The rest of the documentation details each of the object methods. Internal methods are usually preceded
with a _
new()
Title : new(-acefile => $path_to_some_acefile, -verbose => "1")
Usage : $o_consed = Bio::Tools::Alignment::Consed->
new(-acefile => $path_to_some_acefile, -verbose => "1");
Function: Construct the Bio::Tools::Alignment::Consed object. Sets
verbosity for the following procedures, if necessary:
1. Construct a new Bio::Tools::Alignment::Trim object, to
handle quality trimming 2. Read in the acefile and parse it
Returns : A reference to a Bio::Tools::Alignment::Consed object.
Args : A hash. (-acefile) is the filename of an acefile. If a full path
is not specified "./" is prepended to the filename and used from
instantiation until destruction. If you want
Bio::Tools::Alignment::Consed to be noisy during parsing of
the acefile, specify some value for (-verbose).
set_verbose()
Title : set_verbose()
Usage : $o_consed->set_verbose(1);
Function: Set the verbosity level for debugging messages. On instantiation
of the Bio::Tools::Alignment::Consed object the verbosity level
is set to 0 (quiet).
Returns : 1 or 0.
Args : The verbosity levels are:
0 - quiet
1 - noisy
2 - noisier
3 - annoyingly noisy
This method for setting verbosity has largely been superseded by a sub-by-sub way, where for every sub
you can provide a (-verbose) switch. I am doing converting this bit-by-bit so do not be surprised if some
subs do not honour this.
get_filename()
Title : get_filename()
Usage : $o_consed->get_filename();
Function: Returns the name of the acefile being used by the
Bio::Tools::Alignment::Consed object.
Returns : A scalar containing the name of a file.
Args : None.
count_sequences_with_grep()
Title : count_sequences_with_grep()
Usage : $o_consed->count_sequences_with_grep();
Function: Use /bin/grep to scan through the files in the ace project dir
and count sequences in those files. I used this method in the
development of this module to verify that I was getting all of the
sequences. It works, but it is (I think) unix-like platform
dependent.
Returns : A scalar containing the number of sequences in the ace project
directory.
Args : None.
If you are on a non-UNIX platform, you really do not have to use this. It is more of a debugging routine
designed to address very specific problems.
This method was reimplemented to be platform independent with a pure perl implementation. The above note
can be ignored.
get_path()
Title : get_path()
Usage : $o_consed->get_path();
Function: Returns the path to the acefile this object is working with.
Returns : Scalar. The path to the working acefile.
Args : None.
get_contigs()
Title : get_contigs()
Usage : $o_consed->get_contigs();
Function: Return the keys to the Bio::Tools::Alignment::Consed object.
Returns : An array containing the keynames in the
Bio::Tools::Alignment::Consed object.
Args : None.
This would normally be used to get the keynames for some sort of iterator. These keys are worthless in
general day-to-day use because in the Consed acefile they are simply Contig1, Contig2, ...
get_class($contig_keyname)
Title : get_class($contig_keyname)
Usage : $o_consed->get_class($contig_keyname);
Function: Return the class name for this contig
Returns : A scalar representing the class of this contig.
Args : None.
Notes :
get_quality_array($contig_keyname)
Title : get_quality_array($contig_keyname)
Usage : $o_consed->get_quality_array($contig_keyname);
Function: Returns the quality for the consensus sequence for the given
contig as an array. See get_quality_scalar to get this as a scalar.
Returns : An array containing the quality for the consensus sequence with
the given keyname.
Args : The keyname of a contig. Note: This is a keyname. The key would
normally come from get_contigs.
Returns an array, not a reference. Is this a bug? thinking No. Well, maybe. Why was this developed like
this? I was using FreezeThaw for object persistence, and when it froze out these arrays it took a long
time to thaw it. Much better as a scalar.
See get_quality_scalar()get_quality_scalar($contig_keyname)
Title : get_quality_scalar($contig_keyname)
Usage : $o_consed->get_quality_scalar($contig_keyname);
Function: Returns the quality for the consensus sequence for the given
contig as a scalar. See get_quality_array to get this as an array.
Returns : An scalar containing the quality for the consensus sequence with
the given keyname.
Args : The keyname of a contig. Note this is a _keyname_. The key would
normally come from get_contigs.
Why was this developed like this? I was using FreezeThaw for object persistence, and when it froze out
these arrays it took a coon's age to thaw it. Much better as a scalar.
See get_quality_array()freeze_hash()
Title : freeze_hash()
Usage : $o_consed->freeze_hash();
Function: Use Ilya's FreezeThaw module to create a persistent data
object for this Bio::Tools::Alignment::Consed data
structure. In the case of AAFC, we use
Bio::Tools::Alignment::Consed to pre-process bunches of
sequences, freeze the structures, and send in a harvesting
robot later to do database stuff.
Returns : 0 or 1;
Args : None.
This procedure was removed so Consed.pm won't require FreezeThaw.
get_members($contig_keyname)
Title : get_members($contig_keyname)
Usage : $o_consed->get_members($contig_keyname);
Function: Return the _names_ of the reads in this contig.
Returns : An array containing the names of the reads in this contig.
Args : The keyname of a contig. Note this is a keyname. The keyname
would normally come from get_contigs.
See get_contigs()get_members_by_name($some_arbitrary_name)
Title : get_members_by_name($some_arbitrary_name)
Usage : $o_consed->get_members_by_name($some_arbitrary_name);
Function: Return the names of the reads in a contig. This is the name given
to $contig{key} based on what is in the contig. This is different
from the keys retrieved through get_contigs().
Returns : An array containing the names of the reads in the contig with this
name.
Args : The name of a contig. Not a key, but a name.
Highly inefficient. use some other method if possible. See get_contigs()get_contig_number_by_name($some_arbitrary_name)
Title : get_contig_number_by_name($some_arbitrary_name)
Usage : $o_consed->get_contig_number_by_name($some_arbitrary_name);
Function: Return the names of the reads in a contig. This is the name given
to $contig{key} based on what is in the contig. This is different
from the keys retrieved through get_contigs().
Returns : An array containing the names of the reads in the contig with this
name.
Args : The name of a contig. Not a key, but a name.
See get_contigs()get_sequence($contig_keyname)
Title : get_sequence($contig_keyname)
Usage : $o_consed->get_sequence($contig_keyname);
Function: Returns the consensus sequence for a given contig.
Returns : A scalar containing a sequence.
Args : The keyname of a contig. Note this is a key. The key would
normally come from get_contigs.
See get_contigs()set_final_sequence($some_sequence)
Title : set_final_sequence($name,$some_sequence)
Usage : $o_consed->set_final_sequence($name,$some_sequence);
Function: Provides a manual way to set the sequence for a given key in the
contig hash. Rarely used.
Returns : 0 or 1;
Args : The name (not the keyname) of a contig and an arbitrary string.
A method with a questionable and somewhat mysterious origin. May raise the dead or something like that.
_read_file()
Title : _read_file();
Usage : _read_file();
Function: An internal subroutine used to read in an acefile and parse it
into a Bio::Tools::Alignment::Consed object.
Returns : 0 or 1.
Args : Nothing.
This routine creates and saves the filhandle for reading the files in {fh}
set_reverse_designator($some_string)
Title : set_reverse_designator($some_string)
Usage : $o_consed->set_reverse_designator($some_string);
Function: Set the designator for the reverse read of contigs in this
Bio::Tools::Alignment::Consed object. Used to determine if
contigs containing two reads can be named.
Returns : The value of $o_consed->{reverse_designator} so you can check
to see that it was set properly.
Args : An arbitrary string.
May be useful only to me. shrugset_forward_designator($some_string)
Title : set_forward_designator($some_string)
Usage : $o_consed->set_forward_designator($some_string);
Function: Set the designator for the forward read of contigs in this
Bio::Tools::Alignment::Consed object. Used to determine if
contigs containing two reads can be named.
Returns : The value of $o_consed->{forward_designator} so you can check
to see that it was set properly.
Args : An arbitrary string.
May be useful only to me. shrugset_designator_ignore_case("yes")
Title : set_designator_ignore_case("yes")
Usage : $o_consed->set_designator_ignore_case("yes");
Function: Deprecated.
Returns : Deprecated.
Args : Deprecated.
Deprecated. Really. Trust me.
set_trim_points_singlets_and_singletons()
Title : set_trim_points_singlets_and_singletons()
Usage : $o_consed->set_trim_points_singlets_and_singletons();
Function: Set the trim points for singlets and singletons based on
quality. Uses the Bio::Tools::Alignment::Trim object. Use
at your own risk because the Bio::Tools::Alignment::Trim
object was designed specifically for me and is mysterious
in its ways. Every time somebody other then me uses it a
swarm of locusts decends on a small Central American
village so do not say you weren't warned.
Returns : Nothing.
Args : None.
Working on exceptions and warnings here.
See Bio::Tools::Alignment::Trim for more information
set_trim_points_doublets()
Title : set_trim_points_doublets()
Usage : $o_consed->set_trim_points_doublets();
Function: Set the trim points for doublets based on quality. Uses the
Bio::Tools::Alignment::Trim object. Use at your own risk because
the Bio::Tools::Alignment::Trim object was designed specifically
for me and is mysterious in its ways. Every time somebody other
then me uses it you risk a biblical plague being loosed on your
city.
Returns : Nothing.
Args : None.
Notes : Working on exceptions here.
See Bio::Tools::Alignment::Trim for more information
get_trimmed_sequence_by_name($name)
Title : get_trimmed_sequence_by_name($name)
Usage : $o_consed->get_trimmed_sequence_by_name($name);
Function: Returns the trimmed_sequence of a contig with {name} eq $name.
Returns : A scalar- the trimmed sequence.
Args : The {name} of a contig.
Notes :
set_dash_present_in_sequence_name("yes")
Title : set_dash_present_in_sequence_name("yes")
Usage : $o_consed->set_dash_present_in_sequence_name("yes");
Function: Deprecated. Part of an uncompleted thought. ("Oooh! Shiny!")
Returns : Nothing.
Args : "yes" to set {dash_present_in_sequence_name} to 1
Notes :
set_doublets()
Title : set_doublets()
Usage : $o_consed->set_doublets();
Function: Find pairs that have similar names and mark them as doublets
and set the {name}.
Returns : 0 or 1.
Args : None.
A complicated subroutine that iterates over the Bio::Tools::Alignment::Consed looking for contigs of 2.
If the forward and reverse designator are removed from each of the reads in {'member_array'} and the
remaining reads are the same, {name} is set to that name and the contig's class is set as "doublet". If
any of those cases fail the contig is marked as a "pair".
set_singlets
Title : set_singlets
Usage : $o_consed->set_singlets();
Function: Read in a singlets file and place them into the
Bio::Tools::Alignment::Consed object.
Returns : Nothing.
Args : A scalar to turn on verbose parsing of the singlets file.
Notes :
get_singlets()
Title : get_singlets()
Usage : $o_consed->get_singlets();
Function: Return the keynames of the singlets.
Returns : An array containing the keynames of all
Bio::Tools::Alignment::Consed sequences in the class "singlet".
Args : None.
Notes :
set_quality_by_name($name,$quality)
Title : set_quality_by_name($name,$quality)
Usage : $o_consed->set_quality_by_name($name,$quality);
Function: Deprecated. Make the contig with {name} have {'quality'} $quality.
Probably used for testing.
Returns : Nothing.
Args : The name of a contig and a scalar for its quality.
Notes : Deprecated.
set_singlet_quality()
Title : set_singlet_quality()
Usage : $o_consed->set_singlet_quality();
Function: For each singlet, go to the appropriate file in phd_dir and read
in the phred quality for that read and place it into {'quality'}
Returns : 0 or 1.
Args : None.
Notes : This is the next subroutine that will receive substantial revision
in the next little while. It really should eval the creation of
Bio::Tools::Alignment::Phred objects and go from there.
set_contig_quality()
Title : set_contig_quality()
Usage : $o_consed->set_contig_quality();
Function: Deprecated.
Returns : Deprecated.
Args : Deprecated.
Notes : Deprecated. Really. Trust me.
get_multiplets()
Title : get_multiplets()
Usage : $o_consed->get_multiplets();
Function: Return the keynames of the multiplets.
Returns : Returns an array containing the keynames of all
Bio::Tools::Alignment::Consed sequences in the class "multiplet".
Args : None.
Notes :
get_all_members()
Title : get_all_members()
Usage : @all_members = $o_consed->get_all_members();
Function: Return a list of all of the read names in the
Bio::Tools::Alignment::Consed object.
Returns : An array containing all of the elements in all of the
{'member_array'}s.
Args : None.
Notes :
sum_lets($total_only)
Title : sum_lets($total_only)
Usage : $statistics = $o_consed->sum_lets($total_only);
Function: Provide numbers for how many sequences were accounted for in the
Bio::Tools::Alignment::Consed object.
Returns : If a scalar is present, returns the total number of
sequences accounted for in all classes. If no scalar passed
then returns a string that looks like this:
Singt/singn/doub/pair/mult/total : 2,0,1(2),0(0),0(0),4
This example means the following: There were 1 singlets.
There were 0 singletons. There were 1 doublets for a total
of 2 sequences in this class. There were 0 pairs for a
total of 0 sequences in this class. There were 0
multiplets for a total of 0 sequences in this class. There
were a total of 4 sequences accounted for in the
Bio::Tools::Alignment::Consed object.
Args : A scalar is optional to change the way the numbers are returned.
Notes:
write_stats()
Title : write_stats()
Usage : $o_consed->write_stats();
Function: Write a file called "statistics" containing numbers similar to
those provided in sum_lets().
Returns : Nothing. Write a file in $o_consed->{path} containing something
like this:
0,0,50(100),0(0),0(0),100
Where the numbers provided are in the format described in the
documentation for sum_lets().
Args : None.
Notes : This might break platform independence, I do not know.
See sum_lets()get_singletons()
Title : get_singletons()
Usage : @singletons = $o_consed->get_singletons();
Function: Return the keynames of the singletons.
Returns : Returns an array containing the keynames of all
Bio::Tools::Alignment::Consed sequences in the class "singleton".
Args : None.
Notes :
get_pairs()
Title : get_pairs()
Usage : @pairs = $o_consed->get_pairs();
Function: Return the keynames of the pairs.
Returns : Returns an array containing the keynames of all
Bio::Tools::Alignment::Consed sequences in the class "pair".
Args : None.
Notes :
get_name($contig_keyname)
Title : get_name($contig_keyname)
Usage : $name = $o_consed->get_name($contig_keyname);
Function: Return the {name} for $contig_keyname.
Returns : A string. ({name})
Args : A contig keyname.
Notes :
_get_contig_name(\@array_containing_reads)
Title : _get_contig_name(\@array_containing_reads)
Usage : $o_consed->_get_contig_name(\@array_containing_reads);
Function: The logic for the set_doublets subroutine.
Returns : The name for this contig.
Args : A reference to an array containing read names.
Notes : Depends on reverse_designator. Be sure this is set the way you
intend.
get_doublets()
Title : get_doublets()
Usage : @doublets = $o_consed->get_doublets();
Function: Return the keynames of the doublets.
Returns : Returns an array containing the keynames of all
Bio::Tools::Alignment::Consed sequences in the class "doublet".
Args : None.
Notes :
dump_hash()
Title : dump_hash()
Usage : $o_consed->dump_hash();
Function: Use dumpvar.pl to dump out the Bio::Tools::Alignment::Consed
object to STDOUT.
Returns : Nothing.
Args : None.
Notes : I used this a lot in debugging.
dump_hash_compact()
Title : dump_hash_compact()
Usage : $o_consed->dump_hash_compact();
Function: Dump out the Bio::Tools::Alignment::Consed object in a compact way.
Returns : Nothing.
Args : Nothing.
Notes : Cleaner then dumpValue(), dumpHash(). I used this a lot in
debugging.
get_phreds()
Title : get_phreds()
Usage : @phreds = $o_consed->get_phreds();
Function: For each doublet in the Bio::Tools::Alignment::Consed hash, go
and get the phreds for the top and bottom reads. Place them into
{top_phreds} and {bottom_phreds}.
Returns : Nothing.
Args : Nothing.
Requires parse_phd() and reverse_and_complement(). I realize that it would be much more elegant to pull
qualities as required but there were certain "features" in the acefile that required a bit more detailed
work be done to get the qualities for certain parts of the consensus sequence. In order to make _sure_
that this was done properly I wrote things to do all steps and then I used dump_hash() and checked each
one to ensure expected behavior. I have never changed this, so there you are.
parse_phd($read_name)
Title : parse_phd($read_name)
Usage : $o_consed->parse_phd($read_name);
Function: Suck in the contents of a .phd file.
Returns : A reference to an array containing the quality values for the read.
Args : The name of a read.
Notes : This is a significantly weak subroutine because it was always
intended that these functions, along with the functions provided by
get_phreds() be put into the Bio::SeqIO:phd module. This is done
now but the Bio::Tools::Alignment::Consed module has not be
rewritten to reflect this change.
See Bio::SeqIO::phd for more information.
reverse_and_complement(\@source)
Title : reverse_and_complement(\@source)
Usage : $reference_to_array = $o_consed->reverse_and_complement(\@source);
Function: A stub for the recursive routine reverse_recurse().
Returns : A reference to a reversed and complemented array of phred data.
Args : A reference to an array of phred data.
Notes :
reverse_recurse($r_source,$r_destination)
Title : reverse_recurse(\@source,\@destination)
Usage : $o_consed->reverse_recurse(\@source,\@destination);
Function: A recursive routine to reverse and complement an array of
phred data.
Returns : A reference to an array containing reversed phred data.
Args : A reference to a source array and a reverence to a destination
array.
Recursion is kewl, but this sub should likely be _reverse_recurse.
show_missing_sequence()
Title : show_missing_sequence();
Usage : $o_consed->show_missing_sequence();
Function: Used by set_trim_points_doublets() to fill in quality values where
consed (phrap?) set them to 0 at the beginning and/or end of the
consensus sequences.
Returns : Nothing.
Args : None.
Acts on doublets only. Really very somewhat quite ugly. A disgusting kludge. insertpridehere It was
written stepwise with no real plan because it was not really evident why consed (phrap?) was doing this.
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