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github.com/BioJulia/Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl

update docs about Bio.Align

14de59979315c7f98c4cc31118dcfae0125ce709 authored almost 9 years ago by Kenta Sato <[email protected]>
fix iterator and pretty printer of pairwise alignment

efd96ff5ed6f8ac92c9dd9961d4723010c236ac2 authored almost 9 years ago by Kenta Sato <[email protected]>
add `gap` function

dd4e70ceeff64d0749742a2a096b04dd05437b77 authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #141 from BioJulia/fix-gencode

fix genetic code

ecff46e6100554bf2697ab55e0c226fb273aa001 authored almost 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add more tests of `translate` on ambiguous codons

9530e0cd8e13a61add8abeff4be718a1ffbe034e authored almost 9 years ago by Kenta Sato <[email protected]>
update doc of translate (and clean up code)

f9ee222aa12e0e7ccfb249a3b98e611e973f14e8 authored almost 9 years ago by Kenta Sato <[email protected]>
rewrite genetic code tables

a19c64f4b2f2361b43e269fd920945b9760f3e9b authored almost 9 years ago by Kenta Sato <[email protected]>
fix genetic code

990f8fadf12e8e8621f2490b3dc08a83b42aa5c9 authored almost 9 years ago by Kenta Sato <[email protected]>
Removed lines in documentation causing doc build errors.

87baea925a576efeeef7bbee1e417da02ee08487 authored almost 9 years ago by Ward9250 <[email protected]>
Merge pull request #135 from BioJulia/newseq

replace sequence types with BioSequence

430851b4f3f0a2542580ac0c70b716225cf3bb9f authored almost 9 years ago by Ben J. Ward <[email protected]>
merge symbols.md to seq.md

e184ff858c58ac0af58e134f8d334316be93a688 authored almost 9 years ago by Kenta Sato <[email protected]>
do not extend `Base.complement` and `Base.complement!` in Bio.Seq

This is because Base.complement and Bio.Seq.complement are semantically
different from each other.

9b649e67ffe25d0c3b6eacc092ad825103e49221 authored almost 9 years ago by Kenta Sato <[email protected]>
add docs about BioSequence

90845d7fc93f7941c338e5284a04c41ed2deb5bd authored almost 9 years ago by Kenta Sato <[email protected]>
add "Compact representation" section

0cf2232b55c04c1442139d02f1627c131ec7f335 authored almost 9 years ago by Kenta Sato <[email protected]>
faster mismatches

dc4f8cb7465d59ef01cddd5d9916d43b03697af5 authored almost 9 years ago by Kenta Sato <[email protected]>
make Kmer a subtype of Sequence

1748bdc8faae6fc681fd092fd51a297ec3489fe9 authored almost 9 years ago by Kenta Sato <[email protected]>
clean up printers of Kmer

3851da0eb95c190df636c90ad5f1b5336715ed9e authored almost 9 years ago by Kenta Sato <[email protected]>
define eltype for EachKmerIterator

72210e7d8efad24b2af78fae42e95f318553fcbe authored almost 9 years ago by Kenta Sato <[email protected]>
export reverse_complement!

1d9c378631c6bf9ac56defa619d0b967aa0d2f21 authored almost 9 years ago by Kenta Sato <[email protected]>
add tests for `encode` and `decode`

27458099cfbf25e3e3ecd9689ba4ddf3d8272c6f authored almost 9 years ago by Kenta Sato <[email protected]>
test FASTA files that contain gaps and ambiguity

457b82517aea88333629c39c4b1b5b87f976c474 authored almost 9 years ago by Kenta Sato <[email protected]>
add eachindex for BioSequence

deaf70be1a7ca62401831a820eff0a068d59299b authored almost 9 years ago by Kenta Sato <[email protected]>
make reverse faster

47b6ebf786c53ab7abf54f9a4ee7f16ced5b8e13 authored almost 9 years ago by Kenta Sato <[email protected]>
make encode/decode safer

0166a75da7f51b307ead81ad52e8e1367318d222 authored almost 9 years ago by Kenta Sato <[email protected]>
rename a local variable used in @encode_seq macro

e3189fe36e41f32f49fb56cbfcd758eb40438192 authored almost 9 years ago by Kenta Sato <[email protected]>
faster reverse!

0ac6bf01434c4aa03adb052d63180f87fe2a4bfd authored almost 9 years ago by Kenta Sato <[email protected]>
add composition function

rather directly calling `Composition` constructor.

0b89704e04d1940fc29a90ff36ce4fe85de67191 authored almost 9 years ago by Kenta Sato <[email protected]>
support translation of stop codons

b8208bfe2de1a8e5cc5364ea66541ad3c000459b authored almost 9 years ago by Kenta Sato <[email protected]>
make Composition faster

4cc72a8f90996cf56167b346a3c0276c197bbd01 authored almost 9 years ago by Kenta Sato <[email protected]>
make `bitsid` faster

d5b18e7790639e2c3b6db856e17eb989a84068e2 authored almost 9 years ago by Kenta Sato <[email protected]>
make complement! faster for 4-bit encoded sequences

e424c2e451fecba00a0ef157a8534dbb7c711e1b authored almost 9 years ago by Kenta Sato <[email protected]>
inline checkbounds and checkmutability

5cdf7c2074620e9c0f474c2a924e4d83efbe4bcd authored almost 9 years ago by Kenta Sato <[email protected]>
add stop codon and amino acid gap

aa72958d2972f4a23a626a62c7a5449b154ff894 authored almost 9 years ago by Kenta Sato <[email protected]>
add more ambiguous nucleotides and a gap character

b0f95d0b07533da00654f97d7dca8adf71a30df5 authored almost 9 years ago by Kenta Sato <[email protected]>
replace sequence types with BioSequence

151b58a8daacbd93c9c0ec8bf0270787c84273df authored almost 9 years ago by Kenta Sato <[email protected]>
reorder amino acids

standard, non-standard, ambiguous, terminal, then gap.

5db71608c5845637a569ff1f445e5610c6e5219e authored almost 9 years ago by Kenta Sato <[email protected]>
rename AA_Stop to AA_Term

e26dbed62f4e67944c640f39c2adfbb11116edfc authored almost 9 years ago by Kenta Sato <[email protected]>
break long lines

ad220c20e45667dd78049591cfee896cf2d0c541 authored almost 9 years ago by Kenta Sato <[email protected]>
add CharSequence

132fcbdcf8640f15b4d9552bbddfcd5970756370 authored almost 9 years ago by Kenta Sato <[email protected]>
clean up functions of BioSequence

0da9d1776054b9e026ea00553992f3fec2fc3376 authored almost 9 years ago by Kenta Sato <[email protected]>
add MurmurHash3 hash function for BioSequence

ae6ca7a5bfb294379ae516cad021826675130144 authored almost 9 years ago by Kenta Sato <[email protected]>
add copy-on-write sematics of BioSequence

and add more mutating operations.

2128b352894e92c14345a6f2e65297192b0a6ec4 authored almost 9 years ago by Kenta Sato <[email protected]>
small cleanup of submat.jl

c412508d72a9ccdacfa1eee6c6dc8f48e3e22e51 authored almost 9 years ago by Kenta Sato <[email protected]>
include scores of stop in NCBI submats

76a1645b027618f7d2ba265e796d31711f59d190 authored almost 9 years ago by Kenta Sato <[email protected]>
clean up tests of Bio.Seq

80620afecb379bca21ea8031ba5ce7b02ddaf3a0 authored almost 9 years ago by Kenta Sato <[email protected]>
remove an unnecessary test

c0983add15a75cbd4b8a89816ad16cf51ba0e8dc authored almost 9 years ago by Kenta Sato <[email protected]>
clean up concatenation of BioSequene

f2a0f84890c56666eb06187dc78fa1d94eb88c0b authored almost 9 years ago by Kenta Sato <[email protected]>
Resized logo image again

2426157ec9ff4688b503887f024600a2b5545ede authored almost 9 years ago by Ward9250 <[email protected]>
Resized logo image again

a496c2db848759f88e5a0d270ea7b4c5b07c79f5 authored almost 9 years ago by Ward9250 <[email protected]>
resized logo image for manpages

21dad12a7bf99cbe323cd53e325bac38298ed534 authored almost 9 years ago by Ward9250 <[email protected]>
moved logo to images folder, as assets folder is reserved for lapidary

aec1ea257ede11f0a804f1e265cf39f5b5e5879d authored almost 9 years ago by Ward9250 <[email protected]>
Added make instructions to copy logo over

b675b2a3f808ebb782a272cdd12f4d16875a41d2 authored almost 9 years ago by Ward9250 <[email protected]>
Added logo to assets folder

21adec11c63d580aa44d68e94620d4460446ebaf authored almost 9 years ago by Ward9250 <[email protected]>
Edited makedocs.yml

3860dd588b1795dd9e0adc7ea6ec9a239b0cb5e8 authored almost 9 years ago by Ward9250 <[email protected]>
Added reference docs

dc28e8017d673f2b04a8f2df4ca6410c9e53f551 authored almost 9 years ago by Ward9250 <[email protected]>
Added Bio.Seq reference documentation

53bb3a57d48a5fd92e1f4be10bfa47e5460f6b3f authored almost 9 years ago by Ward9250 <[email protected]>
Corrected link to documentation.

54769cd7e277ca151b7a7a2bcdb4bceb8ab4e746 authored almost 9 years ago by Ben J. Ward <[email protected]>
Edited mkdocs.yml to provide markdown extension

219525ab686db02334c8475c2f62e3ad8291b408 authored almost 9 years ago by Ward9250 <[email protected]>
Edited contributing.md

d3a9681069c5e39fb706f07c7e9f27e3e9df66ab authored almost 9 years ago by Ward9250 <[email protected]>
Added contributing section to the docs

96e1b9faba49e38daa68ae02ecb6f4b01f8fb4ca authored almost 9 years ago by Ward9250 <[email protected]>
Fixed path to docs in readme badge

98bee9883c1a0686527c1c68bf1cd73c117d9454 authored almost 9 years ago by Ward9250 <[email protected]>
Added mkdocs material theme

f6e3c65469342a969b9c697a3966cd5123d46066 authored almost 9 years ago by Ward9250 <[email protected]>
Edited mkdocs.yml and removed old docs folder

df41cd1eea62d7a5d7c2a184c57b39d9e34901bb authored almost 9 years ago by Ward9250 <[email protected]>
Switched os to linux

fc7dc90a3be0ab100c637d9bf0cd0f9d4c20cf9d authored almost 9 years ago by Ward9250 <[email protected]>
Corrected travis settings

df07984cc795eba25b53620fc80f4b3af17d0df2 authored almost 9 years ago by Ward9250 <[email protected]>
Edited deploydocs call to use julia 0.4

297806795bd093dc8f020f88f4b1e6761178ff26 authored almost 9 years ago by Ward9250 <[email protected]>
Removed some annoying ds-store files

95f4a0520e80776ddbdb1a4b08436e9d9c69f172 authored almost 9 years ago by Ward9250 <[email protected]>
Merge pull request #139 from BioJulia/lapidocs

Setting up Lapidary.jl to generate BioJulia documentation.

6fca9ae908355b12e725444d22e7a71a89898885 authored almost 9 years ago by Ben J. Ward <[email protected]>
Edited manpages

889396e19b46f4821af313176043c20eb5d34d6f authored almost 9 years ago by Ward9250 <[email protected]>
Added more docs files, and setting up for hosting on gh-pages

a5013221e512f468d58dd15b44e591cdcf502ddf authored almost 9 years ago by Ward9250 <[email protected]>
Added seq and install md files

b5e7d92545f6c600dff1fc22d8f5eebe0642febb authored almost 9 years ago by Ward9250 <[email protected]>
Added make.jl

6291c75c6783ee93384c9c2c32837c92043c76d9 authored almost 9 years ago by Ward9250 <[email protected]>
Merge pull request #131 from jgreener64/strucmin

Struc module - framework for parsing PDB files and dealing with protein structures

1d08cd85fcc42131f6a01d21d351cb926568f06d authored almost 9 years ago by Ben J. Ward <[email protected]>
less restrictive function typing - AbstractString and Integer

f0d0b0cffdd08e81b25edff37f79093417b5e9e6 authored almost 9 years ago by Joe Greener <[email protected]>
Merge pull request #1 from bicycle1885/fix-pdb-filepath

fix filepath of PDB files

fc7c928da11506253f08bf48568f4848b1b67df4 authored almost 9 years ago by Joe Greener <[email protected]>
fix filepath of PDB files

e924fb06bee530c7d0f0e77b7d9c95b72d0ef777 authored almost 9 years ago by Kenta Sato <[email protected]>
remove PDB files; suggested changes made

fb30ad040c73bc10e53cedcc56823b5d14477c17 authored almost 9 years ago by Joe Greener <[email protected]>
function docs; show atom change; tutorial update

b56ef8309499f63d7c05488d763726aad7c7a66b authored almost 9 years ago by Joe Greener <[email protected]>
tests for organise functions and writepdb

64c5ff789f8ad96d52bda58366c049fd7b14d6b9 authored almost 9 years ago by Joe Greener <[email protected]>
tests for parsing/counts/collect/sorting; method type params

591d7b75b2dd20e712db7ae5e27eef543f413780 authored almost 9 years ago by Joe Greener <[email protected]>
some var names; setters; parsing and writing tests

cb253453ccc546ba0a3493558f0ef4056b40cad3 authored almost 9 years ago by Joe Greener <[email protected]>
explicit Base; sort and tests; organise res

0932722b626cd5efde4aecc4d4dbb6435d41f606 authored almost 9 years ago by Joe Greener <[email protected]>
tests for selectors, spatial and some parsing

f91ff19924fd3fc20fd3704291bd039b2b3b1d7e authored almost 9 years ago by Joe Greener <[email protected]>
tests for model scheme and parsing functions; Array -> Vector

17567a1996dd4da2c0f341d1729cc560e38f26ff authored almost 9 years ago by Joe Greener <[email protected]>
typealiases to Vectors; selector arguments rename; other renames

fc0faf2059b3631bef824d4d49dd162fa3640c10 authored almost 9 years ago by Joe Greener <[email protected]>
get/set rename; Set for selectors; rename to Structure

3bd5b5d1d054de11c3b6b250dab88953fa89f534 authored almost 9 years ago by Joe Greener <[email protected]>
No -> number; ASCIIString; haskey; isa

44901ac1f65ade93e441aa6a35aa63da7a0b9052 authored almost 9 years ago by Joe Greener <[email protected]>
basic docs; exports; bugfixes

d8c45bd293f4a4adbad2ba0e63418b8e849a1c06 authored almost 9 years ago by Joe Greener <[email protected]>
organise AtomList improvement

b194c9db17437ad605664df3fa8d4cba78f1e5e2 authored almost 9 years ago by Joe Greener <[email protected]>
getcoordarray; tests into one file

e3558e2eddaaaf7e13ee0a17568fa3bff1693d16 authored almost 9 years ago by Joe Greener <[email protected]>
Store residue/atom lists for faster collections; some docs

9d122d82c6c9da65f9a7624735ac6272651a7094 authored almost 9 years ago by Joe Greener <[email protected]>
formatomlist; many bug fixes

ac2593019cd1dd24f33a088b287abae132c8832d authored almost 9 years ago by Joe Greener <[email protected]>
Merge from master; change test structure

80a77b5556776f2baba49b854898f4a0cf43c549 authored almost 9 years ago by Joe Greener <[email protected]>
arg... fixing; some getter/setters; organise into res

50c7157940544ec91d296889a8da443842afa24b authored almost 9 years ago by Joe Greener <[email protected]>
Merge pull request #130 from BioJulia/newtests

Replace FactCheck with BaseTestNext

ebf7062e38c6fc9ca8c5426679dddaca205b59b1 authored almost 9 years ago by Richard Smith-Unna <[email protected]>
parsing functions; ternary operators; organise

893c063e41e25397497dc93d6f53f5d3d04e2bcb authored almost 9 years ago by Joe Greener <[email protected]>
addtomodel!; show; some model and spatial tests

8dd323d163750a490096f94ae3c0402172600f39 authored almost 9 years ago by Joe Greener <[email protected]>
show; organise; spatial; test outline

9be74f000bebce4c5c99f929ec2b0d23d3676d11 authored almost 9 years ago by Joe Greener <[email protected]>
more getters; organise and unfold

1ad8911d51889113f5f62788c81acafa1b901d99 authored almost 9 years ago by Joe Greener <[email protected]>
type scheme; some getters, iterators and selectors

e2b7fee2cbd6797247880b7e713bc8da24d6e22f authored almost 9 years ago by Joe Greener <[email protected]>