Skip to content

Commit a819898

Browse files
totakketotakke
committed
First commit
0 parents  commit a819898

23 files changed

+2064
-0
lines changed

‎.gitignore

+11
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
/target
2+
/classes
3+
/checkouts
4+
pom.xml
5+
pom.xml.asc
6+
*.jar
7+
*.class
8+
/.lein-*
9+
/.nrepl-port
10+
11+
/.cavia

‎LICENSE

+202
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,202 @@
1+
2+
Apache License
3+
Version 2.0, January 2004
4+
http://www.apache.org/licenses/
5+
6+
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
7+
8+
1. Definitions.
9+
10+
"License" shall mean the terms and conditions for use, reproduction,
11+
and distribution as defined by Sections 1 through 9 of this document.
12+
13+
"Licensor" shall mean the copyright owner or entity authorized by
14+
the copyright owner that is granting the License.
15+
16+
"Legal Entity" shall mean the union of the acting entity and all
17+
other entities that control, are controlled by, or are under common
18+
control with that entity. For the purposes of this definition,
19+
"control" means (i) the power, direct or indirect, to cause the
20+
direction or management of such entity, whether by contract or
21+
otherwise, or (ii) ownership of fifty percent (50%) or more of the
22+
outstanding shares, or (iii) beneficial ownership of such entity.
23+
24+
"You" (or "Your") shall mean an individual or Legal Entity
25+
exercising permissions granted by this License.
26+
27+
"Source" form shall mean the preferred form for making modifications,
28+
including but not limited to software source code, documentation
29+
source, and configuration files.
30+
31+
"Object" form shall mean any form resulting from mechanical
32+
transformation or translation of a Source form, including but
33+
not limited to compiled object code, generated documentation,
34+
and conversions to other media types.
35+
36+
"Work" shall mean the work of authorship, whether in Source or
37+
Object form, made available under the License, as indicated by a
38+
copyright notice that is included in or attached to the work
39+
(an example is provided in the Appendix below).
40+
41+
"Derivative Works" shall mean any work, whether in Source or Object
42+
form, that is based on (or derived from) the Work and for which the
43+
editorial revisions, annotations, elaborations, or other modifications
44+
represent, as a whole, an original work of authorship. For the purposes
45+
of this License, Derivative Works shall not include works that remain
46+
separable from, or merely link (or bind by name) to the interfaces of,
47+
the Work and Derivative Works thereof.
48+
49+
"Contribution" shall mean any work of authorship, including
50+
the original version of the Work and any modifications or additions
51+
to that Work or Derivative Works thereof, that is intentionally
52+
submitted to Licensor for inclusion in the Work by the copyright owner
53+
or by an individual or Legal Entity authorized to submit on behalf of
54+
the copyright owner. For the purposes of this definition, "submitted"
55+
means any form of electronic, verbal, or written communication sent
56+
to the Licensor or its representatives, including but not limited to
57+
communication on electronic mailing lists, source code control systems,
58+
and issue tracking systems that are managed by, or on behalf of, the
59+
Licensor for the purpose of discussing and improving the Work, but
60+
excluding communication that is conspicuously marked or otherwise
61+
designated in writing by the copyright owner as "Not a Contribution."
62+
63+
"Contributor" shall mean Licensor and any individual or Legal Entity
64+
on behalf of whom a Contribution has been received by Licensor and
65+
subsequently incorporated within the Work.
66+
67+
2. Grant of Copyright License. Subject to the terms and conditions of
68+
this License, each Contributor hereby grants to You a perpetual,
69+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
70+
copyright license to reproduce, prepare Derivative Works of,
71+
publicly display, publicly perform, sublicense, and distribute the
72+
Work and such Derivative Works in Source or Object form.
73+
74+
3. Grant of Patent License. Subject to the terms and conditions of
75+
this License, each Contributor hereby grants to You a perpetual,
76+
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
77+
(except as stated in this section) patent license to make, have made,
78+
use, offer to sell, sell, import, and otherwise transfer the Work,
79+
where such license applies only to those patent claims licensable
80+
by such Contributor that are necessarily infringed by their
81+
Contribution(s) alone or by combination of their Contribution(s)
82+
with the Work to which such Contribution(s) was submitted. If You
83+
institute patent litigation against any entity (including a
84+
cross-claim or counterclaim in a lawsuit) alleging that the Work
85+
or a Contribution incorporated within the Work constitutes direct
86+
or contributory patent infringement, then any patent licenses
87+
granted to You under this License for that Work shall terminate
88+
as of the date such litigation is filed.
89+
90+
4. Redistribution. You may reproduce and distribute copies of the
91+
Work or Derivative Works thereof in any medium, with or without
92+
modifications, and in Source or Object form, provided that You
93+
meet the following conditions:
94+
95+
(a) You must give any other recipients of the Work or
96+
Derivative Works a copy of this License; and
97+
98+
(b) You must cause any modified files to carry prominent notices
99+
stating that You changed the files; and
100+
101+
(c) You must retain, in the Source form of any Derivative Works
102+
that You distribute, all copyright, patent, trademark, and
103+
attribution notices from the Source form of the Work,
104+
excluding those notices that do not pertain to any part of
105+
the Derivative Works; and
106+
107+
(d) If the Work includes a "NOTICE" text file as part of its
108+
distribution, then any Derivative Works that You distribute must
109+
include a readable copy of the attribution notices contained
110+
within such NOTICE file, excluding those notices that do not
111+
pertain to any part of the Derivative Works, in at least one
112+
of the following places: within a NOTICE text file distributed
113+
as part of the Derivative Works; within the Source form or
114+
documentation, if provided along with the Derivative Works; or,
115+
within a display generated by the Derivative Works, if and
116+
wherever such third-party notices normally appear. The contents
117+
of the NOTICE file are for informational purposes only and
118+
do not modify the License. You may add Your own attribution
119+
notices within Derivative Works that You distribute, alongside
120+
or as an addendum to the NOTICE text from the Work, provided
121+
that such additional attribution notices cannot be construed
122+
as modifying the License.
123+
124+
You may add Your own copyright statement to Your modifications and
125+
may provide additional or different license terms and conditions
126+
for use, reproduction, or distribution of Your modifications, or
127+
for any such Derivative Works as a whole, provided Your use,
128+
reproduction, and distribution of the Work otherwise complies with
129+
the conditions stated in this License.
130+
131+
5. Submission of Contributions. Unless You explicitly state otherwise,
132+
any Contribution intentionally submitted for inclusion in the Work
133+
by You to the Licensor shall be under the terms and conditions of
134+
this License, without any additional terms or conditions.
135+
Notwithstanding the above, nothing herein shall supersede or modify
136+
the terms of any separate license agreement you may have executed
137+
with Licensor regarding such Contributions.
138+
139+
6. Trademarks. This License does not grant permission to use the trade
140+
names, trademarks, service marks, or product names of the Licensor,
141+
except as required for reasonable and customary use in describing the
142+
origin of the Work and reproducing the content of the NOTICE file.
143+
144+
7. Disclaimer of Warranty. Unless required by applicable law or
145+
agreed to in writing, Licensor provides the Work (and each
146+
Contributor provides its Contributions) on an "AS IS" BASIS,
147+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
148+
implied, including, without limitation, any warranties or conditions
149+
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
150+
PARTICULAR PURPOSE. You are solely responsible for determining the
151+
appropriateness of using or redistributing the Work and assume any
152+
risks associated with Your exercise of permissions under this License.
153+
154+
8. Limitation of Liability. In no event and under no legal theory,
155+
whether in tort (including negligence), contract, or otherwise,
156+
unless required by applicable law (such as deliberate and grossly
157+
negligent acts) or agreed to in writing, shall any Contributor be
158+
liable to You for damages, including any direct, indirect, special,
159+
incidental, or consequential damages of any character arising as a
160+
result of this License or out of the use or inability to use the
161+
Work (including but not limited to damages for loss of goodwill,
162+
work stoppage, computer failure or malfunction, or any and all
163+
other commercial damages or losses), even if such Contributor
164+
has been advised of the possibility of such damages.
165+
166+
9. Accepting Warranty or Additional Liability. While redistributing
167+
the Work or Derivative Works thereof, You may choose to offer,
168+
and charge a fee for, acceptance of support, warranty, indemnity,
169+
or other liability obligations and/or rights consistent with this
170+
License. However, in accepting such obligations, You may act only
171+
on Your own behalf and on Your sole responsibility, not on behalf
172+
of any other Contributor, and only if You agree to indemnify,
173+
defend, and hold each Contributor harmless for any liability
174+
incurred by, or claims asserted against, such Contributor by reason
175+
of your accepting any such warranty or additional liability.
176+
177+
END OF TERMS AND CONDITIONS
178+
179+
APPENDIX: How to apply the Apache License to your work.
180+
181+
To apply the Apache License to your work, attach the following
182+
boilerplate notice, with the fields enclosed by brackets "[]"
183+
replaced with your own identifying information. (Don't include
184+
the brackets!) The text should be enclosed in the appropriate
185+
comment syntax for the file format. We also recommend that a
186+
file or class name and description of purpose be included on the
187+
same "printed page" as the copyright notice for easier
188+
identification within third-party archives.
189+
190+
Copyright [yyyy] [name of copyright owner]
191+
192+
Licensed under the Apache License, Version 2.0 (the "License");
193+
you may not use this file except in compliance with the License.
194+
You may obtain a copy of the License at
195+
196+
http://www.apache.org/licenses/LICENSE-2.0
197+
198+
Unless required by applicable law or agreed to in writing, software
199+
distributed under the License is distributed on an "AS IS" BASIS,
200+
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
201+
See the License for the specific language governing permissions and
202+
limitations under the License.

‎README.md

+109
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,109 @@
1+
# varity
2+
3+
Variant translation library for Clojure.
4+
5+
## Features
6+
7+
* VCF variant -> HGVS
8+
* HGVS -> VCF variant
9+
* Conversion between assemblies
10+
11+
## Installation
12+
13+
With Leiningen/Boot:
14+
15+
```clojure
16+
[varity "0.2.0-SNAPSHOT]
17+
```
18+
19+
## Usage
20+
21+
### Notice
22+
23+
All positions are represented as one-based number, and all ranges are
24+
represented as one-based closed intervals. For example,
25+
26+
```clojure
27+
{:pos 3}
28+
```
29+
30+
represents the third position from the start, and
31+
32+
```clojure
33+
{:chr "chr1", :start 1, :end 3}
34+
```
35+
36+
represents the first three bases of chromosome 1.
37+
38+
### VCF variant to HGVS
39+
40+
`varity.vcf-to-hgvs` provides functions to convert a VCF-style variant into HGVS.
41+
The returned HGVS is data structure of [clj-hgvs](https://github.com/chrovis/clj-hgvs).
42+
43+
```clojure
44+
(require '[varity.vcf-to-hgvs :as v2h])
45+
46+
(v2h/vcf-variant->hgvs "path/to/hg38.fa" "path/to/refGene.txt.gz"
47+
"chr7" 55191822 "T" "G")
48+
;;=> ({:cdna {:kind :cdna,
49+
;; :mutations (#clj_hgvs.mutation.DNASubstitution
50+
;; {:alt "G",
51+
;; :coord #clj_hgvs.coordinate.CDNACoordinate
52+
;; {:offset 0, :position 2573, :region nil},
53+
;; :ref "T",
54+
;; :type ">"}),
55+
;; :transcript "NM_005228"},
56+
;; :protein {:kind :protein,
57+
;; :mutations (#clj_hgvs.mutation.ProteinSubstitution
58+
;; {:alt "Arg",
59+
;; :coord #clj_hgvs.coordinate.ProteinCoordinate
60+
;; {:position 858},
61+
;; :ref "Leu"}),
62+
;; :transcript nil}})
63+
```
64+
65+
Use `clj-hgvs.core/format` to obtain HGVS text.
66+
67+
```clojure
68+
(require '[clj-hgvs.core :as hgvs])
69+
70+
(def l858r (-> (v2h/vcf-variant->protein-hgvs "path/to/hg38.fa"
71+
"path/to/refGene.txt.gz"
72+
"chr7" 55191822 "T" "G")
73+
first))
74+
75+
(hgvs/format l858r {:amino-acid-format :short})
76+
;;=> p.L858R
77+
```
78+
79+
### HGVS to VCF variants
80+
81+
`varity.hgvs-to-vcf` provides functions to convert HGVS into VCF-style variants.
82+
83+
```clojure
84+
(require '[varity.hgvs-to-vcf :as h2v]
85+
'[clj-hgvs.core :as hgvs])
86+
87+
(h2v/hgvs->vcf-variants "path/to/hg38.fa" "path/to/refGene.txt.gz" (hgvs/parse "c.2573T>G") "EGFR")
88+
;;=> ({:chr "chr7", :pos 55191822, :ref "T", :alt "G"})
89+
90+
(h2v/hgvs->vcf-variants "path/to/hg38.fa" "path/to/refGene.txt.gz" (hgvs/parse "p.A222V") "MTHFR")
91+
;;=> ({:chr "chr1", :pos 11796321, :ref "G", :alt "A"})
92+
```
93+
94+
### Conversion between assemblies
95+
96+
To convert a genome coordinate between assemblies,
97+
98+
```clojure
99+
(require '[varity.lift :as lift])
100+
101+
(lift/convert-coord "chr1" 743267 "path/to/hg19ToHg38.over.chain.gz")
102+
;;=> {:chr "chr1", :pos 807887}
103+
```
104+
105+
## License
106+
107+
Copyright 2017 [Xcoo, Inc.](https://xcoo.jp/)
108+
109+
Licensed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0).

‎dev-resources/hg19ToHg38.over.chain.gz

222 KB
Binary file not shown.

‎project.clj

+16
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
(defproject varity "0.2.0-SNAPSHOT"
2+
:description "Variant translation library for Clojure"
3+
:url "https://github.com/chrovis/varity"
4+
:license {:name "Apache License, Version 2.0"
5+
:url "http://www.apache.org/licenses/LICENSE-2.0"}
6+
:min-lein-version "2.7.0"
7+
:dependencies [[org.clojure/clojure "1.8.0" :scope "provided"]
8+
[clj-hgvs "0.1.0"]
9+
[cljam "0.2.1"]
10+
[org.apache.commons/commons-compress "1.13"]
11+
[proton "0.1.1"]]
12+
:test-selectors {:default (complement :slow)
13+
:slow :slow
14+
:all (constantly true)}
15+
:profiles {:dev {:dependencies [[cavia "0.4.0"]]}
16+
:1.9 {:dependencies [[org.clojure/clojure "1.9.0-alpha15"]]}})

0 commit comments

Comments
 (0)