bio-maf 0.3.0 → 0.3.1

data/man/maf_index.1

@@ -28,7 +28,10 @@ The \fImaf\fR input file must be a valid MAF file of any length\.
 The index created is a Kyoto Cabinet TreeDB (B+ tree) database; \fIindex\fR must have a \fB\.kct\fR extension\.
 .
 .SH "OPTIONS"
-TODO
+.
+.TP
+\fB\-a\fR, \fB\-\-all\fR
+All sequences, not just the reference sequence, will be indexed for searching\.
 .
 .TP
 \fB\-d\fR, \fB\-\-dump\fR
@@ -38,25 +41,33 @@ Instead of creating an index, dump out the given \fIindex\fR in human\-readable
 .
 .nf
 
-0 [bin 1195] 80082334:80082368
-  offset 16, length 1087
-  text size: 54
-  sequences in block: 10
-  species vector: 00000000000003ff
+ 0 [bin 1195] 80082334:80082368
+   offset 16, length 1087
+   text size: 54
+   sequences in block: 10
+   species vector: 00000000000003ff
 .
 .fi
 .
 .IP "" 0
 
-.
-.TP
-\fB\-t\fR, \fB\-\-threaded\fR
-Use a separate reader thread to do I/O in parallel with parsing\. Only useful on JRuby\.
 .
 .TP
 \fB\-\-time\fR
 Print elapsed time for index creation\. Mainly useful for measuring performance with different Ruby implementations, I/O subsystems, etc\.
 .
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Run quietly, with warnings suppressed\.
+.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Run verbosely, with additional informational messages\.
+.
+.TP
+\fB\-\-debug\fR
+Log debugging information\.
+.
 .SH "EXAMPLES"
 Build an index on a MAF file:
 .

data/man/maf_index.1.ronn

@@ -29,9 +29,11 @@ The index created is a Kyoto Cabinet TreeDB (B+ tree) database;
 
 ## OPTIONS
 
-TODO
-
- * `-d`, `--dump`:
+ * `-a`, `--all`:
+   All sequences, not just the reference sequence, will be indexed for
+   searching. 
+   
+* `-d`, `--dump`:
    Instead of creating an index, dump out the given <index> in
    human-readable form. Index records will appear like:
    
@@ -41,15 +43,20 @@ TODO
          sequences in block: 10
          species vector: 00000000000003ff
 
- * `-t`, `--threaded`:
-   Use a separate reader thread to do I/O in parallel with
-   parsing. Only useful on JRuby.
-
  * `--time`:
    Print elapsed time for index creation. Mainly useful for measuring
    performance with different Ruby implementations, I/O subsystems,
    etc.
    
+ * `-q`, `--quiet`:
+   Run quietly, with warnings suppressed.
+
+ * `-v`, `--verbose`:
+   Run verbosely, with additional informational messages.
+   
+ * `--debug`:
+   Log debugging information.
+   
 ## EXAMPLES
 
 Build an index on a MAF file:

data/man/maf_tile.1

@@ -43,6 +43,18 @@ The given BED file will be used to provide a list of intervals to process\. If p
 \fB\-o\fR, \fB\-\-output\-base BASE\fR
 The given path will be used as the base name for output files, as described above\.
 .
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Run quietly, with warnings suppressed\.
+.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Run verbosely, with additional informational messages\.
+.
+.TP
+\fB\-\-debug\fR
+Log debugging information\.
+.
 .SH "EXAMPLES"
 Generate an alignment of the \fBhg19\fR, \fBpetMar1\fR, and \fBornAna1\fR sequences from \fBchrY\.maf\fR over the interval 14400 to 15000 on the reference sequence of the MAF file\. Fills in gaps from \fBchrY\.refseq\.fa\.gz\fR\. Writes FASTA output to stdout\.
 .

data/man/maf_tile.1.ronn

@@ -52,6 +52,15 @@ output.
    The given path will be used as the base name for output files, as
    described above.
 
+ * `-q`, `--quiet`:
+   Run quietly, with warnings suppressed.
+
+ * `-v`, `--verbose`:
+   Run verbosely, with additional informational messages.
+   
+ * `--debug`:
+   Log debugging information.
+   
 ## EXAMPLES
 
 Generate an alignment of the `hg19`, `petMar1`, and `ornAna1`

data/spec/bio/maf/index_spec.rb

@@ -43,6 +43,29 @@ module Bio
             buf.string.should == File.read(TestData + 'gap-filled1.fa')
           end
         end
+        it "gives a bio-alignment representation" do
+          access = Access.maf_dir(TestData)
+          interval = GenomicInterval.zero_based('sp1.chr1', 0, 50)
+          aln = access.tile(interval) do |tiler|
+            tiler.reference = TestData + 'gap-sp1.fa'
+            tiler.species = %w(sp1 sp2 sp3)
+            tiler.build_bio_alignment
+          end
+          aln.sequences[0].id.should == 'sp1'
+          aln.sequences[0].to_s.start_with?('CCAGGATGC').should be_true
+        end
+        it "allows setting the fill character" do
+          access = Access.maf_dir(TestData)
+          interval = GenomicInterval.zero_based('sp1.chr1', 0, 50)
+          aln = access.tile(interval) do |tiler|
+            tiler.reference = TestData + 'gap-sp1.fa'
+            tiler.species = %w(sp1 sp2 sp3)
+            tiler.fill_char = '-'
+            tiler.build_bio_alignment
+          end
+          aln.sequences[1].id.should == 'sp2'
+          aln.sequences[1].to_s.start_with?('----------GGGCTG').should be_true
+        end
       end
       describe ".file" do
         it "accepts a MAF file and index" do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-maf
 version: !ruby/object:Gem::Version
-  version: 0.3.0
+  version: 0.3.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-18 00:00:00.000000000 Z
+date: 2012-07-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-alignment
@@ -28,29 +28,29 @@ dependencies:
       - !ruby/object:Gem::Version
         version: 0.0.7
 - !ruby/object:Gem::Dependency
-  name: bio-bigbio
+  name: bio-genomic-interval
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ! '>='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
-  name: bio-genomic-interval
+  name: bio-logger
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: 1.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -58,7 +58,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: 1.0.1
 - !ruby/object:Gem::Dependency
   name: kyotocabinet-ruby
   requirement: !ruby/object:Gem::Requirement
@@ -81,6 +81,7 @@ executables:
 - find_overlaps
 - maf_count
 - maf_dump_blocks
+- maf_extract
 - maf_extract_ranges_count
 - maf_index
 - maf_parse_bench
@@ -112,6 +113,7 @@ files:
 - bin/find_overlaps
 - bin/maf_count
 - bin/maf_dump_blocks
+- bin/maf_extract
 - bin/maf_extract_ranges_count
 - bin/maf_index
 - bin/maf_parse_bench
@@ -157,6 +159,8 @@ files:
 - lib/bio/ucsc/genomic-interval-bin.rb
 - lib/bio/ucsc/ucsc_bin.rb
 - man/.gitignore
+- man/maf_extract.1
+- man/maf_extract.1.ronn
 - man/maf_index.1
 - man/maf_index.1.markdown
 - man/maf_index.1.ronn
@@ -215,7 +219,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2504976576663848022
+      hash: -1336822573836516057
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: