Refseq parser

[Koeng101]

More than just a genbank parser, we should have a refseq parser.

From https://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/Halobacterium_salinarum/latest_assembly_versions/GCF_000006805.1_ASM680v1/README.txt

===========================
Data provided per assembly:
===========================
Sequence and other data files provided per assembly are named according to the 
rule:
[assembly accession.version]_[assembly name]_[content type].[optional format]

File formats and content:

   assembly_status.txt
       A text file reporting the current status of the version of the assembly
       for which data is provided. Any assembly anomalies are also reported.
   *_assembly_report.txt file
       Tab-delimited text file reporting the name, role and sequence 
       accession.version for objects in the assembly. The file header contains 
       meta-data for the assembly including: assembly name, assembly 
       accession.version, scientific name of the organism and its taxonomy ID, 
       assembly submitter, and sequence release date.
   *_assembly_stats.txt file
       Tab-delimited text file reporting statistics for the assembly including: 
       total length, ungapped length, contig & scaffold counts, contig-N50, 
       scaffold-L50, scaffold-N50, scaffold-N75, and scaffold-N90
   *_assembly_regions.txt
       Provided for assemblies that include alternate or patch assembly units. 
       Tab-delimited text file reporting the location of genomic regions and 
       listing the alt/patch scaffolds placed within those regions.
   *_assembly_structure directory
       This directory will only be present if the assembly has internal 
       structure. When present, it will contain AGP files that define how 
       component sequences are organized into scaffolds and/or chromosomes. 
       Other files define how scaffolds and chromosomes are organized into 
       non-nuclear and other assembly-units, and how any alternate or patch 
       scaffolds are placed relative to the chromosomes. Refer to the README.txt
       file in the assembly_structure directory for additional information.
   *_cds_from_genomic.fna.gz
       FASTA format of the nucleotide sequences corresponding to all CDS 
       features annotated on the assembly, based on the genome sequence. See 
       the "Description of files" section below for details of the file format.
   *_feature_count.txt.gz
       Tab-delimited text file reporting counts of gene, RNA, CDS, and similar
       features, based on data reported in the *_feature_table.txt.gz file.
       See the "Description of files" section below for details of the file 
       format.
   *_feature_table.txt.gz
       Tab-delimited text file reporting locations and attributes for a subset 
       of annotated features. Included feature types are: gene, CDS, RNA (all 
       types), operon, C/V/N/S_region, and V/D/J_segment. Replaces the .ptt & 
       .rnt format files that were provided in the old genomes FTP directories.
       See the "Description of files" section below for details of the file 
       format.
   *_gene_expression_counts.txt.gz
       Tab-delimited text file with counts of RNA-seq reads mapped to each gene.
       See "Description of files" section below for details of the file format.
   *_gene_ontology.gaf.gz
       Gene Ontology (GO) annotation of the annotated genes in GO Annotation 
       File (GAF) format. Additional information about the GAF format is 
       available at 
       http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ 
   *_genomic.fna.gz file
       FASTA format of the genomic sequence(s) in the assembly. Repetitive 
       sequences in eukaryotes are masked to lower-case (see below).
       The FASTA title is formatted as sequence accession.version plus 
       description. The genomic.fna.gz file includes all top-level sequences in
       the assembly (chromosomes, plasmids, organelles, unlocalized scaffolds,
       unplaced scaffolds, and any alternate loci or patch scaffolds). Scaffolds
       that are part of the chromosomes are not included because they are
       redundant with the chromosome sequences; sequences for these placed 
       scaffolds are provided under the assembly_structure directory.
   *_genomic.gbff.gz file
       GenBank flat file format of the genomic sequence(s) in the assembly. This
       file includes both the genomic sequence and the CONTIG description (for 
       CON records), hence, it replaces both the .gbk & .gbs format files that 
       were provided in the old genomes FTP directories.
   *_genomic.gff.gz file
       Annotation of the genomic sequence(s) in Generic Feature Format Version 3
       (GFF3). Sequence identifiers are provided as accession.version.
       Additional information about NCBI's GFF files is available at 
       https://ftp.ncbi.nlm.nih.gov/genomes/README_GFF3.txt.
   *_genomic.gtf.gz file
       Annotation of the genomic sequence(s) in Gene Transfer Format Version 2.2
       (GTF2.2). Sequence identifiers are provided as accession.version.
   *_genomic_gaps.txt.gz
       Tab-delimited text file reporting the coordinates of all gaps in the 
       top-level genomic sequences. The gaps reported include gaps specified in
       the AGP files, gaps annotated on the component sequences, and any other 
       run of 10 or more Ns in the sequences. See the "Description of files" 
       section below for details of the file format.
   *_protein.faa.gz file
       FASTA format sequences of the accessioned protein products annotated on
       the genome assembly. The FASTA title is formatted as sequence 
       accession.version plus description.
   *_protein.gpff.gz file
       GenPept format of the accessioned protein products annotated on the 
       genome assembly
   *_rm.out.gz file
       RepeatMasker output; 
       Provided for Eukaryotes 
   *_rm.run file
       Documentation of the RepeatMasker version, parameters, and library; 
       Provided for Eukaryotes 
   *_rna.fna.gz file
       FASTA format of accessioned RNA products annotated on the genome 
       assembly; Provided for RefSeq assemblies as relevant (Note, RNA and mRNA 
       products are not instantiated as a separate accessioned record in GenBank
       but are provided for some RefSeq genomes, most notably the eukaryotes.)
       The FASTA title is provided as sequence accession.version plus 
       description.
   *_rna.gbff.gz file
       GenBank flat file format of RNA products annotated on the genome 
       assembly; Provided for RefSeq assemblies as relevant
   *_rna_from_genomic.fna.gz
       FASTA format of the nucleotide sequences corresponding to all RNA 
       features annotated on the assembly, based on the genome sequence. See 
       the "Description of files" section below for details of the file format.
   *_rnaseq_alignment_summary.txt
       Tab-delimited text file containing counts of alignments that were either
       assigned to a gene or skipped for a specific reason. See "Description of
       files" section below for details of the file format.
   *_rnaseq_runs.txt
       Tab-delimited text file containing information about RNA-seq runs used 
       for gene expression analyses (See *_featurecounts.txt file and *.bw files
       within "RNASeq_coverage_graphs" directory). 
   *_translated_cds.faa.gz
       FASTA sequences of individual CDS features annotated on the genomic 
       records, conceptually translated into protein sequence. The sequence 
       corresponds to the translation of the nucleotide sequence provided in the
       *_cds_from_genomic.fna.gz file. 
   *_wgsmaster.gbff.gz
       GenBank flat file format of the WGS master for the assembly (present only
       if a WGS master record exists for the sequences in the assembly).
   annotation_hashes.txt
       Tab-delimited text file reporting hash values for different aspects
       of the annotation data. See the "Description of files" section below 
       for details of the file format.
   md5checksums.txt file
       file checksums are provided for all data files in the directory

All of this data is provided by refseq for genomes. We should build a parser for getting all of this data into a JSON formatted nice format.

[Koeng101]

This is very nice to have, but not needed right now. Focus needs to be on the API. Closing.