Step 2.7: Export files
(optional)
The process of import and export generates a set of files that will be consistent across different assemblies and therefore useful for use in comparative analyses, converting to BLAST databases, etc. Exported .json
files that can be used for assembly/annotation statistic visualisation.
export_sequences.pl
generates a scaffold level assembly sequence file, together with protein and CDS files for use in Stage 4 as part of the Compara import. Files are written to a subdirectory named exported
cd ~/import
perl ../ei/core/export_sequences.pl ../ei/conf/core-import.ini
cd ~/import
perl ../ei/core/export_json.pl ../ei/conf/core-import.ini
export_json.pl
generates three .json
files:
<assembly_name>.meta.json
contains basic metadata for the assembly and basic summary statistics including assembly span and number of gene models.<assembly_name>.assembly-stats.json
contains an assembly summary in the format used by github.com/rjchallis/assembly_stats to produce a number of individual and comparative views of several assembly statistics.<assembly_name>.codon-usage.json
contains a summary of scaffold, gene, exon, etc. lengths, base composition and codon usage in the format used by github.com/rjchallis/codon_usage to visualise expected and observed codon usage patterns.
These files are written to the web
subdirectory.
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