ezgff 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -54,3 +54,9 @@ build-iPhoneSimulator/
 
 # Used by RuboCop. Remote config files pulled in from inherit_from directive.
 # .rubocop-https?--*
+
+# for python
+__pycache__/
+
+# for Mac
+.DS_Store

data/README.md

@@ -1,39 +1,56 @@
-# ezgff_alpha
+# ezgff
 
-## What is ezgff_alpha
+## What is ezgff?
 
 Utilities for GFF3, the genome annotation format. Useful to explore the gene model features.
 
+
 ## Pre-requisites
 
-  * sqlite3
+  * Sqlite3
+  * Ruby
 
 ## Install
 
 ```bash
-gem ezgff
+gem install ezgff
 ```
 
 ## Quick start
 
-Build database from GFF3 file.
+ezgff provides the command line interface.
+
+You need build an ezgff database from the gff3 file first by using 'build' subcommand. Once you built ezgff db, you can search and retrieve data from the database by using 'search' and 'view' subcommands.
+
+### Build database from GFF3 file.
 
 ```bash
-ezgff build in.gff3
+ezgff build gff3_file
 ```
 
-Retrieve GFF3 reacod by ID.
+This command generates gff3_file.ezdb directory which is the ezgff database that will be specified when you use view and search subcommands.
 
-```bash
-ezgff view data.ezdb cds-WP_010895901.1 --with=ancestors
+### Retrieve GFF3 reacod by ID.
+
+```
+ezgff view DB ID 
 ```
 
 ```
-ezgff view data.ezdb cds-WP_010895901.1 --with=ancestors --format=json |jq
+ezgff view DB ID --with=ancestors
 ```
 
-examples to use jq
+GFF lines with the ID are displayed.
+
+Data can be formated in JSON. Below are examples to work with jq.
+
+```
+ezgff view data.ezdb cds-WP_010895901.1 --with=ancestors --format=json |jq
+```
 
+More complicated example
 ```
-ezgff_alpha/bin/ezgff view GCF_000009605.1_ASM960v1_genomic.gff.ezdb cds-WP_010895901.1  --with=ancestors --format=json  |jq -r '.gff_records | map(select(.type == "gene"))[0] | [.seqid, .start, .end, .attributes.gene] |@csv'
+ezgff view GCF_000009605.1_ASM960v1_genomic.gff.ezdb cds-WP_010895901.1  --with=ancestors --format=json \
+ |jq -r '.gff_records | map(select(.type == "gene"))[0] | [.seqid, .start, .end, .attributes.gene] \
+ |@csv'
 ```

data/lib/ezgff/gffsqlitedb.rb

@@ -103,8 +103,20 @@ module Ezgff
       
           sql = "INSERT INTO gff_records (line_num, record, id, parent, seqid, source, type, start, end, score, strand, phase, attributes, attributes_json)
           VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"
-          values = [i, l.chomp, id, parent, 
-            a[0], a[1], a[2], a[3], a[4], a[5], a[6], a[7], a[8], 
+          values = [
+            i,       # line number
+            l.chomp, # raw record
+            id,      # ID
+            parent,  # parent ID
+            a[0],    # seqid
+            a[1],    # source
+            a[2],    # type
+            a[3],    # start
+            a[4],    # end
+            (a[5] == "." ? nil : a[5]),    # score
+            a[6],    # strand
+            (a[7] == "." ? nil : a[7]),    # phase
+            a[8],    # attributes
             attributes_as_json(l)]
           sq3_db.execute(sql, values)
         end

data/lib/ezgff/version.rb

@@ -1,3 +1,3 @@
 module Ezgff
-  VERSION = "0.0.4"
+  VERSION = "0.0.5"
 end

data/webapi/app/main.py

@@ -0,0 +1,76 @@
+from fastapi import FastAPI
+from fastapi import Query, Path
+from typing import Optional, List
+import subprocess
+import sys
+import json
+from pydantic import BaseModel, Field
+from enum import Enum
+from pydantic.errors import NoneIsNotAllowedError
+import uvicorn
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('-d', '--db', required=True)
+parser.add_argument('-b', '--bind', default='0.0.0.0')
+parser.add_argument('-p', '--port', type=int, default=8000)
+args = parser.parse_args()
+print(args)
+ezdb = args.db
+
+#print(ezdb)
+#print(args)
+
+app = FastAPI()
+
+class OptWith(str, Enum):
+    none = "none"
+    parent = "parent" 
+    children = "children"
+    ancestors = "ancestors"
+    descendants = "descendants"
+
+class GffColumnStrand(str, Enum):
+    plus = "+"
+    minus = "-"
+    unstranded = "."
+    unknown = "?"
+
+class GffRecord(BaseModel):
+    seqid: str = Field(title="seqid", descripion="GFF3 column 1: sequence ID", example="NC_002528.1")
+    source: str = Field(title="source", descripion="GFF3 column 2: algorithm or operating procedure", example="Refseq")
+    type: str = Field(title="type", description="GFF3 column 3: the type of the feature (previously called the \"method\"")
+    start: int = Field(title="start", description="GFF3 column 4: the start coordinate of the feature. 1-based integer.")
+    end: int = Field(title="end", description="GFF3 column 5: the end coordinate of the feature. 1-based integer.")
+    score: Optional[float] = Field(None, description="GFF3 column 6: the score of the feature. A floating point number.")
+    strand: GffColumnStrand = Field(title="strand", description="GFF3 column 7: the strand of the feature. +, -, . (unstranded), ? (unknown) are allowed.")
+    phase: Optional[int] = Field(None, description="GFF3 column 8: phase for CDS. 0, 1, 2 are allowed.")
+    line_num: int = Field(description="Line number in the original GFF3 file. Required and Unique.")
+    id: Optional[str] = Field(None, description="ID")
+    parent_id: Optional[str] = Field(None, description="Parent ID")
+    attributes: Optional[dict] = Field(title="attributes", description="Gff3 column 9: attributes.")
+
+class GffRecords(BaseModel):
+    gff_records: List[GffRecord]
+
+@app.get("/view/{query}", response_model=GffRecords)
+def view(
+    query: str = Path(..., example="NC_002528.1"),
+    w: OptWith = Query("none", description="with"),
+    t: Optional[str] = Query(None, description="type", example="gene")
+    ):
+    return json.loads(run_ezgff(query, w, t))
+
+def run_ezgff(query, w, t):
+    cmd = ["ezgff", "view", ezdb, query, "-f", "json", "-w", w]
+    if t:
+        cmd.extend(["-t", t])
+    print(cmd)
+    proc = subprocess.run(cmd, stdout=subprocess.PIPE)
+    res = proc.stdout
+    print(res)
+    return res
+
+
+if __name__ == "__main__":
+    uvicorn.run(app, host=args.bind, port=args.port)

data/webapi/app/run.py

@@ -0,0 +1,5 @@
+import uvicorn
+ 
+if __name__ == '__main__':
+    # コンソールで [$ uvicorn run:app --reload]でも可
+    uvicorn.run(app="main")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ezgff
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
 platform: ruby
 authors:
 - Shuji Shigenobu
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2021-07-14 00:00:00.000000000 Z
+date: 2021-07-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sqlite3
@@ -91,6 +91,8 @@ files:
 - lib/ezgff.rb
 - lib/ezgff/gffsqlitedb.rb
 - lib/ezgff/version.rb
+- webapi/app/main.py
+- webapi/app/run.py
 homepage: https://github.com/shujishigenobu/ezgff_alpha
 licenses:
 - MIT