bio-fasta_retrieve 0.0.4 → 0.0.5
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/bio-fasta_retrieve.rb +8 -6
- metadata +1 -1
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: d3b63b0ca6955d7354b0ed2efb8abfa5687532fd
|
|
4
|
+
data.tar.gz: 59b6c6ecb9aff21fbb2e02798868ff5f2c2699c7
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: db39c28f937d307baa9ddcc6eb601bd563a1f1644bb70600da2cd19b888bcd33bef4536c98d0eb42d48748393e9fd1b98db57b9c4781ab506b637eda69cd3a65
|
|
7
|
+
data.tar.gz: afe597861c46696c36542687e056431579baa808852dd2239880a2e4643e0fbca76547017f41d4c0a5d3ea96338a21ed6039a21ff3722200f3b7137573db542b
|
data/lib/bio-fasta_retrieve.rb
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
#
|
|
1
2
|
# Copyright:: Copyright (C) 2015
|
|
2
3
|
# Andrei Rozanski <rozanski.andrei@gmail.com>
|
|
3
4
|
# License:: The Ruby License
|
|
@@ -8,12 +9,12 @@
|
|
|
8
9
|
module FastaRetriever
|
|
9
10
|
class Retriever
|
|
10
11
|
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
12
|
+
# Example:
|
|
13
|
+
# >> Retriever.retrieve("hg19","chr1","1000","2000")
|
|
14
|
+
#
|
|
15
|
+
# Arguments:
|
|
16
|
+
# language: (String)
|
|
17
|
+
#
|
|
17
18
|
|
|
18
19
|
require 'bio' # For creation of fasta object.
|
|
19
20
|
require 'nokogiri' # For sequence retrieve and parse.
|
|
@@ -21,6 +22,7 @@ module FastaRetriever
|
|
|
21
22
|
|
|
22
23
|
def initialize;end
|
|
23
24
|
|
|
25
|
+
|
|
24
26
|
#input organism, chromosome, start, end separated by space (i.e. hg19 chr10 1000 2000)
|
|
25
27
|
def self.retrieve(organism,chr,start_coord,end_coord)
|
|
26
28
|
address="http://genome.ucsc.edu/cgi-bin/das/#{organism}/dna?segment=#{chr}:#{start_coord},#{end_coord}"
|