bio-maf 0.3.0-java → 0.3.2-java

data/lib/bio/maf/tiler.rb

@@ -13,16 +13,44 @@ module Bio::MAF
     attr_reader :reference
     # GenomicInterval
     attr_accessor :interval
+
+    # The species of interest to extract from the MAF file. Will be
+    # set as a {Parser#sequence_filter} for parsing. Defaults to the
+    # keys of {#species_map}.
+    #
+    # @return [Array<String>]
     attr_accessor :species
+
+    # A hash mapping species to their desired output names.
+    #
+    # @return [Hash]
     attr_accessor :species_map
 
+    # The character used to fill regions where no sequence data is available for a particular species. Defaults to `*`.
+    # @return [String]
+    attr_reader   :fill_char
+
     def initialize
       @species_map = {}
+      self.fill_char = '*'
+    end
+
+    # Set the character to be used for filling regions with no
+    # sequence data from the MAF file or a reference sequence.
+    # @param c [String] a one-character String to fill with
+    def fill_char=(c)
+      unless c.is_a?(String) && c.length == 1
+        raise ArgumentError, "not a single character: #{c.inspect}" 
+      end
+      @fill_char = c
     end
 
-    # Set the reference sequence.
+    # Set the reference sequence. This can be a {Pathname} or a
+    # {String} giving the path to an optionally-gzipped FASTA file, an
+    # open {IO} stream to a FASTA file, a String containing FASTA
+    # data, or a {FASTARangeReader} instance.
     #
-    # @param source [FASTARangeReader, String, Pathname]
+    # @param source [FASTARangeReader, String, Pathname, #readline]
     def reference=(source)
       ref = case
             when source.is_a?(FASTARangeReader)
@@ -57,6 +85,13 @@ module Bio::MAF
       species || species_map.keys
     end
 
+    def species_for_output
+      species_to_use.collect { |s| species_map[s] || s }
+    end
+
+    # Return an array of tiled sequence data, in the order given by
+    # {#species_to_use}.
+    # @return [Array<String>]
     def tile
       parser.sequence_filter[:only_species] = species_to_use
       # TODO: remove gaps
@@ -88,8 +123,8 @@ module Bio::MAF
                      else
                        'N' * range_size
                      end
-          stars = '*' * range_size
-          nonref_text.each { |t| t << stars }
+          fill_text = fill_char * range_size
+          nonref_text.each { |t| t << fill_text }
         else
           # covered by an alignment block
           t_range = block.ref_seq.text_range(g_range)
@@ -100,8 +135,8 @@ module Bio::MAF
               # got alignment text
               sp_text << seq.text.slice(t_range)
             else
-              # no alignment for this one here, use '*'
-              sp_text << '*' * (t_range.end - t_range.begin)
+              # no alignment for this one here, use the fill char
+              sp_text << fill_char * (t_range.end - t_range.begin)
             end
           end
         end
@@ -109,9 +144,26 @@ module Bio::MAF
       text
     end
 
+    # Tile sequences to build a new {Bio::BioAlignment::Alignment
+    # Alignment} object. This will have one
+    # {Bio::BioAlignment::Sequence Sequence} per entry in {#species}
+    # or {#species_map}, in the same order. Each sequence will have an
+    # {Bio::BioAlignment::Sequence#id id} given by {#species_map} or,
+    # if none is present, the identifier from {#species}.
+    #
+    # @return [Bio::BioAlignment::Alignment]
+    # @api public
+    def build_bio_alignment
+      Bio::BioAlignment::Alignment.new(tile(), species_for_output)
+    end
+
+    # Write a FASTA representation of the tiled sequences to the given
+    # output stream.
+    #
+    # @param [#puts] f the output stream to write the FASTA data to.
+    # @api public
     def write_fasta(f)
-      species_to_use.zip(tile()) do |species, text|
-        sp_out = species_map[species] || species
+      species_for_output.zip(tile()) do |sp_out, text|
         f.puts ">#{sp_out}"
         f.puts text
       end

data/lib/bio/maf/writer.rb

@@ -59,5 +59,31 @@ module Bio::MAF
       end
     end
   end
+
+  FASTA_LINE_LEN = 72
+
+  class FASTAWriter
+
+    def initialize(outf)
+      @f = outf
+    end
+
+    def write_block(block)
+      block.sequences.each do |seq|
+        write_sequence(seq) unless seq.empty?
+      end
+    end
+
+    def write_sequence(seq)
+      @f.puts(">#{seq.fasta_desc}")
+      0.step(seq.text.size, FASTA_LINE_LEN) do |pos|
+        @f.puts(seq.text.slice(pos, FASTA_LINE_LEN))
+      end
+    end
+
+    def close
+      @f.close
+    end
+  end
   
 end

data/man/maf_extract.1

@@ -0,0 +1,268 @@
+.\" generated with Ronn/v0.7.3
+.\" http://github.com/rtomayko/ronn/tree/0.7.3
+.
+.TH "MAF_EXTRACT" "1" "July 2012" "BioRuby" "BioRuby Manual"
+.
+.SH "NAME"
+\fBmaf_extract\fR \- extract blocks from MAF files
+.
+.SH "SYNOPSIS"
+\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
+.
+.P
+\fBmaf_extract\fR \-d MAFDIR \-\-bed BED \fIOPTIONS\fR
+.
+.SH "DESCRIPTION"
+\fBmaf_extract\fR extracts alignment blocks from one or more indexed MAF files, according to either a genomic interval specified with \fB\-\-interval\fR or multiple intervals given in a BED file specified with \fB\-\-bed\fR\.
+.
+.P
+It can either match blocks intersecting the specified intervals with \fB\-\-mode intersect\fR, the default, or extract slices of them which cover only the specified intervals, with \fB\-\-mode slice\fR\.
+.
+.P
+Blocks and the sequences they contain can be filtered with a variety of options including \fB\-\-only\-species\fR, \fB\-\-with\-all\-species\fR, \fB\-\-min\-sequences\fR, \fB\-\-min\-text\-size\fR, and \fB\-\-max\-text\-size\fR\.
+.
+.P
+With the \fB\-\-join\-blocks\fR option, adjacent parsed blocks can be joined if sequence filtering has removed a species causing them to be separated\. The \fB\-\-remove\-gaps\fR option will remove columns containing only gaps (\fB\-\fR)\.
+.
+.P
+Blocks can be output in MAF format, with \fB\-\-format maf\fR (the default), or FASTA format, with \fB\-\-format fasta\fR\. Output can be directed to a file with \fB\-\-output\fR\.
+.
+.P
+This tool exposes almost all the random\-access functionality of the Bio::MAF::Access class\. The exception is MAF tiling, which is provided by maf_tile(1)\.
+.
+.SH "FILES"
+A single MAF file can be processed by specifying it with \fB\-\-maf\fR\. Its accompanying index, created by maf_index(1), is specified with \fB\-\-index\fR\. If \fB\-\-maf\fR is given but no index is specified, the entire file will be parsed to build a temporary in\-memory index\. This facilitates processing small, transient MAF files\. However, on a large file this will incur a great deal of overhead; files expected to be used more than once should be indexed with maf_index(1)\.
+.
+.P
+Alternatively, a directory of indexed MAF files can be specified with \fB\-\-maf\-dir\fR; in this case, they will all be used to satisfy queries\.
+.
+.SH "OPTIONS"
+MAF source options:
+.
+.TP
+\fB\-m\fR, \fB\-\-maf MAF\fR
+A single MAF file to process\.
+.
+.TP
+\fB\-i\fR, \fB\-\-index INDEX\fR
+An index for the file specified with \fB\-\-maf\fR, as created by maf_index(1)\.
+.
+.TP
+\fB\-d\fR, \fB\-\-maf\-dir DIR\fR
+A directory of indexed MAF files\.
+.
+.P
+Extraction options:
+.
+.TP
+\fB\-\-mode (intersect | slice)\fR
+The extraction mode to use\. With \fB\-\-mode intersect\fR, any alignment block intersecting the genomic intervals specified will be matched in its entirety\. With \fB\-\-mode slice\fR, intersecting blocks will be matched in the same way, but columns extending outside the specified interval will be removed\.
+.
+.TP
+\fB\-\-bed BED\fR
+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
+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
+Output options:
+.
+.TP
+\fB\-f\fR, \fB\-\-format (maf | fasta)\fR
+Output will be written in the specified format, either MAF or FASTA\.
+.
+.TP
+\fB\-o\fR, \fB\-\-output OUT\fR
+Output will be written to the file \fIout\fR\.
+.
+.P
+Filtering options:
+.
+.TP
+\fB\-\-only\-species (SP1,SP2,SP3 | @FILE)\fR
+Alignment blocks will be filtered to contain only the specified species\. These can be given as a comma\-separated list or as a file, prefixed with \fB@\fR, from which a list of species will be read\.
+.
+.TP
+\fB\-\-with\-all\-species (SP1,SP2,SP3 | @FILE)\fR
+Only alignment blocks containing all the specified species will be matched\. These can be given as a comma\-separated list or as a file, prefixed with \fB@\fR, from which a list of species will be read\.
+.
+.TP
+\fB\-\-min\-sequences N\fR
+Only alignment blocks containing at least \fIn\fR sequences will be matched\.
+.
+.TP
+\fB\-\-min\-text\-size N\fR
+Only alignment blocks with a text size (including gaps) of at least \fIn\fR will be matched\.
+.
+.TP
+\fB\-\-max\-text\-size N\fR
+Only alignment blocks with a text size (including gaps) of at most \fIn\fR will be matched\.
+.
+.P
+Block processing options:
+.
+.TP
+\fB\-\-join\-blocks\fR
+If sequence filtering with \fB\-\-only\-species\fR removes a species which caused two adjacent blocks to be separate, this option will join them together into a single alignment block\. The filtered blocks must contain the same sequences in contiguous positions and on the same strand\.
+.
+.TP
+\fB\-\-remove\-gaps\fR
+If sequence filtering with \fB\-\-only\-species\fR leaves a block containing columns consisting only of gap characters (\fB\-\fR), these will be removed\.
+.
+.TP
+\fB\-\-parse\-extended\fR
+Parse \fBi\fR lines, giving information on the context of sequence lines, and \fBq\fR lines, giving quality scores\.
+.
+.TP
+\fB\-\-parse\-empty\fR
+Parse \fBe\fR lines, indicating cases where a species does not align with the current block but does align with blocks before and after it\.
+.
+.P
+Logging options:
+.
+.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"
+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\.
+.
+.SH "BUGS"
+No provision exists for writing output to multiple files\.
+.
+.P
+FASTA description lines are always in the format \fB>source:start\-end\fR\.
+.
+.SH "COPYRIGHT"
+\fBmaf_index\fR is copyright (C) 2012 Clayton Wheeler\.
+.
+.SH "SEE ALSO"
+ruby(1), maf_index(1), maf_tile(1)

data/man/maf_extract.1.ronn

@@ -0,0 +1,213 @@
+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] --bed BED [OPTIONS]
+
+`maf_extract` -d MAFDIR --interval SEQ:START-END [OPTIONS]
+
+`maf_extract` -d MAFDIR --bed BED [OPTIONS]
+
+## DESCRIPTION
+
+**maf_extract** extracts alignment blocks from one or more indexed MAF
+files, according to either a genomic interval specified with
+`--interval` or multiple intervals given in a BED file specified with
+`--bed`. 
+
+It can either match blocks intersecting the specified intervals with
+`--mode intersect`, the default, or extract slices of them which cover
+only the specified intervals, with `--mode slice`. 
+
+Blocks and the sequences they contain can be filtered with a variety
+of options including `--only-species`, `--with-all-species`,
+`--min-sequences`, `--min-text-size`, and `--max-text-size`.
+
+With the `--join-blocks` option, adjacent parsed blocks can be joined if
+sequence filtering has removed a species causing them to be
+separated. The `--remove-gaps` option will remove columns containing
+only gaps (`-`).
+
+Blocks can be output in MAF format, with `--format maf` (the default),
+or FASTA format, with `--format fasta`. Output can be directed to a
+file with `--output`.
+
+This tool exposes almost all the random-access functionality of the
+Bio::MAF::Access class. The exception is MAF tiling, which is provided
+by maf_tile(1).
+
+## FILES
+
+A single MAF file can be processed by specifying it with `--maf`. Its
+accompanying index, created by maf_index(1), is specified with
+`--index`. If `--maf` is given but no index is specified, the entire
+file will be parsed to build a temporary in-memory index. This
+facilitates processing small, transient MAF files. However, on a large
+file this will incur a great deal of overhead; files expected to be
+used more than once should be indexed with maf_index(1).
+
+Alternatively, a directory of indexed MAF files can be specified with
+`--maf-dir`; in this case, they will all be used to satisfy queries.
+
+## OPTIONS
+
+MAF source options:
+
+ * `-m`, `--maf MAF`:
+   A single MAF file to process.
+   
+ * `-i`, `--index INDEX`:
+   An index for the file specified with `--maf`, as created by
+   maf_index(1).
+
+ * `-d`, `--maf-dir DIR`:
+   A directory of indexed MAF files.
+
+Extraction options:
+
+ * `--mode (intersect | slice)`:
+   The extraction mode to use. With `--mode intersect`, any alignment
+   block intersecting the genomic intervals specified will be matched
+   in its entirety. With `--mode slice`, intersecting blocks will be
+   matched in the same way, but columns extending outside the
+   specified interval will be removed.
+
+ * `--bed BED`:
+   The specified file will be parsed as a BED file, and each interval
+   it contains will be matched in turn.
+
+ * `--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>.
+
+Output options:
+
+ * `-f`, `--format (maf | fasta)`:
+   Output will be written in the specified format, either MAF or
+   FASTA.
+
+ * `-o`, `--output OUT`:
+   Output will be written to the file <out>.
+
+Filtering options:
+
+ * `--only-species (SP1,SP2,SP3 | @FILE)`:
+   Alignment blocks will be filtered to contain only the specified
+   species. These can be given as a comma-separated list or as a file,
+   prefixed with `@`, from which a list of species will be read.
+
+ * `--with-all-species (SP1,SP2,SP3 | @FILE)`:
+   Only alignment blocks containing all the specified species will be
+   matched. These can be given as a comma-separated list or as a file,
+   prefixed with `@`, from which a list of species will be read.
+
+ * `--min-sequences N`:
+   Only alignment blocks containing at least <n> sequences will be
+   matched.
+   
+ * `--min-text-size N`:
+   Only alignment blocks with a text size (including gaps) of at least
+   <n> will be matched.
+   
+ * `--max-text-size N`:
+   Only alignment blocks with a text size (including gaps) of at most
+   <n> will be matched.
+
+Block processing options:
+
+ * `--join-blocks`:
+   If sequence filtering with `--only-species` removes a species which
+   caused two adjacent blocks to be separate, this option will join
+   them together into a single alignment block. The filtered blocks
+   must contain the same sequences in contiguous positions and on the
+   same strand.
+
+ * `--remove-gaps`:
+   If sequence filtering with `--only-species` leaves a block
+   containing columns consisting only of gap characters (`-`), these
+   will be removed.
+
+ * `--parse-extended`:
+   Parse `i` lines, giving information on the context of sequence
+   lines, and `q` lines, giving quality scores.
+
+ * `--parse-empty`:
+   Parse `e` lines, indicating cases where a species does not align
+   with the current block but does align with blocks before and after
+   it.
+
+Logging options:
+
+ * `-q`, `--quiet`:
+   Run quietly, with warnings suppressed.
+
+ * `-v`, `--verbose`:
+   Run verbosely, with additional informational messages.
+   
+ * `--debug`:
+   Log debugging information.
+
+## EXAMPLES
+
+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
+
+`maf_index` is a Ruby program and relies on ordinary Ruby environment
+variables.
+
+## BUGS
+
+No provision exists for writing output to multiple files.
+
+FASTA description lines are always in the format `>source:start-end`.
+
+## COPYRIGHT
+
+`maf_index` is copyright (C) 2012 Clayton Wheeler.
+
+## SEE ALSO
+
+ruby(1), maf_index(1), maf_tile(1)