bio-maf 0.3.1 → 0.3.2

data/DEVELOPMENT.md

@@ -20,6 +20,10 @@ platform.
 The version is simply set by hand in `bio-maf.gemspec`. Don't forget
 to increment it!
 
+First, verify that you are on the `master` branch:
+
+    $ git branch
+
 Testing the build:
 
     $ rake build

data/README.md

@@ -129,6 +129,10 @@ end
 # => Matched block at 80082713, 54 bases
 ```
 
+This can be done with [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html) as well:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082592-80082766
+
 ### Extract alignment blocks truncated to a given interval
 
 Given a genomic interval of interest, one can also extract only the
@@ -144,6 +148,10 @@ puts "Got #{blocks.size} blocks, first #{blocks.first.ref_seq.size} base pairs."
 # => Got 2 blocks, first 18 base pairs.
 ```
 
+Or, with [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html):
+
+    $ maf_extract -d test/data --mode slice --interval mm8.chr7:80082592-80082766
+
 ### Filter species returned in alignment blocks
 
 ```ruby
@@ -159,6 +167,10 @@ puts "Block has #{block.sequences.size} sequences."
 # => Block has 3 sequences.
 ```
 
+With [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html):
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082592-80082766 --only-species hg18,mm8,rheMac2
+
 ### Extract blocks matching certain conditions
 
 See also the [Cucumber feature][] and [step definitions][] for this.
@@ -176,6 +188,10 @@ n_blocks = access.find(q).count
 # => 1
 ```
 
+With [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html):
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082471-80082730 --with-all-species panTro2,loxAfr1
+
 #### Match only blocks with a certain number of sequences
 
 ```ruby
@@ -186,6 +202,10 @@ n_blocks = access.find(q).count
 # => 1
 ```
 
+With [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html):
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082767-80083008 --min-sequences 6
+
 #### Match only blocks within a text size range
 
 ```ruby
@@ -196,6 +216,10 @@ n_blocks = access.find(q).count
 # => 3
 ```
 
+With [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html):
+
+    $ maf_extract -d test/data --interval mm8.chr7:0-80100000 --min-text-size 72 --max-text-size 160
+
 ### Process each block in a MAF file
 
 ```ruby
@@ -333,6 +357,7 @@ end
 Man pages for command line tools:
 
 * [`maf_index(1)`](http://csw.github.com/bioruby-maf/man/maf_index.1.html)
+* [`maf_extract(1)`](http://csw.github.com/bioruby-maf/man/maf_extract.1.html)
 * [`maf_to_fasta(1)`](http://csw.github.com/bioruby-maf/man/maf_to_fasta.1.html)
 * [`maf_tile(1)`](http://csw.github.com/bioruby-maf/man/maf_tile.1.html)
 
@@ -377,4 +402,3 @@ This Biogem is published at [biogems.info](http://biogems.info/index.html#bio-ma
 ## Copyright
 
 Copyright (c) 2012 Clayton Wheeler. See LICENSE.txt for further details.
-

data/bin/maf_extract

@@ -22,8 +22,11 @@ def handle_list_spec(spec)
 end
 
 def handle_interval_spec(int)
-  parts = int.split(':')
-  Bio::GenomicInterval.zero_based(parts[0], parts[1].to_i, parts[2].to_i)
+  if int =~ /(.+):(\d+)-(\d+)/
+    Bio::GenomicInterval.zero_based($1, $2.to_i, $3.to_i)
+  else
+    raise "Invalid interval specification: #{int}"
+  end
 end
 
 $op = OptionParser.new do |opts|

data/bio-maf.gemspec

@@ -2,7 +2,7 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-maf"
-  s.version = "0.3.1"
+  s.version = "0.3.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Clayton Wheeler"]

data/man/maf_extract.1

@@ -7,13 +7,13 @@
 \fBmaf_extract\fR \- extract blocks from MAF files
 .
 .SH "SYNOPSIS"
-\fBmaf_extract\fR \-m MAF [\-i INDEX] \-\-interval SEQ:START:END \fIOPTIONS\fR
+\fBmaf_extract\fR \-m MAF [\-i INDEX] \-\-interval SEQ:START\-END \fIOPTIONS\fR
 .
 .P
 \fBmaf_extract\fR \-m MAF [\-i INDEX] \-\-bed BED \fIOPTIONS\fR
 .
 .P
-\fBmaf_extract\fR \-d MAFDIR \-\-interval SEQ:START:END \fIOPTIONS\fR
+\fBmaf_extract\fR \-d MAFDIR \-\-interval SEQ:START\-END \fIOPTIONS\fR
 .
 .P
 \fBmaf_extract\fR \-d MAFDIR \-\-bed BED \fIOPTIONS\fR
@@ -69,7 +69,7 @@ The extraction mode to use\. With \fB\-\-mode intersect\fR, any alignment block
 The specified file will be parsed as a BED file, and each interval it contains will be matched in turn\.
 .
 .TP
-\fB\-\-interval SEQ:START:END\fR
+\fB\-\-interval SEQ:START\-END\fR
 A single zero\-based half\-open genomic interval will be matched, with sequence identifier \fIseq\fR, (inclusive) start position \fIstart\fR, and (exclusive) end position \fIend\fR\.
 .
 .P
@@ -141,7 +141,116 @@ Run verbosely, with additional informational messages\.
 Log debugging information\.
 .
 .SH "EXAMPLES"
-TODO
+Extract MAF blocks intersecting with a given interval:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:80082592\-80082766
+.
+.fi
+.
+.IP "" 0
+.
+.P
+As above, but operating on a single file:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-m test/data/mm8_chr7_tiny\.maf \e
+      \-i test/data/mm8_chr7_tiny\.kct \e
+      \-\-interval mm8\.chr7:80082592\-80082766
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Like the first case, but writing output to a file:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:80082592\-80082766 \e
+      \-\-output out\.maf
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Extract a slice of MAF blocks over a given interval:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-mode slice \e
+      \-\-interval mm8\.chr7:80082592\-80082766
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Filter for sequences from only certain species:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:80082592\-80082766 \e
+      \-\-only\-species hg18,mm8,rheMac2
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Extract only blocks with all specified species:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:80082471\-80082730 \e
+      \-\-with\-all\-species panTro2,loxAfr1
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Extract blocks with at least a certain number of sequences:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:80082767\-80083008 \e
+      \-\-min\-sequences 6
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Extract blocks with text sizes in a certain range:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_extract \-d test/data \-\-interval mm8\.chr7:0\-80100000 \e
+      \-\-min\-text\-size 72 \-\-max\-text\-size 160
+.
+.fi
+.
+.IP "" 0
 .
 .SH "ENVIRONMENT"
 \fBmaf_index\fR is a Ruby program and relies on ordinary Ruby environment variables\.

data/man/maf_extract.1.ronn

@@ -3,11 +3,11 @@ maf_extract(1) -- extract blocks from MAF files
 
 ## SYNOPSIS
 
-`maf_extract` -m MAF [-i INDEX] --interval SEQ:START:END [OPTIONS]
+`maf_extract` -m MAF [-i INDEX] --interval SEQ:START-END [OPTIONS]
 
 `maf_extract` -m MAF [-i INDEX] --bed BED [OPTIONS]
 
-`maf_extract` -d MAFDIR --interval SEQ:START:END [OPTIONS]
+`maf_extract` -d MAFDIR --interval SEQ:START-END [OPTIONS]
 
 `maf_extract` -d MAFDIR --bed BED [OPTIONS]
 
@@ -79,7 +79,7 @@ Extraction options:
    The specified file will be parsed as a BED file, and each interval
    it contains will be matched in turn.
 
- * `--interval SEQ:START:END`:
+ * `--interval SEQ:START-END`:
    A single zero-based half-open genomic interval will be matched,
    with sequence identifier <seq>, (inclusive) start position <start>,
    and (exclusive) end position <end>.
@@ -153,7 +153,45 @@ Logging options:
 
 ## EXAMPLES
 
-TODO
+Extract MAF blocks intersecting with a given interval:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082592-80082766
+    
+As above, but operating on a single file:
+
+    $ maf_extract -m test/data/mm8_chr7_tiny.maf \
+          -i test/data/mm8_chr7_tiny.kct \
+          --interval mm8.chr7:80082592-80082766
+
+Like the first case, but writing output to a file:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082592-80082766 \
+          --output out.maf
+
+Extract a slice of MAF blocks over a given interval:
+
+    $ maf_extract -d test/data --mode slice \
+          --interval mm8.chr7:80082592-80082766
+
+Filter for sequences from only certain species:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082592-80082766 \
+          --only-species hg18,mm8,rheMac2
+
+Extract only blocks with all specified species:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082471-80082730 \
+          --with-all-species panTro2,loxAfr1
+
+Extract blocks with at least a certain number of sequences:
+
+    $ maf_extract -d test/data --interval mm8.chr7:80082767-80083008 \
+          --min-sequences 6
+
+Extract blocks with text sizes in a certain range:
+
+    $ maf_extract -d test/data --interval mm8.chr7:0-80100000 \
+          --min-text-size 72 --max-text-size 160
 
 ## ENVIRONMENT
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-maf
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -219,7 +219,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -1336822573836516057
+      hash: 2092820657742105268
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: