This sections of the documentation is designed for users that want to generate data files themselves without using the data preprocessing tool described in [Preparing data].
Most users should not care about this section and go back the to [Preparing data] section that describes how to prepare your data using the provided preprocessing tool!
### # # Viral viz data format demo file # # Lines starting with # are comments and will be ignored by the parser. # # Empty lines are ignored by the parser as well. All empty lines in this file are cosmetic. # # Each line is self-contained and can be parsed individually. The order of the lines should not be important, # although for now I recommend using more or less the same ordering as below. # # Columns are TAB separated # # Last update September 4, 2012 by Thomas Abeel # ### ## # Required configuration information. # # This information is required! # ## # Which sequences are available as reference sequences? config sequence:references=HXB2,V3020 ## # Optional configuration information ## # Which meta data columns need to be initially hidden config metapanel:hidden=HLA,Cohort ## Log-scaling for value meta data columns columns # config metapanel:logscaling:<meta type>=boolean (default false) # For example: config metapanel:logscaling:Viral Load=true ### # Sample based meta data # # All meta data is entered as text, but will be displayed with a appropriate visualization if possible. # ## meta V4139 Cohort=Acute meta V4139 HLA=A0101,A2402,B3801,B4403,C04,C12 ## # Data per view ## # General columns: # View data type specific information ## # Specific extra columns for annotation # annotationType displayName start end extras (key=value;otherkey=listItem1,listItem2) # # Specific columns for sequence # sequence # # Specific columns for variant # position ## ## # Examples, white lines are cosmetic, white space are tabs. # # 'target' is categorical field that can be used for filtering, a menu will be created to filter on this field # # 'intron' for annotation of the type 'gene' allows to specify intron information which will be visually represented # ## aa annotation HXB2 gene VPU 2025 2097 intron=2080:2090 aa annotation HXB2 gene NEF 3005 3161 aa annotation HXB2 gene ENV 2108 2954 intron=2120:2200,2600:2800 aa annotation HXB2 epitope B63_ELDRWEKIRL 11 21 target=B63 aa annotation HXB2 epitope B63_balh 14 24 target=B64;otherkey=1.5 aa sequence HXB2 MGARASVLSGG-----AADRV...very long line, essentially an entire row of a multiple alignment... aa sequence V4141 MGARASVLSGGELDKWEKIRLR...very long line... aa sequence V5239 MGARASVLSGGELDRWEKIRLRPGG...very long line... ## # Variant information. Deletions should be indicated with -=15, insertion should be indicated with for example AT=15 ## aa variant HXB2 683 R=108,T=15,I=11 ## # Coverage information is a diff encoding of the coverage. Position is implicitly assigned. Each value is the difference with the # previous value ## aa coverage HXB2 20,-5,-3,5,2,1,1,0,0,0,0,0,-1,-2,0,0,0,1,...