fangly / amplicopyrighter Goto Github PK

Hi Florent,

We are using the program with an input OTU table containing OTUs at a higher taxonomic rank, e.g 'Root; k__Bacteria; p__Planctomycetes; c__Phycisphaerae; o__Phycisphaerales' (order level).

The Copyrighter program seems currently to not recognise these assignments and gives these a community average GCN value, as evidenced by log messages such as:

Member 'Root; k__Bacteria; p__Planctomycetes; c__Phycisphaerae; o__Phycisphaerales' (ID bc989) got average 16S rRNA count from community '20120800_E3D': 3.32331146069422

What would be nice is if the program used a GCN estimate at the corresponding taxonomic rank. My impression from Figure 1 from the Microbiome paper is that these values have been calculated?

Thanks,
Tim

Error after executing

copyrighter -i otu_table.biom -o copyrighted_otu.biom

Reading input file 'otu_table.biom'
Attribute (weight_files) does not pass the type constraint because: Validation failed for 'ArrayRefOfReadableFileHandles' with value [ "/media/Storage/AmpliCopyrighter/data/201210/:" ] at /usr/lib/perl5/Moose/Meta/Attribute.pm line 1274.
Moose::Meta::Attribute::verify_against_type_constraint('Moose::Meta::Attribute=HASH(0x3d254b0)', 'ARRAY(0x3f776f0)', 'instance', 'Bio::Community::IO::Driver::biom=HASH(0x4080298)') called at /usr/lib/perl5/Moose/Meta/Attribute.pm line 1261
Moose::Meta::Attribute::_coerce_and_verify('Moose::Meta::Attribute=HASH(0x3d254b0)', 'ARRAY(0x3f776f0)', 'Bio::Community::IO::Driver::biom=HASH(0x4080298)') called at /usr/lib/perl5/Moose/Meta/Attribute.pm line 531
Moose::Meta::Attribute::initialize_instance_slot('Moose::Meta::Attribute=HASH(0x3d254b0)', 'Moose::Meta::Instance=HASH(0x44dbe10)', 'Bio::Community::IO::Driver::biom=HASH(0x4080298)', 'HASH(0x210c990)') called at /usr/lib/perl5/Class/MOP/Class.pm line 525
Class::MOP::Class::_construct_instance('Class::MOP::Class::Immutable::Moose::Meta::Class::ANON::S...', 'HASH(0x210c990)') called at /usr/lib/perl5/Class/MOP/Class.pm line 498
Class::MOP::Class::new_object('Class::MOP::Class::Immutable::Moose::Meta::Class::ANON::S...', 'HASH(0x210c990)') called at /usr/lib/perl5/Moose/Meta/Class.pm line 274
Moose::Meta::Class::new_object('Class::MOP::Class::Immutable::Moose::Meta::Class::ANON::S...', 'HASH(0x210c990)') called at /usr/local/share/perl/5.14.2/Bio/Community/IO.pm line 244
Bio::Community::IO::new('Bio::Community::IO', '-file', 'otu_table.biom', '-weight_assign', 'community_average', '-weight_files', 'ARRAY(0x3f776f0)', '-weight_identifier', 'desc') called at /usr/local/bin/copyrighter line 196
main::copyrighter('otu_table.biom', '/media/Storage/AmpliCopyrighter/data/201210/:', 'desc', 'copyrighted_otu.biom', undef, undef) called at /usr/local/bin/copyrighter line 187