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Merge pull request #23 from RNAcentral/import-ena-with-python
Import ena with python
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‎.gitignore‎

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@@ -67,3 +67,4 @@ data/Homo_sapiens.GRCh38.87.chromosome.*.dat
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data/Mus_musculus.GRCm38.87.chromosome.*.dat
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data/pub/
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luigi.cfg
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logging.cfg

‎data/ena/anticodon-in-note.embl‎

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rel_std_pro_04_r133.ncr
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ID CP000102.1:337323..337406:tRNA; SV 1; linear; genomic DNA; STD; PRO; 84 BP.
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XX
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PA CP000102.1
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XX
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PR Project:PRJNA15579;
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XX
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DT 06-JAN-2006 (Rel. 86, Created)
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DT 15-MAY-2014 (Rel. 120, Last updated, Version 6)
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XX
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DE Methanosphaera stadtmanae DSM 3091 tRNA-Leu
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XX
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KW .
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XX
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OS Methanosphaera stadtmanae DSM 3091
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OC Archaea; Euryarchaeota; Methanobacteria; Methanobacteriales;
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OC Methanobacteriaceae; Methanosphaera.
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XX
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RN [1]
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RX DOI; 10.1128/JB.188.2.642-658.2006.
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RX PUBMED; 16385054.
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RA Fricke W.F., Seedorf H., Henne A., Kruer M., Liesegang H., Hedderich R.,
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RA Gottschalk G., Thauer R.K.;
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RT "The genome sequence of Methanosphaera stadtmanae reveals why this human
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RT intestinal archaeon is restricted to methanol and H2 for methane formation
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RT and ATP synthesis";
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RL J. Bacteriol. 188(2):642-658(2006).
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XX
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RN [2]
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RA Fricke W.F., Seedorf H., Henne A., Kruer M., Liesegang H., Hedderich R.,
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RA Gottschalk G., Thauer R.K.;
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RT ;
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RL Submitted (05-AUG-2005) to the INSDC.
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RL Institute of Microbiology and Genetics, Georg August University Goettingen,
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RL Goettingen Genomics Laboratory, Grisebach Str 8, Goettingen D-37077,
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RL Germany
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XX
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DR MD5; 5caa01d86f18febcf564b491596b89dd.
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DR BioSample; SAMN02604180.
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..84
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FT /organism="Methanosphaera stadtmanae DSM 3091"
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FT /strain="DSM 3091"
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FT /mol_type="genomic DNA"
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FT /db_xref="taxon:339860"
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FT tRNA CP000102.1:337323..337406
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FT /operon="trnA"
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FT /locus_tag="Msp_0274"
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FT /product="tRNA-Leu"
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FT /note="codon recognized: CUA"
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XX
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SQ Sequence 84 BP; 13 A; 26 C; 31 G; 14 T; 0 other;
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gcgggggtgc ccgagctggc caaaggggac aggcttagga cctgttggcg taggcctccc 60
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agggttcgaa tccctgctcc cgca 84
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//

‎data/ena/experiment-references.embl‎

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ID HG975378.1:1..299:ncRNA; SV 1; linear; transcribed RNA; STD; HUM; 299 BP.
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XX
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PA HG975378.1
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XX
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PR Project:PRJEB6238;
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XX
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DT 07-MAY-2014 (Rel. 120, Created)
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DT 03-MAR-2015 (Rel. 124, Last updated, Version 2)
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XX
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DE Homo sapiens (human) Small nucleolar RNA 7SL
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XX
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KW RNAcentral; TPA; TPA:specialist_db.
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XX
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OS Homo sapiens (human)
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OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
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OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
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OC Homo.
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XX
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RN [1]
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RP 1-299
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RG lncRNAdb and RNAcentral
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RA ;
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RT ;
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RL Submitted (30-APR-2014) to the INSDC.
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XX
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RN [2]
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RX DOI; 10.1093/nar/gkq1138.
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RX PUBMED; 21112873.
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RA Amaral P.P., Clark M.B., Gascoigne D.K., Dinger M.E., Mattick J.S.;
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RT "lncRNAdb: a reference database for long noncoding RNAs";
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RL Nucleic Acids Res. 39(Database issue):D146-D151(2011).
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XX
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DR lncRNAdb; 140; 7SL.
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DR MD5; 020711a90d35bb197e29e085595dd52e.
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XX
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CC lncRNAdb; 140; 7SL.
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CC
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CC Specialist DB : lncRNAdb (The long non-coding RNA database)
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CC URL : http://www/lncrnadb.org/
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XX
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AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
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AS 1-299 X04248.1 1-299
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..299
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FT /organism="Homo sapiens"
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FT /mol_type="transcribed RNA"
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FT /db_xref="taxon:9606"
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FT ncRNA HG975378.1:1..299
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FT /gene="RN7SL1"
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FT /product="Small nucleolar RNA 7SL"
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FT /note="biotype:SRP_RNA"
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FT /note="ECO:0000305"
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FT /note="SO:0000590"
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FT /note="GO:0006617"
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FT /note="GO:0048501"
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FT /experiment="EXISTENCE: lncRNAdb literature review [PMID:
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FT 12244299,6196367,6181418,6802847,3403542,6084597,10924331,
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FT 7528809,7529207,1704372,20610725,18617187,17881443,
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FT 17164479,8389475,10834842,10684931,15611297,20668672,
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FT 911771,6209580]"
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FT /ncRNA_class="SRP_RNA"
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XX
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SQ Sequence 299 BP; 56 A; 83 C; 105 G; 55 T; 0 other;
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gccgggcgcg gtggcgcgtg cctgtagtcc cagctactcg ggaggctgag gctggaggat 60
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cgcttgagtc caggagttct gggctgtagt gcgctatgcc gatcgggtgt ccgcactaag 120
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ttcggcatca atatggtgac ctcccgggag cgggggacca ccaggttgcc taaggagggg 180
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tgaaccggcc caggtcggaa acggagcagg tcaaaactcc cgtgctgatc agtagtggga 240
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tcgcgcctgt gaatagccac tgcactccag cctgggcaac atagcgagac cccgtctct 299
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//

‎data/ena/function.embl‎

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ID EU410654.1:1..92:ncRNA; SV 1; linear; genomic DNA; STD; PLN; 92 BP.
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XX
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PA EU410654.1
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XX
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DT 19-FEB-2008 (Rel. 94, Created)
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DT 04-JUN-2008 (Rel. 96, Last updated, Version 2)
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XX
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DE Chlamydomonas reinhardtii CrCD10e snoRNA
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XX
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KW .
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XX
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OS Chlamydomonas reinhardtii
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OC Eukaryota; Viridiplantae; Chlorophyta; Chlorophyceae; Chlamydomonadales;
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OC Chlamydomonadaceae; Chlamydomonas.
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XX
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RN [1]
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RP 1-92
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RX DOI; 10.1534/genetics.107.086025.
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RX PUBMED; 18493037.
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RA Chen C.L., Chen C.J., Vallon O., Huang Z.P., Zhou H., Qu L.H.;
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RT "Genomewide analysis of box C/D and box H/ACA snoRNAs in Chlamydomonas
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RT reinhardtii reveals an extensive organization into intronic gene clusters";
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RL Genetics 179(1):21-30(2008).
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XX
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RN [2]
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RP 1-92
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RA Chen C.-L., Chen C.-J., Vallon O., Huang Z.-P., Zhou H., Qu L.-H.;
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RT ;
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RL Submitted (18-JAN-2008) to the INSDC.
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RL Zhongshan University, Key Laboratory of Gene Engineering of the Ministry of
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RL Education, Biotechnology Research Center, Guangzhou 510275, People's
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RL Republic of China
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XX
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DR MD5; 5c4a1c47bfd172e4474c757c89f6ce6c.
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XX
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CC Determined from Chlamydomonas reinhardtii genome in GenBank
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CC Accession Number ABCN00000000.
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..92
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FT /organism="Chlamydomonas reinhardtii"
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FT /mol_type="genomic DNA"
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FT /db_xref="taxon:3055"
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FT ncRNA EU410654.1:1..92
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FT /product="CrCD10e snoRNA"
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FT /function="guide for 26S rRNA methylation at U1043"
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FT /note="C/D box snoRNA"
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FT /ncRNA_class="snoRNA"
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XX
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SQ Sequence 92 BP; 22 A; 28 C; 22 G; 20 T; 0 other;
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gcggcgatga ctgccctcga gtgcctaact cgtcttacct attttcagag tcccctcaag 60
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gggcgcgctg ctgaaacaaa tacacaatga gc 92
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//
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ID AB046489.1:221..306:tRNA; SV 1; linear; genomic DNA; STD; VRT; 86 BP.
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XX
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PA AB046489.1
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XX
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DT 20-NOV-2003 (Rel. 77, Created)
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DT 29-DEC-2010 (Rel. 107, Last updated, Version 2)
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XX
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DE Eurypharynx pelecanoides (pelican eel) tRNA
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XX
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KW .
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XX
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OS Eurypharynx pelecanoides (pelican eel)
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OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
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OC Actinopterygii; Neopterygii; Teleostei; Anguilliformes; Eurypharyngidae;
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OC Eurypharynx.
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OG Mitochondrion
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XX
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RN [1]
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RA Inoue J., Miya M., Tsukamoto K., Nishida M.;
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RT ;
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RL Submitted (23-JUL-2000) to the INSDC.
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RL Contact:Jun Inoue Atmosphere and Ocean Research Institute, The University
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RL of Tokyo; 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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XX
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RN [2]
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RX DOI; 10.1093/molbev/msg206.
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RX PUBMED; 12949142.
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RA Inoue J., Miya M., Tsukamoto K., Nishida M.;
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RT "Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale
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RT gene rearrangements originated within the eels";
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RL Mol. Biol. Evol. 20(11):1917-1924(2003).
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XX
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DR MD5; 84f7c99e40be8ba95932912d86d9ce43.
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..86
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FT /organism="Eurypharynx pelecanoides"
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FT /organelle="mitochondrion"
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FT /isolate="D"
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FT /mol_type="genomic DNA"
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FT /db_xref="taxon:55117"
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FT tRNA complement(AB046489.1:221..306)
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FT /function="tRNA-Pro"
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XX
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SQ Sequence 86 BP; 16 A; 16 C; 25 G; 29 T; 0 other;
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aagttagaga gcgatttaat ttatgacccc ggccttgggg ccttggggtc ttggggatgg 60
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gagtttaatt tcccccctta attttg 86
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//
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ID CP003783.1:1548698..1548818:ncRNA; SV 1; linear; genomic DNA; STD; PRO; 121 BP.
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XX
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PA CP003783.1
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XX
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PR Project:PRJNA172244;
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XX
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DT 29-AUG-2012 (Rel. 113, Created)
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DT 15-MAY-2014 (Rel. 120, Last updated, Version 6)
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XX
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DE Bacillus subtilis QB928 sporulation-specific regulatory RNA
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XX
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KW .
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XX
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OS Bacillus subtilis QB928
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OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
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XX
120+
RN [1]
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RX PUBMED; 23105055.
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RA Yu C.S., Yim K.Y., Tsui S.K., Chan T.F.;
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RT "Complete Genome Sequence of Bacillus subtilis Strain QB928, a Strain
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RT Widely Used in B. subtilis Genetic Studies";
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RL J. Bacteriol. 194(22):6308-6309(2012).
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XX
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RN [2]
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RA Yu C.-S., Yim K.-Y., Mat W.-K., Tsui S.K., Wong J.T., Chan T.-F.;
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RT ;
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RL Submitted (19-AUG-2012) to the INSDC.
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RL School of Life Sciences, The Chinese University of Hong Kong, G12, Run Run
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RL Shaw Science Building, The Chinese University of Hong Kong, Shatin, N.T.,
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RL Hong Kong, China
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XX
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DR MD5; 4d454fc72801b39b5f4d10cbc60aca39.
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DR BioSample; SAMN02603911.
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XX
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CC Bacillus subtilis str. QB928 is available from Bacillus Genetic
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CC Stock Center (BGSC).
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..121
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FT /organism="Bacillus subtilis QB928"
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FT /strain="QB928"
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FT /mol_type="genomic DNA"
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FT /db_xref="taxon:1220533"
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FT ncRNA CP003783.1:1548698..1548818
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FT /gene="csfG"
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FT /locus_tag="B657_miscRNA23"
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FT /product="sporulation-specific regulatory RNA"
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FT /function="1.8 : Sporulation"
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FT /ncRNA_class="other"
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XX
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SQ Sequence 121 BP; 39 A; 23 C; 35 G; 24 T; 0 other;
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ataaaaaaat ccccgcaggc atctgcgggg tccttctatt ccttaatatg ttaaggagaa 60
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ggcaaaggga gaggagaaac cggaggaaga acttatgggg aaacgtaagt cttctccgcg 120
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g 121
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//

‎data/ena/gene_synonym.embl‎

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ID CP000948.1:2011661..2011909:misc_RNA; SV 1; linear; genomic DNA; STD; PRO; 249 BP.
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XX
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PA CP000948.1
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XX
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PR Project:PRJNA20079;
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XX
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DT 26-MAR-2008 (Rel. 95, Created)
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DT 16-MAY-2014 (Rel. 120, Last updated, Version 8)
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XX
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DE Escherichia coli str. K-12 substr. DH10B small RNA
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XX
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KW .
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XX
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OS Escherichia coli str. K-12 substr. DH10B
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OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
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OC Enterobacteriaceae; Escherichia.
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XX
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RN [1]
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RX DOI; 10.1128/JB.01695-07.
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RX PUBMED; 18245285.
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RA Durfee T., Nelson R., Baldwin S., Plunkett G.III., Burland V., Mau B.,
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RA Petrosino J.F., Qin X., Muzny D.M., Ayele M., Gibbs R.A., Csorgo B.,
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RA Posfai G., Weinstock G.M., Blattner F.R.;
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RT "The complete genome sequence of Escherichia coli DH10B: insights into the
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RT biology of a laboratory workhorse";
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RL J. Bacteriol. 190(7):2597-2606(2008).
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XX
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RN [2]
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RA Plunkett G.III.;
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RT ;
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RL Submitted (20-FEB-2008) to the INSDC.
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RL Department of Genetics and Biotechnology, University of Wisconsin, 425G
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RL Henry Mall, Madison, WI 53706, USA
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XX
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DR MD5; 9971e731d14a9b452613a844c1ca14f2.
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DR BioSample; SAMN02604262.
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XX
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CC DH10B and DH10B-T1R are available from Invitrogen Corporation
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CC (http://www.invitrogen.com).
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XX
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FH Key Location/Qualifiers
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FH
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FT source 1..249
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FT /organism="Escherichia coli str. K-12 substr. DH10B"
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FT /strain="K-12"
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FT /sub_strain="DH10B"
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FT /mol_type="genomic DNA"
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FT /db_xref="taxon:316385"
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FT misc_RNA CP000948.1:2011661..2011909
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FT /gene="ryeA"
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FT /gene_synonym="IS091"
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FT /gene_synonym="sraC"
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FT /gene_synonym="tpke79"
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FT /locus_tag="ECDH10B_1978"
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FT /product="small RNA"
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XX
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SQ Sequence 249 BP; 73 A; 48 C; 66 G; 62 T; 0 other;
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aaagtcagcg aaggaaatgc ttctggcttt taacagataa aaagagaccg aacacgattc 60
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ctgtattcgg tccagggaaa tggctcttgg gagagagccg tgcgctaaaa gttggcatta 120
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atgcaggctt agttgccttg ccctttaaga atagatgacg acgccaggtt ttccagtttg 180
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cgtgcaaaat ggtcaataaa aagcgtggtg gtcatcagct gaaatgttaa aaaccgcccg 240
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ttctggtga 249
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//

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