from a contig/singlet, the start of a new one
last;
} elsif ( /^$/ ) { # a blank line
if ($contiginfo{'seqnum'} > 1) {
if ($iscontig) {
# The end of a contig, the start of a read in that contig
$contigobj = $self->_store_contig(\%contiginfo, $contigobj);
} else {
# The end of a read in a contig, the start of a new read in
$self->_store_read(\%readinfo, $contigobj);
undef %readinfo;
}
}
# else it's a singlet and we'll store the singlet and its unique
# sequence all at once later
$iscontig = 0;
} else {
if ($iscontig) {
# Parse contig
if (/^sequence\t(.*)/) {$contiginfo{'sequence'} = $1; next}
elsif (/^lsequence\t(.*)/) {$contiginfo{'lsequence'} = $1; next}
elsif (/^quality\t(.*)/) {$contiginfo{'quality'} = $1; next}
elsif (/^asmbl_id\t(.*)/) {$contiginfo{'asmbl_id'} = $1; next}
elsif (/^seq_id\t(.*)/) {$contiginfo{'seq_id'} = $1; next}
elsif (/^com_name\t(.*)/) {$contiginfo{'com_name'} = $1; next}
elsif (/^type\t(.*)/) {$contiginfo{'type'} = $1; next}
elsif (/^method\t(.*)/) {$contiginfo{'method'} = $1; next}
elsif (/^ed_status\t(.*)/) {$contiginfo{'ed_status'} = $1; next}
elsif (/^redundancy\t(.*)/) {$contiginfo{'redundancy'} = $1; next}
elsif (/^perc_N\t(.*)/) {$contiginfo{'perc_N'} = $1; next}
elsif (/^seq\#\t(.*)/) {$contiginfo{'seqnum'} = $1; next}
elsif (/^full_cds\t(.*)/) {$contiginfo{'full_cds'} = $1; next}
elsif (/^cds_start\t(.*)/) {$contiginfo{'cds_start'} = $1; next}
elsif (/^cds_end\t(.*)/) {$contiginfo{'cds_end'} = $1; next}
elsif (/^ed_pn\t(.*)/) {$contiginfo{'ed_pn'} = $1; next}
elsif (/^ed_date\t(.*\s.*)/) {$contiginfo{'ed_date'} = $1; next}
elsif (/^comment\t(.*)/) {$contiginfo{'comment'} = $1; next}
elsif (/^frameshift\t(.*)/) {$contiginfo{'frameshift'} = $1; next}
else {
$self->throw("Format unknown at line $.:\n$_\nIs your file".
" really a TIGR Assembler tasm-formatted file?");
}
} else {
# Parse read info
if (/^seq_name\t(.*)/) {$readinfo{'seq_name'} = $1; next}
elsif (/^asm_lend\t(.*)/) {$readinfo{'asm_lend'} = $1; next}
elsif (/^asm_rend\t(.*)/) {$readinfo{'asm_rend'} = $1; next}
elsif (/^seq_lend\t(.*)/) {$readinfo{'seq_lend'} = $1; next}
elsif (/^seq_rend\t(.*)/) {$readinfo{'seq_rend'} = $1; next}
elsif (/^best\t(.*)/) {$readinfo{'best'} = $1; next}
elsif (/^comment\t(.*)/) {$readinfo{'comment'} = $1; next}
elsif (/^db\t(.*)/) {$readinfo{'db'} = $1; next}
elsif (/^offset\t(.*)/) {$readinfo{'offset'} = $1; next}
elsif (/^lsequence\t(.*)/) {$readinfo{'lsequence'} = $1; next}
else {
$self->throw("Format unknown at line $.:\n$_\nIs your file".
" really a TIGR Assembler tasm-formatted file?");
}
}
}
}
# Store read info into a singlet or contig
if (defined $contiginfo{'seqnum'}) {
if ($contiginfo{'seqnum'} > 1) {
# This is a read to attach to an existing contig object.
$self->_store_read(\%readinfo, $contigobj);
} elsif ($contiginfo{'seqnum'} == 1) {
# This is a read. Save singlet and read together in a singlet object.
$contigobj = $self->_store_singlet(\%readinfo, \%contiginfo);
} else {
# That should not happen
$self->throw("Unhandled exception");
}
}
return $contigobj;
}
=head2 _qual_hex2dec
Title : _qual_hex2dec
Usage : my dec_quality = $self->_qual_hex2dec($hex_quality);
Function: convert an hexadecimal quality score into a decimal quality score
Returns : string
Args : string
=cut
sub _qual_hex2dec {
my ($self, $qual) = @_;
$qual =~ s/^0x(.*)$/$1/;
$qual =~ s/(..)/hex($1).' '/eg;
return $qual;
}
=head2 _qual_dec2hex
Title : _qual_dec2hex
Usage : my hex_quality = $self->_qual_dec2hex($dec_quality);
Function: convert a decimal quality score into an hexadecimal quality score
Returns : string
Args : string
=cut
sub _qual_dec2hex {
my ($self, $qual) = @_;
$qual =~ s/(\d+)\s*/sprintf('%02X', $1)/eg;
$qual = '0x'.$qual;
return $qual;
}
=head2 _store_contig
Title : _store_contig
Usage : my $contigobj = $self->_store_contig(\%contiginfo, $contigobj);
Function: store information of a contig belonging to a scaffold in the
appropriate object
Returns : Bio::Assembly::Contig object
Args : hash, Bio::Assembly::Contig
=cut
sub _store_contig {
my ($self, $contiginfo, $contigobj) = @_;
# Create a contig
$contigobj = Bio::Assembly::Contig->new(
-id => $$contiginfo{'asmbl_id'},
-strand => 1
);
# Create a gapped consensus sequence and attach it to contig
#$$contiginfo{'llength'} = length($$contiginfo{'lsequence'});
my $consensus = Bio::LocatableSeq->new(
-id => $$contiginfo{'asmbl_id'},
-seq => $$contiginfo{'lsequence'},
-start => 1,
);
$contigobj->set_consensus_sequence($consensus);
# Create an gapped consensus quality score and attach it to contig
$$contiginfo{'quality'} = $self->_qual_hex2dec($$contiginfo{'quality'});
my $qual = Bio::Seq::PrimaryQual->new( -qual => $$contiginfo{'quality'},
-id => $$contiginfo{'asmbl_id'} );
$contigobj->set_consensus_quality($qual);
# Add other misc contig information as features of the contig
my $contigtags = Bio::SeqFeature::Generic->new(
-primary => '_main_contig_feature',
-source => $$contiginfo{'asmbl_id'},
-start => 1,
-end => $contigobj->get_consensus_length(),
-strand => 1,
-tag => { 'seq_id' => $$contiginfo{'seq_id'},
'com_name' => $$contiginfo{'com_name'},
'type' => $$contiginfo{'type'},
'method' => $$contiginfo{'method'},
'ed_status' => $$contiginfo{'ed_status'},
'full_cds' => $$contiginfo{'full_cds'},
'cds_start' => $$contiginfo{'cds_start'},
'cds_end' => $$contiginfo{'cds_end'},
'ed_pn' => $$contiginfo{'ed_pn'},
'ed_date' => $$contiginfo{'ed_date'},
'comment' => $$contiginfo{'comment'},
'frameshift' => $$contiginfo{'frameshift'} }
);
$contigobj->add_features([ $contigtags ], 1);
return $contigobj;
}
=head2 _store_read
Title : _store_read
Usage : my $readobj = $self->_store_read(\%readinfo, $contigobj);
Function: store information of a read belonging to a contig in a contig object
Returns : Bio::LocatableSeq
Args : hash, Bio::Assembly::Contig
=cut
sub _store_read {
my ($self, $readinfo, $contigobj) = @_;
# Create an aligned read object
#$$readinfo{'llength'} = length($$readinfo{'lsequence'});
$$readinfo{'strand'} = ($$readinfo{'seq_rend'} > $$readinfo{'seq_lend'} ? 1 : -1);
my $readobj = Bio::LocatableSeq->new(
# the ids of sequence objects are supposed to include the db name in it, i.e. "big_db|seq1234"
# that's how sequence ids coming from the fasta parser are at least
-display_id => $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'}),
-primary_id => $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'}),
-seq => $$readinfo{'lsequence'},
-start => 1,
-strand => $$readinfo{'strand'},
-alphabet => 'dna'
);
# Add read location and sequence to contig (in 'gapped consensus' coordinates)
$$readinfo{'aln_start'} = $$readinfo{'offset'} + 1; # seq offset is in gapped coordinates
$$readinfo{'aln_end'} = $$readinfo{'aln_start'} + length($$readinfo{'lsequence'}) - 1; # lsequence is aligned seq
my $alncoord = Bio::SeqFeature::Generic->new(
-primary => $readobj->id,
-start => $$readinfo{'aln_start'},
-end => $$readinfo{'aln_end'},
-strand => $$readinfo{'strand'},
-tag => { 'contig' => $contigobj->id() }
);
$contigobj->set_seq_coord($alncoord, $readobj);
# Add quality clipping read information in contig features
# (from 'aligned read' to 'gapped consensus' coordinates)
$$readinfo{'clip_start'} = $contigobj->change_coord('aligned '.$readobj->id, 'gapped consensus', $$readinfo{'seq_lend'});
$$readinfo{'clip_end'} = $contigobj->change_coord('aligned '.$readobj->id, 'gapped consensus', $$readinfo{'seq_rend'});
my $clipcoord = Bio::SeqFeature::Generic->new(
-primary => '_quality_clipping',
-source => $readobj->id,
-start => $$readinfo{'clip_start'},
-end => $$readinfo{'clip_end'},
-strand => $$readinfo{'strand'}
);
$clipcoord->attach_seq($readobj);
$contigobj->add_features([ $clipcoord ], 0);
# Add other misc read information as subsequence feature
my $readtags = Bio::SeqFeature::Generic->new(
-primary => '_main_read_feature',
-source => $readobj->id,
-start => $$readinfo{'aln_start'},
-end => $$readinfo{'aln_end'},
-strand => $$readinfo{'strand'},
-tag => { 'best' => $$readinfo{'best'},
'comment' => $$readinfo{'comment'} }
);
$contigobj->get_features_collection->add_features([$readtags]);
$contigobj->get_features_collection->add_SeqFeature($alncoord, $readtags);
return $readobj;
}
=head2 _store_singlet
Title : _store_singlet
Usage : my $singletobj = $self->_store_read(\%readinfo, \%contiginfo);
Function: store information of a singlet belonging to a scaffold in a singlet object
Returns : Bio::Assembly::Singlet
Args : hash, hash
=cut
sub _store_singlet {
my ($self, $readinfo, $contiginfo) = @_;
# Singlets in TIGR_Assembler are represented as a contig of one sequence
# We try to simulate this duality by playing around with the Singlet object
my $contigid = $$contiginfo{'asmbl_id'};
my $readid = $self->_merge_seq_name_and_db($$readinfo{'seq_name'}, $$readinfo{'db'});
# Create a sequence object
#$$contiginfo{'llength'} = length($$contiginfo{'lsequence'});
my $seqobj = Bio::Seq::Quality->new(
-primary_id => $readid,
-display_id => $readid,
-seq => $$contiginfo{'lsequence'}, # do not use $$readinfo as ambiguities are uppercase
-start => 1,
-strand => $$readinfo{'strand'},
-alphabet => 'dna',
-qual => $self->_qual_hex2dec($$contiginfo{'quality'})
);
# Create singlet from sequence and add it to scaffold
my $singletobj = Bio::Assembly::Singlet->new(
-id => $contigid,
-seqref => $seqobj
);
# Add other misc contig information as features of the singlet
my $contigtags = Bio::SeqFeature::Generic->new(
-primary => '_main_contig_feature',
-source => $contigid,
-start => 1,
-end => $singletobj->get_consensus_length(),
-strand => 1,
-tag => { 'seq_id' => $$contiginfo{'seq_id'},
'com_name' => $$contiginfo{'com_name'},
'type' => $$contiginfo{'type'},
'method' => $$contiginfo{'method'},
'ed_status' => $$contiginfo{'ed_status'},
'full_cds' => $$contiginfo{'full_cds'},
'cds_start' => $$contiginfo{'cds_start'},
'cds_end' => $$contiginfo{'cds_end'},
'ed_pn' => $$contiginfo{'ed_pn'},
'ed_date' => $$contiginfo{'ed_date'},
'comment' => $$contiginfo{'comment'},
'frameshift' => $$contiginfo{'frameshift'} }
);
$singletobj->add_features([ $contigtags ], 1);
# Add read location and sequence to singlet features (in 'gapped consensus' coordinates)
$$readinfo{'aln_start'} = $$readinfo{'offset'} + 1; # seq offset is in gapped coordinates
$$readinfo{'aln_end'} = $$readinfo{'aln_start'} + length($$readinfo{'lsequence'}) - 1; # lsequence is aligned seq
my $alncoord = Bio::SeqFeature::Generic->new(
-primary => '_aligned_coord',
-source => $readid,
-start => $$readinfo{'aln_start'},
-end => $$readinfo{'aln_end'},
-strand => $$readinfo{'strand'},
-tag => { 'contig' => $contigid }
);
$alncoord->attach_seq($singletobj->seqref);
$singletobj->add_features([ $alncoord ], 0);
# Add quality clipping read information in singlet features
# (from 'aligned read' to 'gapped consensus' coordinates)
$$readinfo{'clip_start'} = $$readinfo{'seq_lend'};
$$readinfo{'clip_end'} = $$readinfo{'seq_rend'};
my $clipcoord = Bio::SeqFeature::Generic->new(
-primary => '_quality_clipping',
-source => $readid,
-start => $$readinfo{'clip_start'},
-end => $$readinfo{'clip_end'},
-strand => $$readinfo{'strand'},
-tag => { 'contig' => $contigid }
);
$clipcoord->attach_seq($singletobj->seqref);
$singletobj->add_features([ $clipcoord ], 0);
# Add other misc read information as subsequence feature
my $readtags = Bio::SeqFeature::Generic->new(
-primary => '_main_read_feature',
-source => $readid,
-start => $$readinfo{'aln_start'},
-end => $$readinfo{'aln_end'},
-strand => $$readinfo{'strand'},
-tag => { 'best' => $$readinfo{'best'},
'comment' => $$readinfo{'comment'} }
);
$singletobj->get_features_collection->add_features([$readtags]);
$singletobj->get_features_collection->add_SeqFeature($alncoord, $readtags);
return $singletobj;
}
=head2 write_assembly
Title : write_assembly
Usage : $asmio->write_assembly($assembly)
Function: Write the assembly object in TIGR Assembler compatible format. The
contig IDs are sorted naturally if the Sort::Naturally module is
present, or lexically otherwise. Internally, write_assembly use
the write_contig, write_footer and write_header methods. Use these
methods if you want more control on the writing process.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object
1 to write singlets in the assembly file, 0 otherwise
=cut
=head2 write_contig
Title : write_contig
Usage : $asmio->write_contig($contig)
Function: Write a contig or singlet object in TIGR compatible format. Quality
scores are automatically generated if the contig does not contain
any
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Contig or Singlet object
=cut
sub write_contig {
my ($self, @args) = @_;
my ($contigobj) = $self->_rearrange([qw(CONTIG)], @args);
# Sanity check
if ( !$contigobj || !$contigobj->isa('Bio::Assembly::Contig') ) {
$self->throw("Must provide a Bio::Assembly::Contig or Singlet object when calling write_contig");
}
my $decimal_format = '%.2f';
my $contigid = $contigobj->id;
my $numseqs = $contigobj->num_sequences;
if ( $contigobj->isa('Bio::Assembly::Singlet') ) {
# This is a singlet
my $readid = $contigobj->seqref->id;
my $singletobj = $contigobj;
# Get contig information
my ($contanno) = $singletobj->get_features_collection->get_features_by_type("_main_contig_feature:$contigid");
my %contiginfo;
$contiginfo{'sequence'} = $singletobj->seqref->seq;
$contiginfo{'lsequence'} = $contiginfo{'sequence'};
$contiginfo{'quality'} = $self->_qual_dec2hex(
join ' ', @{$singletobj->get_consensus_quality->qual} );
$contiginfo{'asmbl_id'} = $contigid;
$contiginfo{'seq_id'} = ($contanno->get_tag_values('seq_id'))[0];
$contiginfo{'com_name'} = ($contanno->get_tag_values('com_name'))[0];
$contiginfo{'type'} = ($contanno->get_tag_values('type'))[0];
$contiginfo{'method'} = ($contanno->get_tag_values('method'))[0];
$contiginfo{'ed_status'} = ($contanno->get_tag_values('ed_status'))[0];
$contiginfo{'redundancy'} = sprintf($decimal_format, 1);
$contiginfo{'perc_N'} = sprintf(
$decimal_format, $self->_perc_N($contiginfo{'sequence'}));
$contiginfo{'seqnum'} = 1;
$contiginfo{'full_cds'} = ($contanno->get_tag_values('full_cds'))[0];
$contiginfo{'cds_start'} = ($contanno->get_tag_values('cds_start'))[0];
$contiginfo{'cds_end'} = ($contanno->get_tag_values('cds_end'))[0];
$contiginfo{'ed_pn'} = ($contanno->get_tag_values('ed_pn'))[0];
$contiginfo{'ed_date'} = $self->_date_time;
$contiginfo{'comment'} = ($contanno->get_tag_values('comment'))[0];
$contiginfo{'frameshift'} = ($contanno->get_tag_values('frameshift'))[0];
# Check that no tag value is undef
$contiginfo{'seq_id'} = '' unless defined $contiginfo{'seq_id'};
$contiginfo{'com_name'} = '' unless defined $contiginfo{'com_name'};
$contiginfo{'type'} = '' unless defined $contiginfo{'type'};
$contiginfo{'method'} = '' unless defined $contiginfo{'method'};
$contiginfo{'ed_status'} = '' unless defined $contiginfo{'ed_status'};
$contiginfo{'full_cds'} = '' unless defined $contiginfo{'full_cds'};
$contiginfo{'cds_start'} = '' unless defined $contiginfo{'cds_start'};
$contiginfo{'cds_end'} = '' unless defined $contiginfo{'cds_end'};
$contiginfo{'ed_pn'} = '' unless defined $contiginfo{'ed_pn'};
$contiginfo{'comment'} = '' unless defined $contiginfo{'comment'};
$contiginfo{'frameshift'} = '' unless defined $contiginfo{'frameshift'};
# Print singlet information
$self->_print(
"sequence\t$contiginfo{'sequence'}\n".
"lsequence\t$contiginfo{'lsequence'}\n".
"quality\t$contiginfo{'quality'}\n".
"asmbl_id\t$contiginfo{'asmbl_id'}\n".
"seq_id\t$contiginfo{'seq_id'}\n".
"com_name\t$contiginfo{'com_name'}\n".
"type\t$contiginfo{'type'}\n".
"method\t$contiginfo{'method'}\n".
"ed_status\t$contiginfo{'ed_status'}\n".
"redundancy\t$contiginfo{'redundancy'}\n".
"perc_N\t$contiginfo{'perc_N'}\n".
"seq#\t$contiginfo{'seqnum'}\n".
"full_cds\t$contiginfo{'full_cds'}\n".
"cds_start\t$contiginfo{'cds_start'}\n".
"cds_end\t$contiginfo{'cds_end'}\n".
"ed_pn\t$contiginfo{'ed_pn'}\n".
"ed_date\t$contiginfo{'ed_date'}\n".
"comment\t$contiginfo{'comment'}\n".
"frameshift\t$contiginfo{'frameshift'}\n".
"\n"
);
# Get read information
my ($seq_name, $db) = $self->_split_seq_name_and_db($readid);
my ($clipcoord) = $singletobj->get_features_collection->get_features_by_type("_quality_clipping:$readid");
my ($alncoord) = $singletobj->get_features_collection->get_features_by_type("_aligned_coord:$readid");
my ($readanno) = $singletobj->get_features_collection->get_features_by_type("_main_read_feature:$readid");
my %readinfo;
$readinfo{'seq_name'} = $seq_name;
$readinfo{'asm_lend'} = $alncoord->location->start;
$readinfo{'asm_rend'} = $alncoord->location->end;
$readinfo{'seq_lend'} = $clipcoord->location->start;
$readinfo{'seq_rend'} = $clipcoord->location->end;
$readinfo{'best'} = ($readanno->get_tag_values('best'))[0];
$readinfo{'comment'} = ($readanno->get_tag_values('comment'))[0];
$readinfo{'db'} = $db;
$readinfo{'offset'} = 0;
# ambiguities in read sequence are uppercase
$readinfo{'lsequence'} = uc($contiginfo{'lsequence'});
# Check that no tag value is undef
$readinfo{'best'} = '' unless defined $readinfo{'best'};
$readinfo{'comment'} = '' unless defined $readinfo{'comment'};
# Print read information
$self->_print(
"seq_name\t$readinfo{'seq_name'}\n".
"asm_lend\t$readinfo{'asm_lend'}\n".
"asm_rend\t$readinfo{'asm_rend'}\n".
"seq_lend\t$readinfo{'seq_lend'}\n".
"seq_rend\t$readinfo{'seq_rend'}\n".
"best\t$readinfo{'best'}\n".
"comment\t$readinfo{'comment'}\n".
"db\t$readinfo{'db'}\n".
"offset\t$readinfo{'offset'}\n".
"lsequence\t$readinfo{'lsequence'}\n"
);
$self->_print("|\n");
} else {
# This is a contig
# Get contig information
my ($contanno) = $contigobj->get_features_collection->get_features_by_type("_main_contig_feature:$contigid");
my %contiginfo;
$contiginfo{'sequence'} = $self->_ungap(
$contigobj->get_consensus_sequence->seq);
$contiginfo{'lsequence'} = $contigobj->get_consensus_sequence->seq;
$contiginfo{'quality'} = $self->_qual_dec2hex(
join ' ', @{$contigobj->get_consensus_quality->qual});
$contiginfo{'asmbl_id'} = $contigid;
$contiginfo{'seq_id'} = ($contanno->get_tag_values('seq_id'))[0];
$contiginfo{'com_name'} = ($contanno->get_tag_values('com_name'))[0];
$contiginfo{'type'} = ($contanno->get_tag_values('type'))[0];
$contiginfo{'method'} = ($contanno->get_tag_values('method'))[0];
$contiginfo{'ed_status'} = ($contanno->get_tag_values('ed_status'))[0];
$contiginfo{'redundancy'} = sprintf(
$decimal_format, $self->_redundancy($contigobj));
$contiginfo{'perc_N'} = sprintf(
$decimal_format, $self->_perc_N($contiginfo{'sequence'}));
$contiginfo{'seqnum'} = $contigobj->num_sequences;
$contiginfo{'full_cds'} = ($contanno->get_tag_values('full_cds'))[0];
$contiginfo{'cds_start'} = ($contanno->get_tag_values('cds_start'))[0];
$contiginfo{'cds_end'} = ($contanno->get_tag_values('cds_end'))[0];
$contiginfo{'ed_pn'} = ($contanno->get_tag_values('ed_pn'))[0];
$contiginfo{'ed_date'} = $self->_date_time;
$contiginfo{'comment'} = ($contanno->get_tag_values('comment'))[0];
$contiginfo{'frameshift'} = ($contanno->get_tag_values('frameshift'))[0];
# Check that no tag value is undef
$contiginfo{'seq_id'} = '' unless defined $contiginfo{'seq_id'};
$contiginfo{'com_name'} = '' unless defined $contiginfo{'com_name'};
$contiginfo{'type'} = '' unless defined $contiginfo{'type'};
$contiginfo{'method'} = '' unless defined $contiginfo{'method'};
$contiginfo{'ed_status'} = '' unless defined $contiginfo{'ed_status'};
$contiginfo{'full_cds'} = '' unless defined $contiginfo{'full_cds'};
$contiginfo{'cds_start'} = '' unless defined $contiginfo{'cds_start'};
$contiginfo{'cds_end'} = '' unless defined $contiginfo{'cds_end'};
$contiginfo{'ed_pn'} = '' unless defined $contiginfo{'ed_pn'};
$contiginfo{'comment'} = '' unless defined $contiginfo{'comment'};
$contiginfo{'frameshift'} = '' unless defined $contiginfo{'frameshift'};
# Print contig information
$self->_print(
"sequence\t$contiginfo{'sequence'}\n".
"lsequence\t$contiginfo{'lsequence'}\n".
"quality\t$contiginfo{'quality'}\n".
"asmbl_id\t$contiginfo{'asmbl_id'}\n".
"seq_id\t$contiginfo{'seq_id'}\n".
"com_name\t$contiginfo{'com_name'}\n".
"type\t$contiginfo{'type'}\n".
"method\t$contiginfo{'method'}\n".
"ed_status\t$contiginfo{'ed_status'}\n".
"redundancy\t$contiginfo{'redundancy'}\n".
"perc_N\t$contiginfo{'perc_N'}\n".
"seq#\t$contiginfo{'seqnum'}\n".
"full_cds\t$contiginfo{'full_cds'}\n".
"cds_start\t$contiginfo{'cds_start'}\n".
"cds_end\t$contiginfo{'cds_end'}\n".
"ed_pn\t$contiginfo{'ed_pn'}\n".
"ed_date\t$contiginfo{'ed_date'}\n".
"comment\t$contiginfo{'comment'}\n".
"frameshift\t$contiginfo{'frameshift'}\n".
"\n"
);
my $seqno = 0;
for my $readobj ( $contigobj->each_seq() ) {
$seqno++;
# Get read information
my ($seq_name, $db) = $self->_split_seq_name_and_db($readobj->id);
my ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset)
= $self->_coord($readobj, $contigobj);
my $readanno = ($contigobj->get_features_collection->get_SeqFeatures(
$contigobj->get_seq_coord($readobj) ,
'_main_read_feature:'.$readobj->primary_id) )[0];
my %readinfo;
$readinfo{'seq_name'} = $seq_name;
$readinfo{'asm_lend'} = $asm_lend;
$readinfo{'asm_rend'} = $asm_rend;
$readinfo{'seq_lend'} = $seq_lend;
$readinfo{'seq_rend'} = $seq_rend;
$readinfo{'best'} = ($readanno->get_tag_values('best'))[0];
$readinfo{'comment'} = ($readanno->get_tag_values('comment'))[0];
$readinfo{'db'} = $db;
$readinfo{'offset'} = $offset;
$readinfo{'lsequence'} = $readobj->seq();
# Check that no tag value is undef
$readinfo{'best'} = '' unless defined $readinfo{'best'};
$readinfo{'comment'} = '' unless defined $readinfo{'comment'};
# Print read information
$self->_print(
"seq_name\t$readinfo{'seq_name'}\n".
"asm_lend\t$readinfo{'asm_lend'}\n".
"asm_rend\t$readinfo{'asm_rend'}\n".
"seq_lend\t$readinfo{'seq_lend'}\n".
"seq_rend\t$readinfo{'seq_rend'}\n".
"best\t$readinfo{'best'}\n".
"comment\t$readinfo{'comment'}\n".
"db\t$readinfo{'db'}\n".
"offset\t$readinfo{'offset'}\n".
"lsequence\t$readinfo{'lsequence'}\n"
);
if ($seqno < $contiginfo{'seqnum'}) {
$self->_print("\n");
} else {
$self->_print("|\n")
};
}
}
return 1;
}
=head2 write_header
Title : write_header
Usage : $asmio->write_header($assembly)
Function: In the TIGR Asseformat assembly driver, this does nothing. The
method is present for compatibility with other assembly drivers
that need to write a file header.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object
=cut
sub write_header {
my ($self) = @_;
return 1;
}
=head2 write_footer
Title : write_footer
Usage : $asmio->write_footer($assembly)
Function: Write TIGR footer, i.e. do nothing except making sure that the
file does not end with a '|'.
Returns : 1 on success, 0 for error
Args : A Bio::Assembly::Scaffold object
=cut
sub write_footer {
my ($self) = @_;
# In this implementation, the TIGR file always ends with '|\n'. Remove it.
seek $self->_fh, -length("|\n"), 2;
$self->_print("\n\n");
return 1;
}
=head2 _perc_N
Title : _perc_N
Usage : my $perc_N = $asmio->_perc_N($sequence_string)
Function: Calculate the percent of ambiguities in a sequence.
M R W S Y K X N are regarded as ambiguities in an aligned read
sequence by TIGR Assembler. In the case of a gapped contig
consensus sequence, all lowercase symbols are ambiguities, i.e.:
a c g t u m r w s y k x n.
Returns : decimal number
Args : string
=cut
sub _perc_N {
my ($self, $seq_string) = @_;
$self->throw("Cannot accept an empty sequence") if length($seq_string) == 0;
my $perc_N = 0;
for my $base ( split //, $seq_string ) {
# individual base matches an ambiguity?
if (( $base =~ m/[x|n|m|r|w|s|y|k]/i ) || ( $base =~ m/[a|c|g|t|u]/ ) ) {
$perc_N++;
}
}
$perc_N = $perc_N * 100 / length $seq_string;
return $perc_N;
}
=head2 _redundancy
Title : _redundancy
Usage : my $ref = $asmio->_redundancy($contigobj)
Function: Calculate the fold coverage (redundancy) of a contig consensus
(average number of read base pairs covering the consensus)
Returns : decimal number
Args : Bio::Assembly::Contig
=cut
sub _redundancy {
# redundancy = (sum of all aligned read lengths - ( number of gaps in gapped
# consensus + number of gaps in aligned reads that are also in the consensus ) )
# / length of ungapped consensus
my ($self, $contigobj) = @_;
my $redundancy = 0;
# sum of all aligned read lengths
my $read_tot = 0;
for my $readobj ( $contigobj->each_seq ) {
my $read_length = length($readobj->seq);
$read_tot += $read_length;
}
$redundancy += $read_tot;
# - respected gaps
my $consensus_sequence = $contigobj->get_consensus_sequence->seq;
my @consensus_gaps = ();
$contigobj->_register_gaps($consensus_sequence, \@consensus_gaps);
my $respected_gaps = scalar(@consensus_gaps);
if ($respected_gaps > 0) {
my @cons_arr = split //, $consensus_sequence;
for my $gap_pos_cons ( @consensus_gaps ) {
for my $readobj ( $contigobj->each_seq ) {
my $readid = $readobj->id;
my $read_start = $contigobj->change_coord(
"aligned $readid", 'gapped consensus', $readobj->start);
my $read_end = $contigobj->change_coord(
"aligned $readid", 'gapped consensus', $readobj->end );
# skip this if consensus gap position not within in the read boundaries
next if ( ($gap_pos_cons < $read_start)
|| ($gap_pos_cons > $read_end) );
# does the read position have read have a gap?
my @read_arr = split //, $readobj->seq;
my $gap_pos_read = $contigobj->change_coord(
'gapped consensus', "aligned $readid", $gap_pos_cons);
if ($read_arr[$gap_pos_read-1] eq $cons_arr[$gap_pos_cons-1]) {
$respected_gaps++;
}
}
}
}
$redundancy -= $respected_gaps;
# / length of ungapped consensus
my $contig_length = length($self->_ungap($contigobj->get_consensus_sequence->seq));
$redundancy /= $contig_length;
return $redundancy;
}
=head2 _ungap
Title : _ungap
Usage : my $ungapped = $asmio->_ungap($gapped)
Function: Remove the gaps from a sequence. Gaps are - in TIGR Assembler
Returns : string
Args : string
=cut
sub _ungap {
my ($self, $seq_string) = @_;
$seq_string =~ s/-//g;
return $seq_string;
}
=head2 _date_time
Title : _date_time
Usage : my $timepoint = $asmio->date_time
Function: Get date and time (MM//DD/YY HH:MM:SS)
Returns : string
Args : none
=cut
sub _date_time {
my ($self) = @_;
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);
my $formatted_date_time =
sprintf('%02d', $mon+1).'/'.
sprintf('%02d', $mday).'/'.
sprintf('%02d', $year % 100).
' '.
sprintf('%02d', $hour).':'.
sprintf('%02d', $min).':'.
sprintf('%02d',$sec)
;
return $formatted_date_time;
}
=head2 _split_seq_name_and_db
Title : _split_seq_name_and_db
Usage : my ($seqname, $db) = $asmio->_split_seq_name_and_db($id)
Function: Extract seq_name and db from sequence id
Returns : seq_name, db
Args : id
=cut
sub _split_seq_name_and_db {
my ($self, $id) = @_;
my $seq_name = '';
my $db = '';
if ($id =~ m/(\S+)\|(\S+)/) {
$db = $1;
$seq_name = $2;
} else {
$seq_name = $id;
}
return ($seq_name, $db);
}
=head2 _merge_seq_name_and_db
Title : _merge_seq_name_and_db
Usage : my $id = $asmio->_merge_seq_name_and_db($seq_name, $db)
Function: Construct id from seq_name and db
Returns : id
Args : seq_name, db
=cut
sub _merge_seq_name_and_db {
my ($self, $seq_name, $db) = @_;
my $id = '';
if ($db) {
$id = $db.'|'.$seq_name;
} else {
$id = $seq_name;
}
return $id;
}
=head2 _coord
Title : _coord
Usage : my $id = $asmio->__coord($readobj, $contigobj)
Function: Get different coordinates for the read
Returns : number, number, number, number, number
Args : Bio::Assembly::Seq, Bio::Assembly::Contig
=cut
sub _coord {
my ($self, $readobj, $contigobj) = @_;
my ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset) = (0, 0, 0, 0, 0);
# Get read gapped consensus coordinates from contig and calculate
# asm_lend and asm_rend in ungapped consensus
my $aln_lend = $contigobj->get_seq_coord($readobj)->location->start;
my $aln_rend = $contigobj->get_seq_coord($readobj)->location->end;
$asm_lend = $contigobj->change_coord(
'gapped consensus', 'ungapped consensus', $aln_lend);
$asm_rend = $contigobj->change_coord(
'gapped consensus', 'ungapped consensus', $aln_rend);
# Get gapped consensus coordinates for quality-clipped reads from contig
# annotation and determine seq_lend and seq_rend in unaligned sequence coord
my ($readclip) = $contigobj->get_features_collection->get_features_by_type('_quality_clipping:'.$readobj->primary_id);
my $clip_lend = $readclip->location->start;
my $clip_rend = $readclip->location->end;
$seq_lend = $contigobj->change_coord(
'gapped consensus', 'aligned '.$readobj->id, $clip_lend);
$seq_rend = $contigobj->change_coord(
'gapped consensus', 'aligned '.$readobj->id, $clip_rend);
# Offset
$offset = $aln_lend - 1;
return ($asm_lend, $asm_rend, $seq_lend, $seq_rend, $offset);
}
1;
__END__
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