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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::BaseAlignFeature - Baseclass providing a common abstract implementation for alignment features
SYNOPSIS
my $feat = new Bio::EnsEMBL::DnaPepAlignFeature(
-slice => $slice,
-start => 100,
-end => 120,
-strand => 1,
-hseqname => 'SP:RF1231',
-hstart => 200,
-hend => 220,
-analysis => $analysis,
-cigar_string => '10M3D5M2I',
-align_type => 'ensembl'
);
where $analysis is a Bio::EnsEMBL::Analysis object.
Alternatively if you have an array of ungapped features:
my $feat =
new Bio::EnsEMBL::DnaPepAlignFeature( -features => \@features );
where @features is an array of Bio::EnsEMBL::FeaturePair objects.
There is a method to (re)create ungapped features from the cigar_string:
my @ungapped_features = $feat->ungapped_features();
where @ungapped_features is an array of Bio::EnsEMBL::FeaturePair's.
Bio::EnsEMBL::BaseAlignFeature inherits from:
Bio::EnsEMBL::FeaturePair, which in turn inherits from:
Bio::EnsEMBL::Feature,
thus methods from both parent classes are available.
The cigar_string is a condensed representation of the matches and gaps
which make up the gapped alignment (where CIGAR stands for
Concise Idiosyncratic Gapped Alignment Report).
CIGAR format is: n <matches> [ x <deletes or inserts> m <matches> ]*
where M = match, D = delete, I = insert; n, m are match lengths;
x is delete or insert length.
Spaces are omitted, thus: "23M4I12M2D1M"
as are counts for any lengths of 1, thus 1M becomes M: "23M4I12M2DM"
To make things clearer this is how a blast HSP would be parsed:
>AK014066
Length = 146
Minus Strand HSPs:
Score = 76 (26.8 bits), Expect = 1.4, P = 0.74
Identities = 20/71 (28%), Positives = 29/71 (40%), Frame = -1
Query: 479 GLQAPPPTPQGCRLIPPPPLGLQAPLPTLRAVGSSHHHP*GRQGSSLSSFRSSLASKASA 300
G APPP PQG R P P G + P L + + ++ R +A +
Sbjct: 7 GALAPPPAPQG-RWAFPRPTG-KRPATPLHGTARQDRQVRRSEAAKVTGCRGRVAPHVAP 64
Query: 299 SSPHNPSPLPS 267
H P+P P+
Sbjct: 65 PLTHTPTPTPT 75
The alignment goes from 479 down to 267 in the query sequence on the reverse
strand, and from 7 to 75 in the subject sequence.
The alignment is made up of the following ungapped pieces:
query_seq start 447 , sbjct_seq hstart 7 , match length 33 , strand -1
query_seq start 417 , sbjct_seq hstart 18 , match length 27 , strand -1
query_seq start 267 , sbjct_seq hstart 27 , match length 147 , strand -1
When assembled into a DnaPepAlignFeature where:
(seqname, start, end, strand) refer to the query sequence,
(hseqname, hstart, hend, hstrand) refer to the subject sequence,
these ungapped pieces are represented by the cigar string:
33M3I27M3I147M
with start 267, end 479, strand -1, and hstart 7, hend 75, hstrand 1.CAVEATS
AlignFeature cigar strings have the opposite 'sense'
('D' and 'I' swapped) compared with Exonerate cigar strings.
Exonerate modules in Bio::EnsEMBL::Analysis use this convention:
The longer genomic sequence specified by:
exonerate: target
AlignFeature: (sequence, start, end, strand)
A shorter sequence (such as EST or protein) specified by:
exonerate: query
AlignFeature: (hsequence, hstart, hend, hstrand)
The resulting AlignFeature cigar strings have 'D' and 'I'
swapped compared with the Exonerate output, i.e.:
exonerate: M 123 D 1 M 11 I 1 M 39
AlignFeature: 123MI11MD39MMETHODS
new
Arg [..] : List of named arguments. (-cigar_string , -features, -align_type) defined
in this constructor, others defined in FeaturePair and
SeqFeature superclasses. Either cigar_string or a list
of ungapped features should be provided - not both.
Example : $baf = new BaseAlignFeatureSubclass(-cigar_string => '3M3I12M', -align_type => 'ensembl');
Description: Creates a new BaseAlignFeature using either a cigar string or
a list of ungapped features. BaseAlignFeature is an abstract
baseclass and should not actually be instantiated - rather its
subclasses should be.
Returntype : Bio::EnsEMBL::BaseAlignFeature
Exceptions : thrown if both feature and cigar string args are provided
thrown if neither feature nor cigar string args are provided
warn if cigar string is provided without cigar type
Caller : general
Status : Stablecigar_string
Arg [1] : string $cigar_string
Example : $feature->cigar_string( "12MI3M" );
Description: get/set for attribute cigar_string.
cigar_string describes the alignment:
"xM" stands for x matches (or mismatches),
"xI" for x inserts into the query sequence,
"xD" for x deletions from the query sequence
where the query sequence is specified by (seqname, start, ...)
and the subject sequence by (hseqname, hstart, ...).
An "x" that is 1 can be omitted.
See the SYNOPSIS for an example.
Returntype : string
Exceptions : none
Caller : general
Status : Stablealign_type
Arg [1] : type $align_type
Example : $feature->align_type( "ensembl" );
Description: get/set for attribute align_type.
align_type specifies which cigar string
is used to describe the alignment:
The default is 'ensembl'
Returntype : string
Exceptions : none
Caller : general
Status : Stablealignment_length
Arg [1] : None
Description: return the alignment length (including indels) based on the alignment_type ('ensembl', 'mdtag')
Returntype : int
Exceptions :
Caller :
Status : Stable_ensembl_cigar_alignment_length
Arg [1] : None
Description: return the alignment length (including indels) based on the cigar_string
Returntype : int
Exceptions :
Caller :
Status : Stableungapped_features
Args : none
Example : @ungapped_features = $align_feature->get_feature
Description: converts the internal cigar_string into an array of
ungapped feature pairs
Returntype : list of Bio::EnsEMBL::FeaturePair
Exceptions : cigar_string not set internally
Caller : general
Status : Stablestrands_reversed
Arg [1] : int $strands_reversed
Description: get/set for attribute strands_reversed
0 means that strand and hstrand are the original strands obtained
from the alignment program used
1 means that strand and hstrand have been flipped as compared to
the original result provided by the alignment program used.
You may want to use the reverse_complement method to restore the
original strandness.
Returntype : int
Exceptions : none
Caller : general
Status : Stable
reverse_complement
Args : none
Description: reverse complement the FeaturePair based on the cigar type
modifing strand, hstrand and cigar_string in consequence
Returntype : none
Exceptions : none
Caller : general
Status : Stable_ensembl_reverse_complement
Args : none
Description: reverse complement the FeaturePair for ensembl cigar string,
modifing strand, hstrand and cigar_string in consequence
Returntype : none
Exceptions : none
Caller : general
Status : Stabletransform
Arg 1 : String $coordinate_system_name
Arg [2] : String $coordinate_system_version
Example : $feature = $feature->transform('contig');
$feature = $feature->transform('chromosome', 'NCBI33');
Description: Moves this AlignFeature to the given coordinate system.
If the feature cannot be transformed to the destination
coordinate system undef is returned instead.
Returntype : Bio::EnsEMBL::BaseAlignFeature;
Exceptions : wrong parameters
Caller : general
Status : Medium Risk_parse_ensembl_cigar
Args : none
Description: PRIVATE (internal) method - creates ungapped features from
internally stored cigar line in ensembl format
Returntype : list of Bio::EnsEMBL::FeaturePair
Exceptions : none
Caller : ungapped_features
Status : Stable_parse_features
Arg [1] : listref Bio::EnsEMBL::FeaturePair $ungapped_features
Description: creates internal cigar_string and start,end hstart,hend
entries.
Returntype : none, fills in values of self
Exceptions : argument list undergoes many sanity checks - throws under many
invalid conditions
Caller : new
Status : Stable_hit_unit
Args : none
Description: abstract method, overwrite with something that returns
one or three
Returntype : int 1,3
Exceptions : none
Caller : internal
Status : Stable_query_unit
Args : none
Description: abstract method, overwrite with something that returns
one or three
Returntype : int 1,3
Exceptions : none
Caller : internal
Status : Stable_mdtag_alignment_length
Arg [1] : None
Description: return the alignment length (including indels) based on the mdtag (mdz) string
Returntype : int
Exceptions : none
Caller : internal
Status : Stable_get_mdz_chunks
Arg [1] : mdtag string - MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer: SAM/BAM specification)
Description: parses the mdtag string and group it according the type
eg: MD:Z:35^VIVALE31^GRPLIQPRRKKAYQLEHTFQGLLGKRSLFTE10 returns ['35', '^', 'VIVALE', '31', '^', 'GRPLIQPRRKKAYQLEHTFQGLLGKRSLFTE', '10']
Returntype : array of strings
Exceptions : none
Caller : internal
Status : Stable_get_mdz_alignment_length
Arg [1] : array of strings
Description: calculate the alignment length from the given chunks
Returntype : array of strings
Exceptions : none
Caller : internal
Status : Stable_get_mdz_chunk_type
Arg [1] : char
Description: get the chunk type
Returntype : string
Exceptions : none
Caller : internal
Status : Stable_mdz_alignment_string
Arg [1] : input sequence
Arg [2] : MD Z String for mismatching positions. Regex : [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)* (Refer: SAM/BAM specification)
eg: MD:Z:96^RHKTDSFVGLMGKRALNS0V14
Example : $pf->alignment_strings
Description: Allows to rebuild the alignment string of both the seq and hseq sequence
Returntype : array reference containing 2 strings
the first corresponds to seq
the second corresponds to hseq
Exceptions : none
Caller : general
Status : Stable