bio-1.4.1

https://rubygems.org

id: 11288

number: 1.4.1

platform: ruby

spec_sha256: ee006b7db51b8637f80dff696f77820343e32fb0cca6e4eba5eb9be76ad1b46d

sha256: 71f49c1585d223518047b0614edb997daab67e957e02aa9f700fc7c23053804b

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

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

position: 13

version_data_entries_count: 600

uploaded_at: 2010-10-22 05:32:47 UTC

indexed: true

has_extensions:

extensions:

Gem size: 1.28 MB

Version Data Entries

Total: 600

Unpacked size: 5.05 MB

Full Name	Mode	Size	SHA
lib/bio/util/restriction_enzyme/double_stranded.rb	644	10.6 KB	5d70feb8d68c4580c82efc1582d9084ce5ce5c35d6832753b579f4807e7518ca
test/unit/bio/util/restriction_enzyme/test_single_strand.rb	644	5.02 KB	9b3348b3e537492f8558b4d66c743dff875e19480942c37ea8f2036ca6c17d3a
lib/bio/db/medline.rb	644	7.42 KB	55f56e7e641cc0eb24f6bd5dd639135d11f7c3b00f78c1786f87f56fed0751aa
test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb	644	7.7 KB	efadc0c9037ad1205c09a1a8177cf60f3a59f45eea852a1892698bb69d741e6b
lib/bio/appl/tcoffee.rb	644	1.46 KB	5d6065494772947211a2b8d1b5d50e84aae79c591238ba640f86fdce51a2b706
test/data/sim4/simple2-A4.sim4	644	672 Bytes	dce2c8000b726b2ead80fae52e4765da3572e174534e691e919d38d9787fd301
test/unit/bio/test_shell.rb	644	461 Bytes	854ea2dd1413610f58f6edefacbeecb68227a3268746128b7c1b1d2062ad3a4d
test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb	644	5.07 KB	f8fb8b389728d100a83117ef13cc8f1786a809ee9a0b96454f0cc86f333496de
lib/bio/db/lasergene.rb	644	8.81 KB	ab810df2b17490d5b9e55de9e96999ccb14ca3d2e8bb19614a8ff34f169d1f44
test/unit/bio/sequence/test_aa.rb	644	2.53 KB	15d484c50fa839ee6108254bc0e8a6551964a55a2f4ea5adcfc4d5343eebc92d
lib/bio/io/dbget.rb	644	5.19 KB	e9f4133b481f5e2e4ed1f528522f145b9249d6fafc5b40a7c8e43e813cb5cc8c
lib/bio/shell/plugin/obda.rb	644	870 Bytes	b5999d927691ff7a320fb474e3d2376e0d302feefb657efa9bc3e2d544967407
sample/any2fasta.rb	755	1.33 KB	2b781b7bdf098238d5fe0772f5cabeae4130d09755ba1c8f9fa05d9cd9338a32
sample/fsplit.rb	755	1.11 KB	400c70b8905f27f74fd581c8c9accf5ab24748c9725131890d3e8a560dd4b80b
test/unit/bio/appl/paml/codeml/test_rates.rb	644	1.4 KB	fe7b2055f05e01cfbb8cb01c6fea59fe5c2ec794fd8306f2cd6af9ecaa1c6e69
LEGAL	644	4.41 KB	5260182d652bef11239763707e13a8c23e06b5d9f8610d60c75ebe7fe9aae36d
RELEASE_NOTES.rdoc	644	3.03 KB	bb8a82d5abd538bd6ad8ddd0aa9b10c55ab09d09e4a9720bb86d4934d2e2a636
bin/br_pmfetch.rb	755	9.87 KB	0d44e2b56f2c4c0b759acbecac01e557343eace38a2d05f616d6d72aa17a9fba
doc/ChangeLog-before-1.3.1	644	127 KB	9f6d16df3336cbca579e1fd90d0bba50878442fb5403a9ea3a7f0d13f1c51823
lib/bio/appl/paml/common.rb	644	11.1 KB	6ab2be5c82923922eb79afe7ba71c40e5be8032b732ec9b5d282b9599a123372
lib/bio/compat/references.rb	644	3.59 KB	2c9b0a6ae3aac34d26693af51bdfaf847df0d4813d6d8984f9c11de8151fe744
lib/bio/db/embl/uniprot.rb	644	951 Bytes	af4e716ecf160c6d3b1e48b8bdba8e449f388d0babc972a77f76d5294bea7d9a
lib/bio/db/fasta.rb	644	7.17 KB	a71804800c414d75da4e3c0c2c398fa90a04ec6dd0356afe7bd386809549e7d1
lib/bio/db/fastq/format_fastq.rb	644	5.37 KB	353d58684154823306f46966bcda7f2269ea804455ec0ba998aacd6d25cd047f
lib/bio/db/go.rb	644	9.85 KB	56ab7ddd3a8b014be517a77a1bc905355124fc833779831886cf4c2e9606e4b7
lib/bio/db/kegg/kgml.rb	644	5.86 KB	e434a73f1002214e20d3be9691f0620156b0cde3908bfa0bdea0601521fe53f4
lib/bio/io/fetch.rb	644	6.52 KB	1c940010dc593ae8d4e899dea631476724463498db97194f4b720ec67ae9acf0
lib/bio/io/flatfile/buffer.rb	644	5.84 KB	3f9dc74600896dafff3dbb9b4594a5dc23592d4f89b27d548cf475e272dea56b
lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml	644	215 Bytes	f729f88b0e7b5f80f1460f30cd59cb6d4c48c9f0b19ef147c7d706019f4a6939
lib/bio/shell/script.rb	644	476 Bytes	5be184d23bb6de666291ff4bfefdd1293d1dbc5cacd63b00ac8c3124e3322c90
lib/bio/shell/setup.rb	644	2.5 KB	8fe1225a57c89d14f61594b0cd2f6411bb3a33f90ce805780e19be7e3e349a25
lib/bio/tree.rb	644	25.9 KB	f8f0a731323ee10e16564fc173060bdcde430fbf52e2446a17b0981c779c1b00
lib/bio/util/restriction_enzyme/string_formatting.rb	644	2.83 KB	222f84fb60277208e57b30341fa3f7ba2867ea461c01aeff4c1b001d6cc4bc8d
sample/demo_prosite.rb	644	2.12 KB	b5d1ad86818fcd67e730037829d480ac976f1c4cfdb64420d67cd481809e0ac2
sample/demo_targetp_report.rb	644	3.27 KB	29e1c7c9fa0b3bf213064bafb5d586133e6469196e3658aaa8e6fe0f5148cf82
sample/gbtab2mysql.rb	755	3.99 KB	92b5b3f0f9ab26f44e193bd51adca9ad1c41dbbeff05cf7395cfc02d40fd8624
test/data/HMMER/hmmsearch.out	644	3.67 KB	575ce8e79d16903c9cf7670748e88bad399066ef5b9bb35f93cb36298d76b8f9
test/data/KEGG/map00030.pathway	644	2.8 KB	0caa06a4c62491f9ed9e9d0b87a6ec31f1ccd8cc0e9516975d5affea68d450e8
test/data/fastq/error_qual_tab.fastq	644	609 Bytes	c2a85269fc0b2f6b0b8dc02d6026b583b82638fcc8e76f2888bbcef1da57f015
test/data/fastq/error_short_qual.fastq	644	607 Bytes	f92205c3a8e15c4cb233fd3de4876f2ef0d34ab5693db30a9da6149bcdebe0dd
test/data/fastq/longreads_as_illumina.fastq	644	8.19 KB	3be788dd8a50564cb7b2bdddd3005c41dc85ec866242f8979d1223b97f370447
test/data/fastq/misc_rna_original_sanger.fastq	644	774 Bytes	b50686397fc812ecf7c726901acc1f127be1d29dcb6039bf35970e378ba51893
test/data/fastq/solexa_full_range_as_sanger.fastq	644	450 Bytes	10b0c1a68a40b726229f23f0989637e6479513965bb9c450ac81eee1ce796808
test/data/genscan/sample.report	644	2.7 KB	f13ec60b9b006881654cb13344f92618f94d669cfa2fde890be41f37f3f38ad8
test/data/meme/db	644	0 Bytes	e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855
test/data/phyloxml/bcl_2.xml	644	105 KB	677e9a0520f5f260f41c31fe69946eab6ac30c924a4ceb9e97ed0b82825c7061
test/data/refseq/nm_126355.entret	644	3.4 KB	60a6bdd9418cc8b9bfc96a1017f412db4f6baddfb3bd9a33c17297bbfc89aee7
test/data/soft/GDS100_partial.soft	755	4.41 KB	1bfefad740153929f2e57e33eb45487558e52da5e577f6a1c690c06f7af5ed0b
test/unit/bio/appl/bl2seq/test_report.rb	644	3.52 KB	1f478235c31f939714066745348a7a032110be2e9483822e85e40ae0c8993358
test/unit/bio/appl/meme/mast/test_report.rb	644	1.15 KB	33e2f7b746315e46468e66a0e59bf83f323eca9cc935a4c85a146f00a3d4b0b3
test/unit/bio/appl/paml/test_codeml.rb	644	5.31 KB	5e6bc2dd067a706f06ecab978dc95326f651fc46bd4ed3d4e84bcd1acdbf2793
test/unit/bio/db/kegg/test_compound.rb	644	7.86 KB	890fb8731a62a2819b41fb93a374cd9039007a1bd4397c75a0e5db028c1d4bbb
test/unit/bio/db/test_medline.rb	644	8.68 KB	74750181d3aacf9d3c2997861bda082d08fe4ca1731792d09705fa3ddae3fb2b
test/unit/bio/db/test_prosite.rb	644	18 KB	b244e49a2fcd841894ec25a9ed3cacda768f61575863a44f2edde1f3ff94e921
test/unit/bio/io/test_ensembl.rb	644	2.42 KB	e647416048e81ed635f1e57c60d35cedd8429c129aac849440f416f1c724d395
test/unit/bio/sequence/test_na.rb	644	8.01 KB	dbc562dc4a5a8daa94fdf5616a9f06a1625909f56dd0521fff9f6cbd0ba4cff7
test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb	644	3.12 KB	e0e643a36525596fa30b8c4d5831ebdd4d5a3dc3ccf1df72281abfeaeea06a56
test/unit/bio/util/test_color_scheme.rb	644	965 Bytes	d214c1911f0a1c35e1b78e8c62be9642392077df2ad622ac354f1882d6b34758
lib/bio/db/embl/swissprot.rb	644	1014 Bytes	a48b17fc793812516ddf692232b14e62e0f87bd8a9dfe3a5631eda69a5848ae3
lib/bio/data/aa.rb	644	4.89 KB	378b8e509427b76a1936c0a8ac05803ef6d42a3ed94b7897ae4b0c44a3fbfbea
sample/demo_kegg_drug.rb	644	1.27 KB	6852a6cccce5590fae8c7963961eccde179204ad461dc350be5256f147612264
doc/Changes-0.7.rd	644	12.8 KB	dc32dba9fc065d700458cedbb493c30ca341afcd4541e53ad81b956cb8ee2263
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb	644	949 Bytes	d9f9349d45f95f3e753b7b8650da42e032ac0bc3db6a8c5db0d4ec9b4c7a8573
bin/bioruby	755	979 Bytes	bbe0535bab46e968088196c828fe6700e289594fbf124ae16f0db556d14d882b
bioruby.gemspec	644	25.3 KB	bfa3568217f925895b5acba4ad8885848a4a0a5cfeb714bee453cf1476534293
lib/bio/io/biosql/ar-biosql.rb	644	12.4 KB	b1702ec502c7c4440bf754e052e87028dd7879726f8b3f997146493933590627
sample/demo_aminoacid.rb	644	2.92 KB	5d66a56b5c310f5bddd0e2440baa20cf5a2ca1013c25d5b90b05c3f85130b7f1
sample/demo_ncbi_rest.rb	644	3.48 KB	ede3b871491e386f854e9bddce1f08e7c05e04f36efb5bce28bfaff080d36329
sample/demo_tmhmm_report.rb	644	1.36 KB	a6517a2b8fac40759b81953333a3309cf1b89aaae0fe31a194c021947ed965bf
test/unit/bio/test_map.rb	644	8.1 KB	609d4551a3506a90e086c24b1daeff3a34762bca796640213f4aea7e5916586f
bin/br_bioflat.rb	755	7.17 KB	8d87c3730fe70eac916f8915b9472fde9ccace80208b0e01cda83f66d7780199
sample/demo_sosui_report.rb	644	1.87 KB	450026b68483c8a78bce3df8be796b49e371c137e4078c9a39322dd7698dd600
lib/bio/appl/blast/format8.rb	644	1.94 KB	e5de459c710c3a819f17ed3f6e37ff708dd34b040ab063191418911d01581e0b
test/data/fastq/misc_rna_as_illumina.fastq	644	774 Bytes	8c421caeb94ff3a46da42307e67f8ad21ef02763793f2a695872651e2b203635
test/unit/bio/util/restriction_enzyme/test_analysis.rb	644	8.81 KB	00bb1a18e1a7a7e09c43eed2cd7cbd51d704e8de443de2f9dae8d4bde9ff8fda
lib/bio/appl/blast.rb	644	15.1 KB	f51bc601534771d4899a95d9d30aab59aeef5953aa4e4b01a196af5c2e118fa8
lib/bio/appl/bl2seq/report.rb	644	4.4 KB	6e2e7bd629b56949f9f38e53ec9fc4749f04e4f19a02bebfaa5954269b0f4802
lib/bio/appl/phylip/alignment.rb	644	3.36 KB	74ab9a941fc46def4555c416d5502eaf884d8fe7da4499b14a57df98c5d15ec2
lib/bio/appl/psort.rb	644	12.1 KB	57e9e08d484f82b9b0481fb4a045b6279b3145655d6f58b71695e191d9e913cf
lib/bio/shell/plugin/blast.rb	644	789 Bytes	363a9cd26d862b6fc7d7dd6cba92eb1e5f8a1e85252768e14f22ba6691b141d8
lib/bio/shell/plugin/flatfile.rb	644	2.29 KB	8c296ec5abb50e2071a047b4a4cb34f32dd436dd17dffd6915e34ab0e88fd3c7
sample/demo_ddbjxml.rb	644	5.37 KB	e328c5e621c4b9065c905cde8a0c72d0d5941b2866851838119ec5953ae016bb
sample/genome2rb.rb	755	910 Bytes	c163eac8c0477dd2b7f93400518da3f656d11de834693f82c432add97876cb06
sample/pmsearch.rb	755	1.32 KB	485c955f5493b3056e13c335572cde72f9f676ae80a2a70b06b7f22a3d1e3422
COPYING.ja	644	2.06 KB	ff6bcad6dd598e328541552b374cda4dc8390c1862da051495fb3afacd562c88
ChangeLog	644	158 KB	43a610195d77d1296cade9c3f98ff06c1b986c112b8d2d3a617bb2ec61b84ea4
doc/Tutorial.rd	644	50 KB	12e78a6b97b35c77349c5647df66fb918bf974f853cfc52eced34be737c859ac
extconf.rb	644	42 Bytes	f7e2d00da8d1364f842b3ca91d711ec3f63f2208dc4a9541c6518e2055b8348c
lib/bio/appl/fasta.rb	644	5.84 KB	1c08a4018fc4e34f195ee25c0dfd0d25172bb9565579e68752ec51412da6699e
lib/bio/appl/paml/baseml.rb	644	2.74 KB	57e1ba4b3a8b914c9165e6ac4c99e9c8d3229bc6bab99c4befc99e0fbe4c8808
lib/bio/appl/paml/common_report.rb	644	844 Bytes	a6bf1e607f9d94f754900c1e5d14d1a42dbaf70b9f123ef8f37cefd5bcef7163
lib/bio/db/fasta/fasta_to_biosequence.rb	644	1.51 KB	be1fbf4bc481f11772ca1961afb6187ee7a40073254fefad0010a42d88a6d731
lib/bio/db/kegg/pathway.rb	644	6.07 KB	04aa7ee9d0b3cb18bbcf7c8d5d19455f774e488d40a6caf41f531160f3b9b746
lib/bio/io/biosql/config/database.yml	644	379 Bytes	d395d83802b9d76d291add20f85d110a8a63918dc3b62dc13849b311dbf110a4
lib/bio/io/ddbjxml.rb	644	10.5 KB	e2f68dbe43b6d87aa27ce01486054fd702db45beaf6a470b4168d3c9981963fd
lib/bio/io/flatfile.rb	644	13.3 KB	84792c667f395994d596ffed28458790133c913524acbe3f9e65d70cbd023d5b
lib/bio/sequence/format.rb	644	10.5 KB	90b765e2c04ff21bcb70effea13ecb5dcf9ce886ed9cd4f94521f0daa8513efa
lib/bio/sequence/quality_score.rb	644	5.78 KB	a8649c9f40a30f0126d20a9ae756bdbb5127f1df6527f65d68deaf8012f267b4
sample/demo_das.rb	644	2.23 KB	f193aaa863e90aba9bff5f2be0ae191a552f6693b81df4b13451149ff751dc9a
sample/demo_kegg_compound.rb	644	1.24 KB	e9dc8cc8a04054bcc59f1b07f479771dc26ec51fd0aa8f264299655d04957f20
sample/fastasort.rb	755	1.75 KB	1b62217e8944bd9815b230caadb3665dd82d70885ef67643795c21e616a8a831
test/data/KEGG/G00024.glycan	644	2.32 KB	203ec01248d66a18e40a046c9f30c0a4bcd2a124cdd40599a29c785280c78c2e
test/data/KEGG/M00118.module	644	2.16 KB	fe02348b75b75f0ec88b67e2c0c15a8d193807cdfc7706c978460f1ecfed678b
test/data/KEGG/hsa00790.pathway	644	3.05 KB	6ca9a6e9170fee93de9269641f4aa9c416cb3b5122761810af94707600d4613f
test/data/fastq/error_no_qual.fastq	644	482 Bytes	28b8205b4b3ed0d76ff1e2aec7ffffb0ca506cb99f057b4270ba37f7a5a51129
test/data/fastq/wrapping_as_illumina.fastq	644	963 Bytes	cceaae4b9273ceabe155ab40724f96d56c725b920fa94ddeb0a0c21f9fc8e0ae
test/functional/bio/io/test_soapwsdl.rb	644	1.03 KB	c33b7939624b2b8f57b4742613d1c7973320e2fd99432a7190e7710f234fd687
test/unit/bio/appl/meme/test_mast.rb	644	2.75 KB	853e762224db2d84f48178ab9dd23ff9f3b43079f0c927c2a7e353e3ce8407cb
test/unit/bio/appl/sim4/test_report.rb	644	21.4 KB	c19a66d6d6196a357be8bd692e64d542bb9a63d9ac01df575a770640d72eb201
test/unit/bio/io/test_ddbjxml.rb	644	2.3 KB	3a9cefebea194d7b6135694b0d0cd516dfe68b40bbb894aa684fc93a8ce0f690
lib/bio/db/rebase.rb	644	13.8 KB	d5913b0ba399fcf4f694e7efab6be6aa09ef5b2c449be4ec2b1c165bcfae7ebe
sample/genome2tab.rb	755	1.65 KB	5325f258867cc7f73710c9773bde73c12dbce2e4edbb3e2e8bc91c887cf06ad3
test/data/fastq/sanger_full_range_as_solexa.fastq	644	550 Bytes	a7ce416a53df877a08592025830be338b345330c61064ce2499532f6a2497d40
test/functional/bio/io/test_togows.rb	644	6.82 KB	5697434f93feca1b391ecec69f7a8ba2ee5a2f58e07b49afc35b993d9d9fea56
test/unit/bio/io/test_togows.rb	644	4.25 KB	b8c24ed5c5d252734ff423b105ad7666d6eb5dffb275c9c19fb1dfe49b2d291c
lib/bio/appl/mafft/report.rb	644	6.51 KB	1d4b4cfee1e66e52d7c39cb7f3086148d38b815d44f843f33a30d4042e42db33
lib/bio/appl/paml/codeml/report.rb	644	17.4 KB	cb467c82d09fe246ab3dbbec4c00c3809c954d572f3ef8215ee0168747de6f17
lib/bio/db/pdb.rb	644	594 Bytes	75fb017faf8c188ceb846336c581b5455cffe63c4cc6ff6d3e26e264a1d3325c
lib/bio/io/flatfile/splitter.rb	644	8.24 KB	16cdfff3260ceea21e3993cb0983e4b9dfeeca0aa75cae5a4b91684b41f6baba
lib/bio/shell/core.rb	644	12.6 KB	d1664b180dfdb34a7ba30ed62cfdcfed288ba17c58e58e007943a34c1a1120aa
lib/bio/shell/plugin/codon.rb	644	5.95 KB	ca5ea167f8b0dffd44bbe810c3ca77b22e8eda146da319a12267d5d4b06e192c
lib/bio/shell/plugin/keggapi.rb	644	4.76 KB	d57e48fcc23204e607171447424ecd3075768acd171cc87ed1b99510cf934b6c
lib/bio/util/restriction_enzyme/single_strand.rb	644	6.62 KB	68d63e357dbced77555563e5a043942d9e4e3a78ffe48b6b11fde80308065135
sample/biofetch.rb	755	12.2 KB	0e2e2a35cc2970bf0cefaa6d4befb431082a0391228435cb9f15df3ded3970c9
sample/color_scheme_na.rb	644	2.01 KB	8a184ec205da562d16d8f1b81ed89ca7ee61d44b1c29bcb104d3d3baad4fdf1e
test/data/embl/AB090716.embl	644	2.47 KB	0cf0a12b44f6472a021abcf4dc38f2f8a64d6dd4049463056057968e2ce0f0f4
test/data/fastq/sanger_full_range_original_sanger.fastq	644	550 Bytes	daa8500ee0d0b8242c65991f4965b1ec445cf9f57565b838d3ba760e5313cb00
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