NAME

Stockholm.pm

SYNOPSIS

Lightweight Perl module encapsulating a Stockholm multiple alignment.

Author: Ian Holmes with minor modifications by Christopher Bottoms

(This is modified from the original Stockholm.pm from the DART suite, see https://github.com/ihh/dart/blob/master/perl/Stockholm.pm. Modifications allowed for passing a generic consensus annotation to the constructor.)

For more detail on Stockholm format itself, see the following URL:

http://biowiki.org/StockholmFormat

METHODS

new

my $stock = Stockholm->new();

Creates an empty Stockholm object.

from_file

my $stock = Stockholm->from_file ($filename);

Creates a new Stockholm object and reads it from a file.

from_filehandle

my $stock = Stockholm->from_filehandle ($filehandle);

Creates a new Stockholm object and reads it from a filehandle.

to_file

$stock->to_file ($filename);

Writes a Stockholm object to a file.

to_string

print $stock->to_string ($maxcols)
print $stock->to_string ($maxcols, ARG1=>VAL1, ARG2=>VAL2 ...)
print $stock->to_string (MAXCOLS=>$maxcols, ARG1=>VAL1, ARG2=>VAL2 ...)

Returns the object as a Stockholm-formatted string.

ARGs can include... MAXCOLS -- limit maximum number of columns (can also be specified as a single scalar arg) NOSEQDATA -- don\'t print any sequence data (can be used this to compress output)

copy

my $newStock = $stock->copy();

Does a deep-copy, duplicating all information.

columns

my $cols = $stock->columns()

Returns the number of columns in this alignment.

sequences

my $rows = $stock->sequences()

Returns the number of sequences (i.e. rows) in this alignment.

seqname

my $rowName = $stock->seqname->[$rowIndex];

Returns a reference to an array of sequence names.

seqdata

my $row = $stock->seqdata->{$rowName};

Returns a reference to a hash of alignment rows, keyed by sequence name.

gf

my @gf = @{$stock->gf->{FEATURE}};
my @gf = @{$stock->gf_FEATURE};

Returns a reference to an array of all the lines beginning '#=GF FEATURE ...'

gc

my $gc = $stock->gc->{FEATURE};
my $gc = $stock->gc_FEATURE;

Returns the line beginning '#=GC FEATURE ...'

gs

my @gs = @{$stock->gs->{FEATURE}->{SEQNAME}};
my @gs = @{$stock->gs_FEATURE->{SEQNAME}};

Returns a reference to an array of all the lines beginning '#=GS SEQNAME FEATURE ...'

gr

my $gr = $stock->gr->{FEATURE}->{SEQNAME};
my $gr = $stock->gr_FEATURE->{SEQNAME};

Returns the line beginning '#=GR SEQNAME FEATURE ...'

add_gf

$stock->add_gf (FEATURE, $line)
$stock->add_gf (FEATURE, $line1, $line2, ...)
$stock->add_gf (FEATURE, @lines)
$stock->add_gf (FEATURE, "$line1\n$line2\n$...")

Add '#=GF FEATURE' annotation, preserving the order of the '#=GF' lines (damn those crazy context-sensitive Stockholm semantics!)

Each list entry gets printed on its own line.

set_gf

$stock->set_gf (FEATURE, $line)
$stock->set_gf (FEATURE, $line1, $line2, ...)
$stock->set_gf (FEATURE, @lines)
$stock->set_gf (FEATURE, "$line1\n$line2\n$...")

Set a '#=GF FEATURE ...' annotation. The difference between this and 'add_gf' is that here, if this sequence and feature have an annotation already, it will be overwritten instead of appended to.

As with add_gf, each list entry gets printed on its own line.

get_gf

my $gf = $stock->get_gf (FEATURE)

Concatenates and returns all lines beginning '#=GF FEATURE ...'

add_gs

$stock->add_gs (SEQNAME, FEATURE, $line)
$stock->add_gs (SEQNAME, FEATURE, $line1, $line2, ...)
$stock->add_gs (SEQNAME, FEATURE, @lines)
$stock->add_gs (SEQNAME, FEATURE, "$line1\n$line2\n$...")

Add a GS annotation: '#=GS SEQNAME FEATURE ...'

If such a line already exists for this sequence and feature, append to it.

Each list entry gets printed on its own line.

set_gs

$stock->set_gs (SEQNAME, FEATURE, $line)
$stock->set_gs (SEQNAME, FEATURE, $line1, $line2, ...)
$stock->set_gs (SEQNAME, FEATURE, @lines)
$stock->set_gs (SEQNAME, FEATURE, "$line1\n$line2\n$...")

Set a GS annotation: '#=GS SEQNAME FEATURE ...'

The difference between this and 'add_gs' is that here, if this sequence and feature have an annotation already, it will be overwritten instead of appended to.

Each list entry gets printed on its own line.

get_gs

my $gs = $stock->get_gs (SEQNAME, FEATURE)

Concatenates and returns all lines beginning '#=GS SEQNAME FEATURE ...'

drop_columns

my $success = $stock->drop_columns (@columns)

Drops a set of columns from the alignment and the GC and GR annotations. Note that this may break annotations where the column annotations are not independent (e.g. you might drop one base in an RNA base pair, but not the other). The caller is responsible for making sure the set of columns passed in does not mess up the annoation.

Arguments: a list of scalar, zero-based column indices to drop.

Returns success of operation (1 for success, 0 for failure)

empty

my $isEmpty = $stock->empty

Returns true if the alignment is empty (i.e. there are no sequences).

subseq

my $subseq = $stock->subseq (SEQNAME, $startPos)
my $subseq = $stock->subseq (SEQNAME, $startPos, $length)

Returns a subsequence of the named alignment row.

Note that the co-ordinates are with respect to the alignment columns (starting at zero), NOT sequence positions. That is, gaps are counted.

If $length is omitted, this call returns the subsequence from $startPos to the end of the row.

get_column

my $column = $stock->get_column ($colNum)

Extracts the specified column and returns it as a string.

The column number $colNum uses zero-based indexing.

map_align_to_seq_coords

my ($start, $end) = $stock->map_align_to_seq_coords ($colStart, $colEnd, $seqName);
die "Failed" unless defined ($start);

my ($start, $end) = $stock->map_align_to_seq_coords ($colStart, $colEnd, $seqName, $seqStart);
die "Failed" unless defined ($start);

Given a range of column indices ($colStart, $colEnd), returns the coordinates of sequence $seqName contained within that range, accounting for gaps.

Returns start and end coordinates as a 2-ple list, or returns the empty list if there is no sequence in the given range (i.e. range contains all gaps in $seqName).

You can provide $seqStart, which is the coordinate of the first non-gap character in $seqName. If you don\'t, the default is that the sequence starts at 1.

is_gap

my $isGap = $stock->is_gap (SEQNAME, $colNum)

Return true if a given (SEQNAME,column) co-ordinate is a gap.

subalign

my $substock = $stock->subalign ($start, $len)
my $substock = $stock->subalign ($start, $len, $strand)

Returns a Stockholm object representing a sub-alignment of the current alignment, starting at column $start (zero-based) and containing $len columns.

If $strand is supplied and is equal to '-', then the sub-alignment will be reverse-complemented.

concatenate

$stock->concatenate ($stock2)

Concatenates another alignment onto the end of this one.

is_flush

my $flush = $stock->is_flush()

Returns true if the alignment is "flush", i.e. all sequence and annotation lines have the same length.

add_row

my $new_row_index = $stock->add_row ($seqname, $rowdata);

Adds a new row to a Stockholm alignment.

Copyright (C) 1989, 1991 Free Software Foundation, Inc.
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cpanm Bio::App::SELEX::RNAmotifAnalysis

perl -MCPAN -e shell
install Bio::App::SELEX::RNAmotifAnalysis