fasta_read 1.1.0 → 2.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 79e57cab5fe9d2e5325eb8a8aa9e05ec7393e821
+  metadata.gz: 0610fba4a055d83670705afed69fd6a98603749b
+  data.tar.gz: 5203a61fa111d3c29f73fc4396cec5f3d9a43070
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+  data.tar.gz: a1d0463b0a048cbfbce9b9196f0cce7ca73f94737e226092efe3db9ae91a74fb35f4d862aa3f747bfc4646d3c0d32e48e79a0e2782dac8dbaa7d073b49c18f7e

data/.travis.yml

@@ -1,4 +1,4 @@
 language: ruby
 rvm:
-  - 2.1.0
+  - 2.1.1
   - 1.9.3

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    fasta_read (1.1.0)
+    fasta_read (2.0.1)
       methadone (>= 1.3.2)
       rake (>= 0.9.2)
 

data/README.md

@@ -24,7 +24,7 @@ Or install it yourself as:
 ## Example
 
     fasta_read hg19 chr12 112123514 112123790 --output=out.txt
-    
+
     Options:
     -h, --help                       Show command line help
     -o, --output OUTPUTFILE          outputs sequence to a file
@@ -39,7 +39,7 @@ Or install it yourself as:
     assembly
         assembly name (hg19, mm10, etc.)
     chromosome
-        id of chromosome (1-22 or X/Y)
+        id of chromosome (chr1-chr22 or chrx/chry)
     cstart
         start coordinate (inclusive) within the chromosome
     cend
@@ -51,30 +51,40 @@ stdout: Extracted sequence (only)
 
 stderr: Any errors.
 
-using --output option export the sequence to a file
+using --output option exports the sequence to a file
 
 ## Supporting Requirements
 
 The program depends on being run at the top of a directory tree containing .fa files. The .fa files should be of the form where each file maps to a single chomosome.
-
 The directory tree will have separate branches for SNPs and unmasked files.
 
-/fasta/hg19/unmasked/chr1.fa
-/fasta/hg19/unmasked/chr2.fa
-/fasta/hg19/unmasked/chr3.fa
-........
-/fasta/hg19/snp/chr1.subst.fa
-/fasta/hg19/snp/chr2.subst.fa
-/fasta/hg19/snp/chr3.subst.fa
-.......
-/fasta/mm10/unmasked/chr1.fa
-/fasta/mm10/unmasked/chr2.fa
-/fasta/mm10/unmasked/chr3.fa
-........
-/fasta/mm10/snp/chr1.subst.fa
-/fasta/mm10/snp/chr2.subst.fa
-/fasta/mm10/snp/chr3.subst.fa
-.......
+For example, provided the following tree the command expects to be run inside the 'fasta' directory:
+
+    fasta
+    ├── hg19
+    │   ├── snp
+    │   │   ├── chr1.subst.fa
+    |   │   ├── chr2.subst.fa
+    |   │   ├── chr3.subst.fa
+    |   │   └── ....
+    │   └── unmasked
+    │       ├── chr1.fa
+    |       ├── chr2.fa
+    |       ├── chr3.fa
+    |       └── ....
+    └── mm10
+        ├── snp
+        │   ├── chr1.subst.fa
+        │   ├── chr2.subst.fa
+        │   ├── chr3.subst.fa
+        │   └── ....
+        └── unmasked
+            ├── chr1.fa
+            ├── chr2.fa
+            ├── chr3.fa
+            └── ....
+
+Fasta files can be downloaded at:
 
 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/
 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/snp138Mask/

data/bin/fasta_read

@@ -9,12 +9,10 @@ class App
   include Methadone::CLILogging
 
   main do |assembly, chromosome, cstart, cend|
-    snp = masked_unmasked(options)[0]
-    subst = masked_unmasked(options)[1]
-    path = "fasta/#{assembly}/#{snp}/chr#{chromosome + subst}.fa"
+    path = "#{assembly}/#{snp_or_unmasked(options)[0]}/#{chromosome + snp_or_unmasked(options)[1]}.fa"
     exit_now_with!(assembly_or_chromosome(assembly, chromosome)) unless File.exist?(path)
     fasta = IO.read(path)
-    debug("About to read #{assembly} #{snp} chr#{chromosome}:#{cstart}-#{cend}")
+    debug("About to read #{assembly} #{snp_or_unmasked(options)[0]} chr#{chromosome}:#{cstart}-#{cend}")
     sequence = FastaRead::Sequence.new(fasta, chromosome, cstart, cend).process
     if options[:output]
       File.open(options[:output], "w") do |file|
@@ -26,12 +24,12 @@ class App
     info "#{sequence.length} base pairs"
   end
 
-  def self.masked_unmasked(options)
+  def self.snp_or_unmasked(options)
     options[:snp] ? ["snp", ".subst"] : ["unmasked", ""]
   end
 
   def self.assembly_or_chromosome(assembly, chromosome)
-    Dir.exist?("fasta/#{assembly}") ? [chromosome, "chromosome"] : [assembly, "assembly"]
+    Dir.exist?("#{assembly}") ? [chromosome, "chromosome"] : [assembly, "assembly"]
   end
 
   def self.exit_now_with!(value_and_argument)
@@ -41,17 +39,47 @@ class App
 
   # Declare command-line interface here
 
-  description "Extract DNA Fasta sequence from assembly files."
+  description <<-EOF
+    Extract DNA Fasta sequence from assembly files.
+
+    The program depends on being run at the top of a directory tree containing .fa files. The .fa files should be of the form where each file maps to a single chomosome.
+    The directory tree will have separate branches for SNPs and unmasked files.
+
+    For example, provided the following tree the command expects to be run inside the 'fasta' directory:
+
+        └── fasta
+            ├── hg19
+            │   ├── snp
+            │   │   ├── chr1.subst.fa
+            |   │   ├── chr2.subst.fa
+            |   │   ├── chr3.subst.fa
+            |   │   └── ....
+            │   └── unmasked
+            │       ├── chr1.fa
+            |       ├── chr2.fa
+            |       ├── chr3.fa
+            |       └── ....
+            └── mm10
+                ├── snp
+                │   ├── chr1.subst.fa
+                │   ├── chr2.subst.fa
+                │   ├── chr3.subst.fa
+                │   └── ....
+                └── unmasked
+                    ├── chr1.fa
+                    ├── chr2.fa
+                    ├── chr3.fa
+                    └── ....
+    EOF
+
   #
   # Accept flags via:
   # on("--flag VAL","Some flag")
   # options[flag] will contain VAL
-  options['multiple-lines'] = true
   #
   # Specify switches via:
   on "-o OUTPUTFILE", "--output", "outputs sequence to a file"
   on "--snp", "return the sequence from the SNP-masked assembly"
-  on "--multiple-lines", "return the sequence from the SNP-masked assembly"
 
   # on("--[no-]switch","Some switch")
   #
@@ -59,7 +87,7 @@ class App
   #
   # Require an argument
   arg :assembly,   "assembly name (hg19, mm10, etc.)"
-  arg :chromosome, "id of chromosome (1-22 or X/Y)"
+  arg :chromosome, "id of chromosome (chr1-chr22 or chrx/chry)"
   arg :cstart,     "start coordinate (inclusive) within the chromosome"
   arg :cend,       "end coordinate within the chromosome"
   #

data/features/fasta_read.feature

@@ -4,7 +4,7 @@ Feature: My bootstrapped app kinda works
   So I don't have to do it myself
 
   Background:
-    Given a file named "fasta/hg19/unmasked/chr1.fa" with:
+    Given a file named "hg19/unmasked/chr1.fa" with:
       """
       >chr1
       AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
@@ -13,7 +13,7 @@ Feature: My bootstrapped app kinda works
       GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
       C
       """
-    And a file named "fasta/hg19/snp/chr1.subst.fa" with:
+    And a file named "hg19/snp/chr1.subst.fa" with:
       """
       AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
       CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
@@ -26,7 +26,6 @@ Feature: My bootstrapped app kinda works
     When I get help for "fasta_read"
     Then the exit status should be 0
       And the banner should be present
-      And there should be a one line summary of what the app does
       And the banner should include the version
       And the banner should document that this app takes options
       And the following options should be documented:
@@ -41,7 +40,7 @@ Feature: My bootstrapped app kinda works
         |cend      |which is required|
 
   Scenario Outline: files with one line stream
-    Given a file named "fasta/hg19/unmasked/chr1.fa" with:
+    Given a file named "hg19/unmasked/chr1.fa" with:
       """
       >chr1
       AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
@@ -50,7 +49,7 @@ Feature: My bootstrapped app kinda works
       GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
       C
       """
-    And a file named "fasta/hg19/snp/chr1.subst.fa" with:
+    And a file named "hg19/snp/chr1.subst.fa" with:
       """
       >chr1
       AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
@@ -61,17 +60,16 @@ Feature: My bootstrapped app kinda works
       """
     When I successfully run `fasta_read <options>`
     Then the output should contain "<output>"
-    Then the output should not contain "<noutput>"
 
     Scenarios: unmasked
-      |options     |output    |noutput|
-      |hg19 1 0 200|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|ccaga  |
+      |options        |output                   |
+      |hg19 chr1 0 200|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|
     Scenarios: snp
-      |options            |output    |noutput|
-      |hg19 1 0 200 --snp|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|ccaga  |
+      |options            |output    |
+      |hg19 chr1 0 200 --snp|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|
 
   Scenario: Export to file
-    When I successfully run `fasta_read hg19 1 0 200 --output=out.txt`
+    When I successfully run `fasta_read hg19 chr1 0 200 --output=out.txt`
     Then the file "out.txt" should contain:
     """
     AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
@@ -82,5 +80,5 @@ Feature: My bootstrapped app kinda works
     Then the stderr should contain "<output>"
     Scenarios: incorrect assembly/chromosome
       |options                      |output                                                  |
-      |foo 12 0 3 --log-level=debug |the 'foo' assembly doesn't exist in directory structure |
-      |hg19 99 0 3 --log-level=debug|the '99' chromosome doesn't exist in directory structure|
+      |foo chr12 0 3 --log-level=debug |the 'foo' assembly doesn't exist in directory structure |
+      |hg19 chr99 0 3 --log-level=debug|the 'chr99' chromosome doesn't exist in directory structure|

data/lib/fasta_read/sequence.rb

@@ -5,11 +5,9 @@ module FastaRead
     include Methadone::Main
     include Methadone::CLILogging
 
-    attr_reader :separate_lines
-
     def initialize(fasta, chromosome, cstart, cend)
       @fasta =  fasta.gsub("\n", "")
-      @chromosome = ">chr#{chromosome}"
+      @chromosome = ">#{chromosome}"
       @cstart = cstart.to_i
       @cend =   cend.to_i
     end

data/lib/fasta_read/version.rb

@@ -1,3 +1,3 @@
 module FastaRead
-  VERSION = "1.1.0"
+  VERSION = "2.0.1"
 end

data/spec/fasta_read/sequence_spec.rb

@@ -5,13 +5,13 @@ module FastaRead
     let(:fasta) {">chr1\nAATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT\nCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC\nACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG\nGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT\nC"}
     describe "#real_cstart" do
       context "when @cstart is > 0" do
-        subject {Sequence.new(fasta, "12", "5", "200").real_cstart}
+        subject {Sequence.new(fasta, "chr12", "5", "200").real_cstart}
         it "should add file header string length" do
           expect(subject).to eq 10
         end
       end
       context "when @cstart is 0" do
-        subject {Sequence.new(fasta, "1", "0", "200").real_cstart}
+        subject {Sequence.new(fasta, "chr1", "0", "200").real_cstart}
         it "should not subtract 1" do
           expect(subject).to eq 5
         end
@@ -19,14 +19,14 @@ module FastaRead
     end
 
     describe "#real_cend" do
-      subject {Sequence.new(fasta, "1", "0", "200").real_cend}
+      subject {Sequence.new(fasta, "chr1", "0", "200").real_cend}
       it "should subtract 1 and add file header string length" do
         expect(subject).to eq 204
       end
     end
 
     describe "#process" do
-      subject {Sequence.new(fasta, "1", "0", "200").process}
+      subject {Sequence.new(fasta, "chr1", "0", "200").process}
       describe "with a continuous character stream" do
         it "builds a character sequence" do
           expect(subject).to eq "AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: fasta_read
 version: !ruby/object:Gem::Version
-  version: 1.1.0
+  version: 2.0.1
 platform: ruby
 authors:
 - Andrea D'Amico
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-04-05 00:00:00.000000000 Z
+date: 2014-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: methadone