Class: Bio::TwoBit

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/twobit.rb,
lib/bio/twobit/version.rb,
lib/bio/twobit/metadata.rb,
lib/bio/twobit/cache_path.rb,
lib/bio/twobit/downloader.rb,
lib/bio/twobit/references/cb3.rb,
lib/bio/twobit/references/ci2.rb,
lib/bio/twobit/references/dm6.rb,
lib/bio/twobit/references/dp3.rb,
lib/bio/twobit/references/fr2.rb,
lib/bio/twobit/references/hs1.rb,
lib/bio/twobit/references/mm9.rb,
lib/bio/twobit/references/rn6.rb,
lib/bio/twobit/references/ce11.rb,
lib/bio/twobit/references/hg19.rb,
lib/bio/twobit/references/hg38.rb,
lib/bio/twobit/references/mm10.rb,
lib/bio/twobit/references/mm39.rb,
lib/bio/twobit/reference_genome.rb,
lib/bio/twobit/references/caepb2.rb,
lib/bio/twobit/references/ailmel1.rb,
lib/bio/twobit/references/allmis1.rb,
lib/bio/twobit/references/anocar2.rb,
lib/bio/twobit/references/anogam3.rb,
lib/bio/twobit/references/apimel2.rb,
lib/bio/twobit/references/aplcal1.rb,
lib/bio/twobit/references/aptman1.rb,
lib/bio/twobit/references/aquchr2.rb,
lib/bio/twobit/references/balacu1.rb,
lib/bio/twobit/references/bostau7.rb,
lib/bio/twobit/references/braflo1.rb,
lib/bio/twobit/references/caejap1.rb,
lib/bio/twobit/references/caerem3.rb,
lib/bio/twobit/references/caljac4.rb,
lib/bio/twobit/references/calmil1.rb,
lib/bio/twobit/references/canfam4.rb,
lib/bio/twobit/references/canfam6.rb,
lib/bio/twobit/references/cersim1.rb,
lib/bio/twobit/references/chlsab2.rb,
lib/bio/twobit/references/chohof1.rb,
lib/bio/twobit/references/chrpic1.rb,
lib/bio/twobit/references/dasnov3.rb,
lib/bio/twobit/references/dipord1.rb,
lib/bio/twobit/references/droana2.rb,
lib/bio/twobit/references/droere1.rb,
lib/bio/twobit/references/drogri1.rb,
lib/bio/twobit/references/dromoj2.rb,
lib/bio/twobit/references/droper1.rb,
lib/bio/twobit/references/drosec1.rb,
lib/bio/twobit/references/drosim1.rb,
lib/bio/twobit/references/drovir2.rb,
lib/bio/twobit/references/droyak2.rb,
lib/bio/twobit/references/ebovir3.rb,
lib/bio/twobit/references/echtel2.rb,
lib/bio/twobit/references/equcab3.rb,
lib/bio/twobit/references/erieur2.rb,
lib/bio/twobit/references/felcat9.rb,
lib/bio/twobit/references/gadmor1.rb,
lib/bio/twobit/references/galgal6.rb,
lib/bio/twobit/references/geofor1.rb,
lib/bio/twobit/references/gorgor6.rb,
lib/bio/twobit/references/hetgla2.rb,
lib/bio/twobit/references/latcha1.rb,
lib/bio/twobit/references/loxafr3.rb,
lib/bio/twobit/references/maceug2.rb,
lib/bio/twobit/references/macfas5.rb,
lib/bio/twobit/references/manpen1.rb,
lib/bio/twobit/references/melgal1.rb,
lib/bio/twobit/references/melund1.rb,
lib/bio/twobit/references/micmur2.rb,
lib/bio/twobit/references/mondom5.rb,
lib/bio/twobit/references/myoluc2.rb,
lib/bio/twobit/references/nanpar1.rb,
lib/bio/twobit/references/naslar1.rb,
lib/bio/twobit/references/neosch1.rb,
lib/bio/twobit/references/nomleu3.rb,
lib/bio/twobit/references/ochpri3.rb,
lib/bio/twobit/references/orenil2.rb,
lib/bio/twobit/references/ornana2.rb,
lib/bio/twobit/references/orycun2.rb,
lib/bio/twobit/references/orylat2.rb,
lib/bio/twobit/references/otogar3.rb,
lib/bio/twobit/references/oviari4.rb,
lib/bio/twobit/references/panpan3.rb,
lib/bio/twobit/references/pantro6.rb,
lib/bio/twobit/references/papanu4.rb,
lib/bio/twobit/references/papham1.rb,
lib/bio/twobit/references/petmar3.rb,
lib/bio/twobit/references/ponabe2.rb,
lib/bio/twobit/references/ponabe3.rb,
lib/bio/twobit/references/pripac1.rb,
lib/bio/twobit/references/procap1.rb,
lib/bio/twobit/references/ptevam1.rb,
lib/bio/twobit/references/saccer3.rb,
lib/bio/twobit/references/saibol1.rb,
lib/bio/twobit/references/sarhar1.rb,
lib/bio/twobit/references/sorara2.rb,
lib/bio/twobit/references/spetri2.rb,
lib/bio/twobit/references/strpur2.rb,
lib/bio/twobit/references/taegut2.rb,
lib/bio/twobit/references/tarsyr2.rb,
lib/bio/twobit/references/tetnig2.rb,
lib/bio/twobit/references/thasir1.rb,
lib/bio/twobit/references/triman1.rb,
lib/bio/twobit/references/tupbel1.rb,
lib/bio/twobit/references/turtru2.rb,
lib/bio/twobit/references/uusfur1.rb,
lib/bio/twobit/references/vicpac2.rb,
lib/bio/twobit/references/wuhcor1.rb,
lib/bio/twobit/references/danrer10.rb,
lib/bio/twobit/references/danrer11.rb,
lib/bio/twobit/references/rhemac10.rb,
lib/bio/twobit/references/susscr11.rb,
lib/bio/twobit/references/xentro10.rb,
lib/bio/twobit/references/crigrichov2.rb,
ext/bio/twobit/twobit.c

Overview

Reader for .2bit files (i.e., from UCSC genome browser)

Direct Known Subclasses

ReferenceGenome

Defined Under Namespace

Classes: AilMel1, AllMis1, AnoCar2, AnoGam3, ApiMel2, AplCal1, AptMan1, AquChr2, BalAcu1, BosTau7, BraFlo1, CachePath, CaeJap1, CaePb2, CaeRem3, CalJac4, CalMil1, CanFam4, CanFam6, Cb3, Ce11, CerSim1, ChlSab2, ChoHof1, ChrPic1, Ci2, CriGriChoV2, DanRer10, DanRer11, DasNov3, DipOrd1, Dm6, Downloader, Dp3, DroAna2, DroEre1, DroGri1, DroMoj2, DroPer1, DroSec1, DroSim1, DroVir2, DroYak2, EboVir3, EchTel2, EquCab3, EriEur2, FelCat9, Fr2, GadMor1, GalGal6, GeoFor1, GorGor6, HetGla2, Hg19, Hg38, Hs1, LatCha1, LoxAfr3, MacEug2, MacFas5, ManPen1, MelGal1, MelUnd1, Metadata, MicMur2, Mm10, Mm39, Mm9, MonDom5, MyoLuc2, NanPar1, NasLar1, NeoSch1, NomLeu3, OchPri3, OreNil2, OrnAna2, OryCun2, OryLat2, OtoGar3, OviAri4, PanPan3, PanTro6, PapAnu4, PapHam1, PetMar3, PonAbe2, PonAbe3, PriPac1, ProCap1, PteVam1, ReferenceGenome, RheMac10, Rn6, SacCer3, SaiBol1, SarHar1, SorAra2, SpeTri2, StrPur2, SusScr11, TaeGut2, TarSyr2, TetNig2, ThaSir1, TriMan1, TupBel1, TurTru2, UusFur1, VicPac2, WuhCor1, XenTro10

Constant Summary collapse

VERSION = 
"0.2.2"

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fname, masked: false) ⇒ TwoBit

Returns a new instance of TwoBit.



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# File 'lib/bio/twobit.rb', line 29

def initialize(fname, masked: false)
  raise "TwoBit::new() does not take block; use TwoBit::open() instead" if block_given?

  fname = fname.to_path if fname.respond_to?(:to_path)
  @fname = fname
  if masked
    mskd = 1
    @masked = true
  else
    mskd = 0
    @masked = false
  end
  initialize_raw(fname, mskd)
end

Instance Attribute Details

#metadata ⇒ Object (readonly)

Returns the value of attribute metadata.



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# File 'lib/bio/twobit.rb', line 13

def metadata
  @metadata
end

Class Method Details

.open(*args, **kwargs) ⇒ Object 



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# File 'lib/bio/twobit.rb', line 16

def open(*args, **kwargs)
  file = new(*args, **kwargs)
  return file unless block_given?

  begin
    yield file
  ensure
    file.close
  end
  file
end

Instance Method Details

#bases(chrom, start = 0, stop = 0, fraction: true) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/bio/twobit.rb', line 63

def bases(chrom, start = 0, stop = 0, fraction: true)
  raise ArgumentError, "negative start position" if start.negative?
  raise ArgumentError, "negative stop position" if stop.negative?

  bases_raw(chrom, start, stop, fraction ? 1 : 0)
end

#chroms ⇒ Object 



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# File 'ext/bio/twobit/twobit.c', line 214

static VALUE
twobit_chroms(VALUE self)
{
	TwoBit *tb = getTwoBit(self);

	if (!tb)
	{
		rb_raise(rb_eRuntimeError, "The 2bit file handle is not open!");
		return Qnil;
	}

	uint32_t i;
	VALUE val;
	VALUE chroms = rb_hash_new();

	for (i = 0; i < tb->hdr->nChroms; i++)
	{
		val = UINT32_2NUM(tb->idx->size[i]);
		if (!val)
			goto error;
		rb_hash_aset(chroms, rb_str_new2(tb->cl->chrom[i]), val);
	}

	return chroms;

error:
	rb_raise(rb_eRuntimeError, "Received an error while adding an item to the output hash!");
	return Qnil;
}

#clear_cache! ⇒ Object 



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# File 'lib/bio/twobit.rb', line 84

def clear_cache!
  cache_path.remove
end

#close ⇒ Object 



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# File 'ext/bio/twobit/twobit.c', line 111

static VALUE
twobit_close(VALUE self)
{
	TwoBit *tb = getTwoBit(self);
	if (tb)
	{
		twobitClose(tb);
		DATA_PTR(self) = NULL;
	}

	return Qnil;
}

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'ext/bio/twobit/twobit.c', line 124

static VALUE
twobit_closed_question_mark(VALUE self)
{
	TwoBit *tb = getTwoBit(self);
	if (tb)
	{
		return Qfalse;
	}
	else
	{
		return Qtrue;
	}
}

#hard_masked_blocks(chrom, start = 0, stop = 0) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/bio/twobit.rb', line 70

def hard_masked_blocks(chrom, start = 0, stop = 0)
  raise ArgumentError, "negative start position" if start.negative?
  raise ArgumentError, "negative stop position" if stop.negative?

  hard_masked_blocks_raw(chrom, start, stop)
end

#info ⇒ Object 



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# File 'ext/bio/twobit/twobit.c', line 138

static VALUE
twobit_info(VALUE self)
{
	TwoBit *tb = getTwoBit(self);

	if (!tb)
	{
		rb_raise(rb_eRuntimeError, "The 2bit file handle is not open!");
		return Qnil;
	}

	uint32_t i, j, foo;
	VALUE val;
	VALUE info = rb_hash_new();

	// file size
	val = UINT64_2NUM(tb->sz);
	if (!val)
		goto error;
	rb_hash_aset(info, rb_str_new2("file_size"), val);

	// nContigs
	val = UINT32_2NUM(tb->hdr->nChroms);
	if (!val)
		goto error;
	rb_hash_aset(info, rb_str_new2("nChroms"), val);

	// sequence length
	foo = 0;
	for (i = 0; i < tb->hdr->nChroms; i++)
	{
		foo += tb->idx->size[i];
	}
	val = UINT32_2NUM(foo);
	if (!val)
		goto error;
	rb_hash_aset(info, rb_str_new2("sequence_length"), val);

	// hard-masked length
	foo = 0;
	for (i = 0; i < tb->hdr->nChroms; i++)
	{
		for (j = 0; j < tb->idx->nBlockCount[i]; j++)
		{
			foo += tb->idx->nBlockSizes[i][j];
		}
	}
	val = UINT32_2NUM(foo);
	if (!val)
		goto error;
	rb_hash_aset(info, rb_str_new2("hard_masked_length"), val);

	// soft-masked length
	if (tb->idx->maskBlockStart)
	{
		foo = 0;
		for (i = 0; i < tb->hdr->nChroms; i++)
		{
			for (j = 0; j < tb->idx->maskBlockCount[i]; j++)
			{
				foo += tb->idx->maskBlockSizes[i][j];
			}
		}
		val = UINT32_2NUM(foo);
		if (!val)
			goto error;
		rb_hash_aset(info, rb_str_new2("soft_masked_length"), val);
	}

	return info;

error:
	rb_raise(rb_eRuntimeError, "Received an error while gathering information on the 2bit file!");
	return Qnil;
}

#masked? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/twobit.rb', line 48

def masked?
  @masked
end

#path ⇒ Object 



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# File 'lib/bio/twobit.rb', line 44

def path
  @fname
end

#sequence(chrom, start = 0, stop = 0) ⇒ Object Also known as: seq

Since “end” is a reserved word in Ruby, use “stop” instead.

Raises:

  • (ArgumentError) 


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# File 'lib/bio/twobit.rb', line 54

def sequence(chrom, start = 0, stop = 0)
  raise ArgumentError, "negative start position" if start.negative?
  raise ArgumentError, "negative stop position" if stop.negative?

  sequence_raw(chrom, start, stop)
end

#soft_masked_blocks(chrom, start = 0, stop = 0) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/bio/twobit.rb', line 77

def soft_masked_blocks(chrom, start = 0, stop = 0)
  raise ArgumentError, "negative start position" if start.negative?
  raise ArgumentError, "negative stop position" if stop.negative?

  soft_masked_blocks_raw(chrom, start, stop)
end