bio-1.4.3.0001

https://rubygems.org

id: 11291

number: 1.4.3.0001

platform: ruby

spec_sha256: 080af7257a1f60e8e22edaaa90a4979db7d052f7f35fff9e4db62d1713be65bc

sha256: 273455d8b7f0fd450cdf00798879002dbbd53c7f9a385b3d5d77e2fa1a7ebbf8

created_at: 2024-05-13 08:13:57 UTC

updated_at: 2024-05-23 19:20:24 UTC

position: 10

version_data_entries_count: 635

uploaded_at: 2013-05-24 19:12:57 UTC

indexed: true

has_extensions:

extensions:

Gem size: 1.42 MB

Version Data Entries

Total: 635

Unpacked size: 5.65 MB

Full Name	Mode	Size	SHA
test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb	644	3.45 KB	ba6116356af552be39457a0aee054aaf529774d8c905da6ee399141fe6ad335a
lib/bio/appl/clustalw.rb	644	5.98 KB	1e51eff966b274cec63a5d10e2ac61cb598b9125163c63ac4b9a443b23c1d1d5
lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb	644	803 Bytes	4a22c7c7063b42ca96f2809acae97ace54e65ac5ea93d7160ccff2c3bef7dc73
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb	644	1.13 KB	becf3bf68fa08f81e54b9bbe60f241b1dc0e6a5d316480f6f477f4f7bdbf9dff
test/data/paml/codeml/models/aa.aln	644	1.35 KB	1002a03b17cedbcd23b826f98da8e2f957868ee34bbe635e2a3bfda32d57a063
test/data/refseq/nm_126355.entret	644	3.4 KB	60a6bdd9418cc8b9bfc96a1017f412db4f6baddfb3bd9a33c17297bbfc89aee7
test/unit/bio/db/kegg/test_pathway.rb	644	43.2 KB	606f888b6f0324edd0406e862a2574702b690a8d8c5c776dd42cbd9dac9179e1
test/unit/bio/db/kegg/test_reaction.rb	644	2.99 KB	c7084af4afbb8495119c99989df5e0d1504ce64a908448dc8b5b15cbde1c8a56
test/unit/bio/io/test_flatfile.rb	644	12.9 KB	cf5883c0606271c205719b03f62cbf7d69f2df717622ad2b7c8a7a9177b57d39
test/unit/bio/appl/meme/mast/test_report.rb	644	1.15 KB	33e2f7b746315e46468e66a0e59bf83f323eca9cc935a4c85a146f00a3d4b0b3
COPYING	644	2.45 KB	d18b5463859ebbe78e33e13bf7a6241d4d69a7c484f677d7aea7f8bbac039531
sample/demo_ncbi_rest.rb	644	3.48 KB	ede3b871491e386f854e9bddce1f08e7c05e04f36efb5bce28bfaff080d36329
sample/psortplot_html.rb	644	4.95 KB	75a7811ea4d6aa05206b50aaea0643dc7d2d9b3813955d1d84904f227a9ceafb
bin/bioruby	755	979 Bytes	bbe0535bab46e968088196c828fe6700e289594fbf124ae16f0db556d14d882b
lib/bio/appl/mafft/report.rb	644	6.51 KB	1d4b4cfee1e66e52d7c39cb7f3086148d38b815d44f843f33a30d4042e42db33
lib/bio/appl/paml/yn00.rb	644	2.79 KB	17fc612d7db16c1035adc7979da1d611a667210fb0a6bc94f50e7b6b600649cb
lib/bio/db/fasta/format_qual.rb	644	6.09 KB	11435edd1f11ef00ae7a83405555d774386902a62d886d3261cf13ef77ed86e3
lib/bio/db/kegg/taxonomy.rb	644	8.5 KB	ad8789074dfa2c0331e0f3aa876c4acb61fc5558ca133ec83cc2782dbc85677f
lib/bio/io/biosql/ar-biosql.rb	644	12.4 KB	b1702ec502c7c4440bf754e052e87028dd7879726f8b3f997146493933590627
lib/bio/io/higet.rb	644	1.3 KB	8d6daf64f8d2f1395102a877163cb75af7f1a35f2415ca702047e83c3bdc14aa
lib/bio/io/sql.rb	644	2.61 KB	654ee925ca98024162982c5a6aa4b258761b8667179dd4990abd26d9c6e9c4ae
lib/bio/shell/plugin/ncbirest.rb	644	1.55 KB	cb5a45ca35fe491e7fed017bdba9ff2aafda05865ae3fa1be79f5d959bf6f669
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif	644	1.51 KB	e008bc0bca2fa6f9b9c113fad73551230961baec88c06b20997ec50171bb2b6b
lib/bio/util/color_scheme.rb	644	4.94 KB	a2e614c3205ad4e364eb422b703efe3184afe8261515565588406c4a17ecbc30
lib/bio/util/restriction_enzyme/enzymes.yaml	644	87.5 KB	56ed1fd2f2d5557604da2044f3d491ccc5b845c43b4b307b395fb89e3798b346
sample/demo_fastaformat.rb	644	2.43 KB	e5522eca1e7c5fdb2c853df473ef6f1c607bd65ee646cd8bcd8648af5f03dcd3
sample/demo_kegg_genome.rb	644	1.44 KB	f929c3029ba2de4487f047221a1059c43c972467687be02683e250ceac6d2255
sample/demo_litdb.rb	644	832 Bytes	52bc6ee01104e8a5785ce9ebe94ccee7d341fa7f79b90bcde433a82cc27e4665
sample/genes2nuc.rb	755	955 Bytes	0caf11a1a36cc66aa4dfcf92ff53af12ce4990b663a2096d907243b736b67267
test/data/KEGG/T00070.genome	644	1.16 KB	2ba3a3e622afbce769db9dae9f26fd90a274ccdac4427bab461c200cae479cac
test/data/KEGG/rn00250.pathway	644	6.12 KB	e684bcf769a8da079baa4ae3090d2d711a9db50322965464aabc0982af2b23d7
test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq	644	984 Bytes	7f6e883493ac3be2114dfe4794e4a324bb67e7e9064c211bed60a6527c783b33
test/data/fastq/error_long_qual.fastq	644	609 Bytes	4649efbe152fcc28e1c39b2721ce52f147252a7ee0b55ceb22d535dae1277d48
test/data/fastq/error_qual_null.fastq	644	610 Bytes	72af9fe18e7f35688f717b685771f6da3fb1534d54f3af0437be97ecf4c617eb
test/data/fastq/error_trunc_at_plus.fastq	644	548 Bytes	785fe4189c44bb5503b51a9e26ac58127cfb8cdea2ebe244213d2bf5deae7b0d
test/data/fastq/illumina_full_range_as_sanger.fastq	644	426 Bytes	4148a8f6ae111de3d10933e1055dadb932e6f93926f75cf3983d36646fe37e90
test/data/fastq/longreads_as_solexa.fastq	644	8.19 KB	a922d878e416ecc7df755f0e263dfe31078bebf298f1c85e6a5c980a6cc38bf5
test/data/fastq/misc_rna_as_solexa.fastq	644	774 Bytes	073dd9509de2be068bae20cae68c546727c8043de53298a3093afbffa9dda3f2
test/data/genbank/CAA35997.gp	644	2.01 KB	b4b7f655fe65d35ea050d4d0d8fba18caa5bd156db50438f6be0b3c480ad95a2
test/data/go/selected_component.ontology	644	553 Bytes	7ca3d2f1c054079ebf3b61c1dd87af6a6a8b99c9f93662a6ee92151ca6997f6b
test/data/go/selected_wikipedia2go	644	798 Bytes	5715946c196b7b6ca89bafa343ee944358b6ae1e4ac51f2c284d50c4401f900b
test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml	644	1.86 KB	2446e2a045b8648e528d9ee46deec710e9930b7bf17da2aaa063ec5a51ed5c67
test/network/bio/appl/test_pts1.rb	644	2.43 KB	5344321f243479c9202184d8e93edeeeb35c61153ec79332bfc8726b8a646a55
test/unit/bio/appl/tmhmm/test_report.rb	644	3.2 KB	58ff701c8d1aacc023648e8acfd3c13698b82d77097ab212158b2ef529de792d
test/unit/bio/db/pdb/test_pdb.rb	644	100 KB	9dc3411672ad0b195e4e6ae00fcd110986a6a582a6e50f1506d8459c3094596b
test/unit/bio/db/test_newick.rb	644	9.92 KB	825a44b21570a540114e637260b1cf3559b3cd61d19fec00e613d6fb387a128a
test/unit/bio/db/test_phyloxml.rb	644	24.3 KB	780602e5b2880e9543f0c263a55e008f3340a04d34053145ea61d9dd3db30512
test/unit/bio/sequence/test_sequence_masker.rb	644	4.72 KB	9117e63f9f2bcc13ee0cdec24473315aea47b9af4fca1ac2077563551bd918e3
test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb	644	10.2 KB	b81fe69319e35852270f6bf71d7a15478c7db84bc7d77d210f8b49bfe8dbb92d
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb	644	2.2 KB	dd35fc665ed061594953f2a98495febde2b1cf9a53c927a096d94af1c2b96f68
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb	644	1.47 KB	bf40d893499726b091be88692cbb7a7072503cba1528527f34d0c2fc5fd7cbc8
sample/demo_kegg_glycan.rb	644	1.5 KB	7716f364760283313fcd39d9b86f34ba6dafed0799855657cc834982b3316f32
lib/bio/db/rebase.rb	644	13.8 KB	d5913b0ba399fcf4f694e7efab6be6aa09ef5b2c449be4ec2b1c165bcfae7ebe
lib/bio/io/soapwsdl.rb	644	2.3 KB	a986284bdf999c960ba417a7ce244c8d8cfcd22faa60b1ca333c03fb0dca2550
sample/demo_targetp_report.rb	644	3.27 KB	29e1c7c9fa0b3bf213064bafb5d586133e6469196e3658aaa8e6fe0f5148cf82
lib/bio/db/embl/embl_to_biosequence.rb	644	1.7 KB	68591ecd39e1f856e9c55abd8b471514f64db35b8e14ef39eb3a1470c1e91096
lib/bio/data/na.rb	644	3.62 KB	850ef4c7403ac98b365d1988c407c61b9a3dd4b5b6762baec2b037bb5066553e
lib/bio/util/restriction_enzyme/analysis.rb	644	9.64 KB	48976b6810297a7cef36018626d762f9313ea22da0dae58ef69dc7a6b1297f67
test/data/fastq/error_short_qual.fastq	644	607 Bytes	f92205c3a8e15c4cb233fd3de4876f2ef0d34ab5693db30a9da6149bcdebe0dd
test/unit/bio/db/test_go.rb	644	6.61 KB	8912b4976008031c10cea41aae5e9542a758bcab32876274e541d70a296e8859
test/unit/bio/sequence/test_common.rb	644	11.3 KB	d1b0d9553b83b4c833cce9f63a5e1eac728c8e86710feeb167196f92262d7776
lib/bio/appl/paml/baseml.rb	644	2.74 KB	57e1ba4b3a8b914c9165e6ac4c99e9c8d3229bc6bab99c4befc99e0fbe4c8808
lib/bio/appl/paml/common.rb	644	11.1 KB	6ab2be5c82923922eb79afe7ba71c40e5be8032b732ec9b5d282b9599a123372
test/unit/bio/util/test_sirna.rb	644	6.15 KB	9ba9f1f45a142fc8e66da61734830136a50da8ca05f01a07de9e3e315be87e29
lib/bio/io/ddbjrest.rb	644	12.7 KB	640b9959b15eb43fe9d51c6f82d6f694659030c7f9e6d420bbebf2b4c6ecf4df
sample/enzymes.rb	755	2 KB	6e6056acba8725e95dd245dc889c3f5d388001b0111923bc973edb6600fecb53
sample/demo_keggapi.rb	644	14.5 KB	b12fd6ba43895bbbec3004680cc2f01d5356b24ec432c0398b6322aa4c12ae69
lib/bio/appl/blast/report.rb	644	17.2 KB	0242ed44c1a18694e40171ad4d2143d85ff1485f396c1b00c7125feba8a3284c
lib/bio/appl/paml/baseml/report.rb	644	660 Bytes	9a4c272ea61596c13451459b6dcf3b386a3149ca20f972bd1b2ac0177ab82734
lib/bio/appl/psort/report.rb	644	12.4 KB	a6d4f66696a5cc9a34df56e9c6921098ae27f2c0e38284e58ceb1b558cdac8d9
lib/bio/appl/spidey/report.rb	644	19 KB	e7ec75fc26c812cc81deaa8653dfba4418ce4910a4ae63cc6dc6e938673b17df
lib/bio/db/lasergene.rb	644	8.81 KB	ab810df2b17490d5b9e55de9e96999ccb14ca3d2e8bb19614a8ff34f169d1f44
lib/bio/io/biosql/biosql.rb	644	1.86 KB	c29f8a0148670bdf1ffddce08bcb3fba49cc6dc759b74f387fdd4159f81612e1
lib/bio/io/ensembl.rb	644	5.69 KB	44668eb1edef70d1df9aaac87d582b155986f00507261b236984132e8383846d
lib/bio/io/flatfile/indexer.rb	644	26.8 KB	07b629888b34645ac50a2b011dcb61506c655648b79580040cead344291bce5b
lib/bio/util/color_scheme/nucleotide.rb	644	690 Bytes	826ecc72308f879c325103e36a5dbe51fe67ec5b9fcf32e73c133ceeaf80376e
sample/test_phyloxml_big.rb	644	5.93 KB	fd6a5a8c459d8eed7ede672216c807c073459d824dd0606fed06ca0dbe1f29e3
test/bioruby_test_helper.rb	644	2.32 KB	d73db275a0f04547b7caa393d326d61f3fa72835fef530540495115ad87c46d5
test/data/KEGG/C00025.compound	644	5.2 KB	837ef41867587872d0b0a53f66f7b50093249569516e0f815721b722b0f32871
test/data/KEGG/G01366.glycan	644	545 Bytes	e103e8ecab1b285dd603215f6ce8a30e8fc7ca3f625c01967b7c5a4029bd42c7
test/data/KEGG/b0529.gene	644	2.52 KB	faa9f0534c9b79d8632ac5b0558371a67b97bbea47d96d170e81373038f5e12e
test/data/KEGG/test.kgml	644	1.7 KB	5626abada68ac5bc6dce2da889970ba8d24fcc91050e59b4ee79d7eeaecdb3ae
test/data/blast/b0002.faa.m7	644	5.52 KB	bb7d1c37f92f8a36527c02efb6f6352294eb1acf688ea6caedb7b934f9817e8f
test/data/fastq/error_qual_vtab.fastq	644	608 Bytes	24629e256f3ad949817c8e0c1f5e117c1d62fc64b96d74fa0b9ffb9a52b56274
test/data/sim4/simple-A4.sim4	644	661 Bytes	ab1a4c389192697f64269ca4af532edd7ee94977ef0ca5c64694bef727bb6768
test/functional/bio/test_command.rb	644	10.2 KB	8ae5128f5efbe7ef1844c4ea0728d60498484e8507d28f2eadfa05ddf43e840d
test/network/bio/io/test_pubmed.rb	644	3.74 KB	5813b92453cfef93ab75f0844013d8e654e86f5835245325679ba7f8071d3761
test/unit/bio/appl/blast/test_report.rb	644	37.3 KB	82dc5cb52532a8c968db51b4dd2c9ec8efa8e2474510c85179f2688df976c275
test/unit/bio/data/test_codontable.rb	644	2.32 KB	7cda469bbeb6e38b0efc78aba38672493332ed436f4302feb79e8ba5ff18d3b6
test/unit/bio/db/fasta/test_defline.rb	644	7.77 KB	e28017019d7bfc8e06647d624384b5ac88568702792a2905b7439be0d122ec74
test/unit/bio/db/kegg/test_drug.rb	644	6 KB	7f6996d9f6ba6d2b1df27d5e0a32d3c3363533bbdec344b2903bb726be41ddee
test/unit/bio/db/test_medline.rb	644	8.72 KB	ff1f25de1fee160868cf3ef24ffc5194a7da49a98903d9d33955ff15d7adc3c4
test/unit/bio/db/test_soft.rb	644	6.58 KB	08a0cd71551b0c03667ef21988b94e31aade89384eb601e4e9f5f0c3897599d8
test/unit/bio/io/test_ddbjxml.rb	644	2.3 KB	3a9cefebea194d7b6135694b0d0cd516dfe68b40bbb894aa684fc93a8ce0f690
test/unit/bio/test_shell.rb	644	461 Bytes	854ea2dd1413610f58f6edefacbeecb68227a3268746128b7c1b1d2062ad3a4d
lib/bio/util/restriction_enzyme/range/cut_range.rb	644	579 Bytes	d6eb663412027fe3eedd58b7a61893efa3eb63b717f8130c8e0d84c829cac176
lib/bio/appl/bl2seq/report.rb	644	4.41 KB	8df8c2691cfe2544eb1ce8047169453d863d489b4bb2471ce9b99f0c291d40ce
lib/bio/appl/clustalw/report.rb	644	5.01 KB	08379d9f1c9232aef9f53c022a6daff068423ec51941346846481f52a4d69b6d
lib/bio/appl/targetp/report.rb	644	3.86 KB	ea6395dcc172bed3f4fefa7d6632b622c9494d6c5b4d747002f0f23a25b52f3a
lib/bio/db/aaindex.rb	644	7.03 KB	59a361d682cb7ee281146d798d1637e6790eab5e603cf45cc5eb2a080c0eeaa1
lib/bio/db/embl/swissprot.rb	644	1014 Bytes	a48b17fc793812516ddf692232b14e62e0f87bd8a9dfe3a5631eda69a5848ae3
lib/bio/db/fasta.rb	644	8.64 KB	975b8d13b8c7205a14247ab86bd5bea5b5b6ba29bad619b692af9ab76603b317
lib/bio/db/genbank/genbank_to_biosequence.rb	644	1.75 KB	f09815c7600e410e67356fddcf4ccc7f7c1894b1903a942a5c86cebaf1d36413
lib/bio/sequence.rb	644	15.9 KB	7508f4467236cac107728cfda58dc1d015a741539426251b6943fd711afa43b9
lib/bio/sequence/adapter.rb	644	3.7 KB	40e2012097a720593ac504c1c63a65e11b2f0f306ad51dbac4b74ec5457cc447
lib/bio/shell/core.rb	644	12.7 KB	c8f5cf3df686d73216b340084031a3f4ddba7bb8b9217057a5583c438c185b11
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png	644	6.79 KB	483e2f19ce8966c8490191c261d40e3bafcff790c1abdf21060307e31ef2372d
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml	644	142 Bytes	f636303863e9caae6ad5b285d102c3b2f8451353c15d3163f7333e5c10512141
lib/bio/util/color_scheme/turn.rb	644	1.24 KB	bd3eccff3a257ba853884956d26e8da73b68412375bf9531af7964a991ced74e
lib/bio/util/restriction_enzyme/cut_symbol.rb	644	2.67 KB	2a6790db38055526a6e31eadaa4ad293ce81974c2d98fe8e94499179d6235750
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb	644	1.75 KB	e03d803b8352255ec227013a1639d0a9e8511ddfbbf11939e82984ee7f208382
sample/demo_aminoacid.rb	644	2.92 KB	5d66a56b5c310f5bddd0e2440baa20cf5a2ca1013c25d5b90b05c3f85130b7f1
sample/demo_blast_report.rb	644	10.1 KB	af533f7e723ee515ebfd88e973bd52efb89dc883b365a9606656c9c9ceb3f162
sample/demo_kegg_drug.rb	644	1.27 KB	6852a6cccce5590fae8c7963961eccde179204ad461dc350be5256f147612264
sample/demo_pubmed.rb	644	2.99 KB	c3160b959f0d89fbc64be4974461341d2ccd14eacd9d4d9c9c97bf62498522b9
sample/fastagrep.rb	755	1.78 KB	cb2f5248e1106048f2428cef80577fbab52ec65ee81ae33dbfb5de02ee90ecbb
sample/genome2rb.rb	755	910 Bytes	c163eac8c0477dd2b7f93400518da3f656d11de834693f82c432add97876cb06
sample/ssearch2tab.rb	755	2.24 KB	f48f03ed7e929175411bdb75df185c16b906a9fd5fc0f3e7c8feb1a95536a25a
sample/vs-genes.rb	755	5.82 KB	88f460be7dd0ea6961a364efb8ffa2037dd20636234803968dbd99db783cfaa9
test/data/KEGG/D00063.drug	644	3.92 KB	d7941a74bd701f93ab057f6e4ab21cd043d7e53c4885a85be8d352f7329df3d8
test/data/KEGG/M00118.module	644	2.16 KB	fe02348b75b75f0ec88b67e2c0c15a8d193807cdfc7706c978460f1ecfed678b
test/data/KEGG/R00006.reaction	644	730 Bytes	74cfc3e7fb48400b5dcbbafd58647809acb42fba4aaf5fb53dc83c901269b9bf
test/data/aaindex/PRAM900102	644	1.08 KB	62991a1bd9b197111da30dd3bd8f2a637c435778aef8d2bbb548c5e0fa8ea69d
test/data/blast/b0002.faa.m0	644	5.15 KB	2479b6f0b728c354edbf01fe600cd7884308e1e6a22913a7420e23af75cbfd75
test/data/fastq/error_qual_unit_sep.fastq	644	608 Bytes	a819e7f2a4d33695eb1916112d4ca95ab16bd58f7fcf1ef4798d854b59ceeae3
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sample/demo_kegg_reaction.rb	644	1.47 KB	3b5f4b0c869458395fe10b94ad20139efe265c5d4312cf4f7e7f7dfcb7904987
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sample/demo_psort_report.rb	644	1.42 KB	2ed41494c85b0f89a81c42c485740ec1220c0e2a82618a2c42365a5dd6c59141
sample/demo_tmhmm_report.rb	644	1.36 KB	a6517a2b8fac40759b81953333a3309cf1b89aaae0fe31a194c021947ed965bf
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setup.rb	644	35.8 KB	7939fe536eccf4be96abbcaf9034003b1991388c07f79548c16abb766b889230
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test/data/fastq/solexa_full_range_as_illumina.fastq	644	450 Bytes	cea9449b8602d7a29b6eaa45a0ecb2edd3e25cb3273f1476e05ffd3766da7cbb
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test/data/genbank/SCU49845.gb	644	10.2 KB	e9a1e1626188afc7168680a9c0039be85f1298f140165d6cb67c707b0b6fd660
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test/data/sanger_chromatogram/test_chromatogram_abif.ab1	644	223 KB	8dcd2b30c70cc4ca455868b9f0df5dc588c54ff0be00066810c11442acd6effc
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test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf	644	46.4 KB	db84e92dc2aacbf0d84f003593494292e8799a4677c003f6b7d19ff4abfd0061
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test/unit/bio/appl/paml/codeml/test_report.rb	644	7.06 KB	2778e99bc756aadb5867dc5c4a9d71264224fda2764cf6aac2fdcd1545f60301
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test/unit/bio/db/genbank/test_genbank.rb	644	24.7 KB	48e3f9ec7e0112107058415eda8480bf424b4a69f9b4cf24ad7617c604c72014
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