Class: Bio::CGRanges

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/cgranges.rb,
lib/bio/cgranges/version.rb,
ext/bio/cgranges/cgranges.c

Overview

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

Defined Under Namespace

Classes: IndexedError, NoIndexError

Constant Summary collapse

VERSION = 
"0.0.4"

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Bio::CGRanges

Create a new cgranges object



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# File 'ext/bio/cgranges/cgranges.c', line 99

static VALUE
cgranges_init(VALUE self)
{
  cgranges_t *cr = NULL;

  cr = cr_init();
  DATA_PTR(self) = cr;

  rb_ivar_set(self, rb_intern("@indexed"), Qfalse);

  return self;
}

Instance Method Details

#add(rb_ctg, rb_st, rb_en, rb_label) ⇒ Bio::CGRanges

Add a genomic interval to the cgranges object.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

  • label (Fixnum) —

    The label of the interval.

Returns:



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# File 'ext/bio/cgranges/cgranges.c', line 120

static VALUE
cgranges_add(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en, VALUE rb_label)
{
  cgranges_t *cr = get_cgranges(self);
  cr_intv_t *intv = NULL;
  char *ctg = NULL;
  int32_t st = 0;
  int32_t en = 0;
  int32_t label = 0;

  if (RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eIndexedError, "Cannot add intervals to an indexed CGRanges");
    return Qnil;
  }

  ctg = StringValueCStr(rb_ctg);
  st = NUM2INT32(rb_st);
  en = NUM2INT32(rb_en);
  label = NUM2INT32(rb_label);

  intv = cr_add(cr, ctg, st, en, label);

  if (!intv)
  {
    rb_raise(rb_eRuntimeError, "Error adding interval");
    return Qnil;
  }

  return self;
}

#contain(rb_ctg, rb_st, rb_en) ⇒ Array

Containment query.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Array) —

    An array of [contig, start, end, label] arrays.



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# File 'ext/bio/cgranges/cgranges.c', line 273

static VALUE
cgranges_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  cgranges_t *cr = get_cgranges(self);
  char *ctg = NULL;
  int32_t st = 0;
  int32_t en = 0;

  int64_t *b = NULL;
  int64_t m_b = 0;
  int64_t n = 0;

  if (!RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eNoIndexError, "CGRanges not indexed");
    return Qnil;
  }

  ctg = StringValueCStr(rb_ctg);
  st = NUM2INT32(rb_st);
  en = NUM2INT32(rb_en);

  n = cr_contain(cr, ctg, st, en, &b, &m_b);

  if (n < 0)
  {
    free(b);
    rb_raise(rb_eRuntimeError, "Error finding contained");
    return Qnil;
  }

  VALUE result = rb_ary_new2(n);

  for (int64_t i = 0; i < n; i++)
  {
    VALUE rb_intv = rb_ary_new3(
        4, rb_ctg, INT32_2NUM(cr_start(cr, b[i])), INT32_2NUM(cr_end(cr, b[i])), INT32_2NUM(cr_label(cr, b[i])));
    rb_ary_push(result, rb_intv);
  }
  free(b);

  return result;
}

#count_contain(rb_ctg, rb_st, rb_en) ⇒ Fixnum

Get the number of contained intervals.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Fixnum) —

    The number of contained intervals.



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# File 'ext/bio/cgranges/cgranges.c', line 324

static VALUE
cgranges_count_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  cgranges_t *cr = get_cgranges(self);
  char *ctg = NULL;
  int32_t st = 0;
  int32_t en = 0;

  int64_t *b = NULL;
  int64_t m_b = 0;
  int64_t n = 0;

  if (!RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eNoIndexError, "CGRanges not indexed");
    return Qnil;
  }

  ctg = StringValueCStr(rb_ctg);
  st = NUM2INT32(rb_st);
  en = NUM2INT32(rb_en);

  n = cr_contain(cr, ctg, st, en, &b, &m_b);

  if (n < 0)
  {
    free(b);
    rb_raise(rb_eRuntimeError, "Error finding contained");
    return Qnil;
  }
  free(b);

  return INT64_2NUM(n);
}

#count_overlap(rb_ctg, rb_st, rb_en) ⇒ Fixnum

Get the number of overlapping intervals.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Fixnum) —

    The number of overlapping intervals.



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# File 'ext/bio/cgranges/cgranges.c', line 231

static VALUE
cgranges_count_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  cgranges_t *cr = get_cgranges(self);
  char *ctg = NULL;
  int32_t st = 0;
  int32_t en = 0;

  int64_t *b = NULL;
  int64_t m_b = 0;
  int64_t n = 0;

  if (!RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eNoIndexError, "CGRanges not indexed");
    return Qnil;
  }

  ctg = StringValueCStr(rb_ctg);
  st = NUM2INT32(rb_st);
  en = NUM2INT32(rb_en);

  n = cr_overlap(cr, ctg, st, en, &b, &m_b);

  if (n < 0)
  {
    free(b);
    rb_raise(rb_eRuntimeError, "Error finding overlaps");
    return Qnil;
  }
  free(b);

  return INT64_2NUM(n);
}

#coverage(ctg, rb_st, rb_en, mode: :overlap) ⇒ Array

Calculate breadth of coverage. This is a wrapper method for ‘coverage_overlap` and `coverage_contain`.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

  • mode (Symbol) (defaults to: :overlap) —

    :overlap or :contain (default: :overlap)

Returns:

  • (Array) —

    The breadth of coverage and the number of intervals.

See Also:



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# File 'lib/bio/cgranges.rb', line 19

def coverage(ctg, rb_st, rb_en, mode: :overlap)
  case mode
  when :overlap
    coverage_overlap(ctg, rb_st, rb_en)
  when :contain
    coverage_contain(ctg, rb_st, rb_en)
  else
    raise ArgumentError, "unknown mode: #{mode}"
  end
end

#coverage_contain(rb_ctg, rb_st, rb_en) ⇒ Array

Calculate breadth of coverage. (Containment) same as coverage(contig, start, end, mode: contain)

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Array) —

    The breadth of coverage and the number of intervals.

See Also:



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# File 'ext/bio/cgranges/cgranges.c', line 446

static VALUE
cgranges_coverage_contain(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  VALUE result;
  result = cgranges_coverage(self, rb_ctg, rb_st, rb_en, 1);
  return result;
}

#coverage_overlap(rb_ctg, rb_st, rb_en) ⇒ Array

Calculate breadth of coverage. (Overlap) Same as coverage(contig, start, end, mode: overlap)

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Array) —

    The breadth of coverage and the number of intervals.

See Also:



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# File 'ext/bio/cgranges/cgranges.c', line 429

static VALUE
cgranges_coverage_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  VALUE result;
  result = cgranges_coverage(self, rb_ctg, rb_st, rb_en, 0);
  return result;
}

#index ⇒ Bio::CGRanges

Index.

Returns:



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# File 'ext/bio/cgranges/cgranges.c', line 156

static VALUE
cgranges_index(VALUE self)
{
  if (RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eIndexedError, "CGRanges already indexed");
    return Qnil;
  }

  cgranges_t *cr = get_cgranges(self);
  cr_index(cr);

  rb_ivar_set(self, rb_intern("@indexed"), Qtrue);

  return self;
}

#overlap(rb_ctg, rb_st, rb_en) ⇒ Array

Overlap query.

Parameters:

  • contig (String) —

    The contig name

  • start (Fixnum) —

    The start position of the interval.

  • end (Fixnum) —

    The end position of the interval.

Returns:

  • (Array) —

    An array of [contig, start, end, label] arrays.



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# File 'ext/bio/cgranges/cgranges.c', line 180

static VALUE
cgranges_overlap(VALUE self, VALUE rb_ctg, VALUE rb_st, VALUE rb_en)
{
  cgranges_t *cr = get_cgranges(self);
  char *ctg = NULL;
  int32_t st = 0;
  int32_t en = 0;

  int64_t *b = NULL;
  int64_t m_b = 0;
  int64_t n = 0;

  if (!RTEST(rb_ivar_get(self, rb_intern("@indexed"))))
  {
    rb_raise(rb_eNoIndexError, "CGRanges not indexed");
    return Qnil;
  }

  ctg = StringValueCStr(rb_ctg);
  st = NUM2INT32(rb_st);
  en = NUM2INT32(rb_en);

  n = cr_overlap(cr, ctg, st, en, &b, &m_b);

  if (n < 0)
  {
    free(b);
    rb_raise(rb_eRuntimeError, "Error finding overlaps");
    return Qnil;
  }

  VALUE result = rb_ary_new2(n);

  for (int64_t i = 0; i < n; i++)
  {
    VALUE rb_intv = rb_ary_new3(
        4, rb_ctg, INT32_2NUM(cr_start(cr, b[i])), INT32_2NUM(cr_end(cr, b[i])), INT32_2NUM(cr_label(cr, b[i])));
    rb_ary_push(result, rb_intv);
  }
  free(b);

  return result;
}