Bioperl adding tags to BAM aligned reads

[jonasZ]

Hi everybody,

I have a bam file and use bioperl (Bio:B::Sam) to work with it.
Now i wanted to ask if there is any possibility to add tags to alignments in this File?

i use

        
my $iterator     = $bam->features(-iterator => 1, -flags    => {M_UNMAPPED=>0});

while (my $align = $iterator->next_seq) { 
        ...
}

to loop through the aligned reads and I am searching for anthing like

$align->addTag(key=>value)

and i have one more question: is it possible to get the coverage of a segment using only the read start positions?

Thx
bye

[SES]

I'm not sure about the first question, but for coverage you can use Bio:B::Sam::Segment (ignore smilie)

 $segment = $sam->segment($seqid,$start,$end);

to get coverage for the whole region.

 # get coverage across this region
 my ($coverage)       = $segment->features('coverage');
 my @data_points      = $coverage->coverage;

From the above, it looks like all you would need is $data_points[0] to get coverage at the start positions. Is that what you need?
You may want to post this question to the bioperl list ([email protected]) if you don't find an answer on this forum. Someone will definitely help you there.

[jonasZ]

no, that's not what i meant. your code would give you the coverage of the startposition of one segment. What i want is the coverage of the whole segment considering only startpositions of the reads. That means each read is considered as it would have length 1.

[Fabien Campagne]

Adding optional attributes to Goby alignment entries

I am not sure about BAM alignments, but it is possible to add custom 'tags' to Goby alignment entries. You would simply do:

            final IterateAlignments iterator = new IterateAlignments() {

                public void processAlignmentEntry(final AlignmentReader alignmentReader, final Alignments.AlignmentEntry alignmentEntry) {

                    int tagValue =???

                    final Alignments.AlignmentEntry revisedEntry = Alignments.AlignmentEntry.newBuilder()
                            .mergeFrom(alignmentEntry).setMyTagValue(tagValue).build();

                    // do something with  revisedEntry
                }
            };
            final String[] basenames = {"input1.entries", "input2.entries"};

            iterator.parseIncludeReferenceArgument("1,2,X");
            iterator.iterate(basenames);

This assumes the attribute MyTagValue/my_tag_value has been defined on the alignment entry. You can simply

1. add an optional tag attribute to the protobuff schema definition file (see goby/protobuf/Alignments.proto in the the Goby source code distribution), such as:

optional int32 my_tag_value=1001;

2. run protobuf/gensrc.sh to update the code to the new schema and you are ready to go. When defining pipeline specific attributes, please make the attributes optional and give attribute keys larger than 1000 (1001 in the example above).

3. Create a new AlignmentEntry builder (revisedEntry), initialize it with values from alignmentEntry (calling mergeFrom), then set any new attributes as needed on revisedEntry. The call to build instructs the builder we are done making changes and returns a read-only alignment entry, which can be written to file, for instance or processed in some other way.

[jonasZ]

hmm but that's java...

as I said i am using bioperl and bam files....
thx for your help, but that doesn't help me that much :-\