Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Genbank parser fixes #389

Closed
wants to merge 16 commits into from
Closed

Genbank parser fixes #389

Show file tree
Hide file tree
Changes from 8 commits
Commits
Show all changes
16 commits
Select commit Hold shift + click to select a range
158fcf1
Added generic collections module
abondrn Oct 30, 2023
8862a6c
Switched Feature.Attributes to use multimap
abondrn Oct 30, 2023
ef07e94
Fixed tests
abondrn Oct 30, 2023
cac1e55
Ran linter
abondrn Oct 30, 2023
8025bc2
Added copy methods
abondrn Oct 30, 2023
1f49f9d
Adds new functional test that addresses case where there is a partial…
abondrn Oct 30, 2023
8112866
Ran linter
abondrn Oct 30, 2023
fec8796
Add capability to compute sequence features and marshal en masse
abondrn Oct 30, 2023
9ce9f4f
Add methods to convert polyjson -> genbank
abondrn Oct 30, 2023
89a2ba4
Removed generic collections library in favor of hand-rolled multimap,…
abondrn Oct 30, 2023
b88d7b8
Propogate handrolled multimap to test files
abondrn Oct 30, 2023
b4c3a37
Responded to more comments
abondrn Oct 30, 2023
8b82d7b
Reduced new example genbank file
abondrn Oct 31, 2023
f523651
Resolved lint errors, added test StoreFeatureSequences and fixed unco…
abondrn Oct 31, 2023
1270ec8
Added multimap.go file doc
abondrn Oct 31, 2023
9c322f6
Responded to more comments
abondrn Oct 31, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 12 additions & 0 deletions CONTRIBUTING.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,18 @@ In order to simplify the development experience, and environment setup, the poly

Whether you're a beginner with Go or you're an experienced developer, You should see the suggestions popup automatically when you goto the *Plugins* tab in VSCode. Using these plugins can help accelerate the development experience and also allow you to work more collaboratively with other poly developers.

## Local Checks

Poly runs numerous CI/CD checks via Github Actions before a PR can be merged. In order to make your PR mergeable, your PR must pass all of these checks.

A quick way to check your PR will pass is to run:

```sh
gofmt -s -w . && go test ./...
```

Additionally, you may want to [install](https://golangci-lint.run/usage/install/#local-installation) and run the linter.

Koeng101 marked this conversation as resolved.
Show resolved Hide resolved
# How to report a bug

### Security disclosures
Expand Down
10,207 changes: 10,207 additions & 0 deletions data/NC_001141.2.gb
View file
Open in desktop
Koeng101 marked this conversation as resolved.
Show resolved Hide resolved

Large diffs are not rendered by default.

2 changes: 2 additions & 0 deletions go.mod
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,9 @@ require (
require (
github.com/davecgh/go-spew v1.1.1 // indirect
github.com/mattn/go-sqlite3 v1.14.13 // indirect
github.com/segmentio/fasthash v1.0.3 // indirect
github.com/spaolacci/murmur3 v1.1.0 // indirect
github.com/zyedidia/generic v1.2.1 // indirect
abondrn marked this conversation as resolved.
Show resolved Hide resolved
)

require (
Expand Down
4 changes: 4 additions & 0 deletions go.sum
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,13 +20,17 @@ github.com/mroth/weightedrand v0.4.1 h1:rHcbUBopmi/3x4nnrvwGJBhX9d0vk+KgoLUZeDP6
github.com/mroth/weightedrand v0.4.1/go.mod h1:3p2SIcC8al1YMzGhAIoXD+r9olo/g/cdJgAD905gyNE=
github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
github.com/segmentio/fasthash v1.0.3 h1:EI9+KE1EwvMLBWwjpRDc+fEM+prwxDYbslddQGtrmhM=
github.com/segmentio/fasthash v1.0.3/go.mod h1:waKX8l2N8yckOgmSsXJi7x1ZfdKZ4x7KRMzBtS3oedY=
github.com/sergi/go-diff v1.2.0 h1:XU+rvMAioB0UC3q1MFrIQy4Vo5/4VsRDQQXHsEya6xQ=
github.com/sergi/go-diff v1.2.0/go.mod h1:STckp+ISIX8hZLjrqAeVduY0gWCT9IjLuqbuNXdaHfM=
github.com/spaolacci/murmur3 v1.1.0 h1:7c1g84S4BPRrfL5Xrdp6fOJ206sU9y293DDHaoy0bLI=
github.com/spaolacci/murmur3 v1.1.0/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA=
github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk=
github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
github.com/zyedidia/generic v1.2.1 h1:Zv5KS/N2m0XZZiuLS82qheRG4X1o5gsWreGb0hR7XDc=
github.com/zyedidia/generic v1.2.1/go.mod h1:ly2RBz4mnz1yeuVbQA/VFwGjK3mnHGRj1JuoG336Bis=
golang.org/x/exp v0.0.0-20230310171629-522b1b587ee0 h1:LGJsf5LRplCck6jUCH3dBL2dmycNruWNF5xugkSlfXw=
golang.org/x/exp v0.0.0-20230310171629-522b1b587ee0/go.mod h1:CxIveKay+FTh1D0yPZemJVgC/95VzuuOLq5Qi4xnoYc=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
Expand Down
4 changes: 2 additions & 2 deletions io/genbank/example_test.go
View file
Open in desktop
Koeng101 marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"os"
"path/filepath"

"github.com/TimothyStiles/poly/io/genbank"

Check failure on line 9 in io/genbank/example_test.go

View workflow job for this annotation

GitHub Actions / lint 

could not import github.com/TimothyStiles/poly/io/genbank (-: # github.com/TimothyStiles/poly/io/genbank [github.com/TimothyStiles/poly/io/genbank.test]
)

// This example shows how to open a genbank file and search for a gene given
Expand All @@ -14,8 +14,8 @@
func Example_basic() {
sequences, _ := genbank.Read("../../data/puc19.gbk")
for _, feature := range sequences.Features {
if feature.Attributes["gene"] == "bla" {
fmt.Println(feature.Attributes["note"])
if feature.Type == "CDS" && feature.Attributes.Has("gene") && feature.Attributes.Get("gene")[0] == "bla" {
fmt.Println(feature.Attributes.Get("note")[0])
}
}
// Output: confers resistance to ampicillin, carbenicillin, andrelated antibiotics
Expand Down
Loading
Loading