{"__v":13,"_id":"5735b5f2eceb872200abbc6e","category":{"__v":0,"_id":"5735a32931a73b1700887c94","project":"5735936aafab441700723a50","version":"5735936aafab441700723a53","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-05-13T09:49:29.176Z","from_sync":false,"order":2,"slug":"quick-start","title":"Stage 2 - Core Import"},"parentDoc":null,"project":"5735936aafab441700723a50","user":"573592b84b0ab120000b7d44","version":{"__v":12,"_id":"5735936aafab441700723a53","project":"5735936aafab441700723a50","createdAt":"2016-05-13T08:42:18.615Z","releaseDate":"2016-05-13T08:42:18.615Z","categories":["5735936aafab441700723a54","5735a32931a73b1700887c94","5735b55beceb872200abbc6c","5735b56eb667601700d3bd6f","5735b9ba4b0ab120000b7dd4","5735b9c94b0ab120000b7dd5","5735cb131f16241700c8a0f7","5735e5c4e4824c3400aa1f21","5735e5d9e4824c3400aa1f23","5735e5f2ec67f6290013ac72","573ecfe0804f901700a9dfc7","573f276c7eeb8b190094ca7d"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":false,"codename":"","version_clean":"1.0.0","version":"1.0"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-05-13T11:09:38.576Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":7,"body":"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.  \n\n``export_sequences.pl`` generates a scaffold level assembly sequence file, together with protein and CDS files for use in [Stage 4](doc:stage-4-requirements) as part of the Compara import.  Files are written to a subdirectory named ``exported``\n\n```\ncd ~/import\nperl ../ei/core/export_sequences.pl ../ei/conf/core-import.ini\n```\n\n```\ncd ~/import\nperl ../ei/core/export_json.pl ../ei/conf/core-import.ini\n```\n\n``export_json.pl`` generates three ``.json`` files:\n  - ``<assembly_name>.meta.json`` contains basic metadata for the assembly and basic summary statistics including assembly span and number of gene models.\n  - ``<assembly_name>.assembly-stats.json`` contains an assembly summary in the format used by [github.com/rjchallis/assembly_stats](https://github.com/rjchallis/assembly_stats) to produce a number of individual and comparative views of several assembly statistics.\n  - ``<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](https://github.com/rjchallis/codon_usage) to visualise expected and observed codon usage patterns.\n\n\nThese files are written to the ``web`` subdirectory.","excerpt":"(optional)","slug":"step-27-export-files","type":"basic","title":"Step 2.7: Export files"}

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](doc:stage-4-requirements) 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](https://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](https://github.com/rjchallis/codon_usage) to visualise expected and observed codon usage patterns. These files are written to the ``web`` subdirectory.