Module: SequenceServer::Links

Includes:
ERB::Util
Included in:
BLAST::Hit
Defined in:
lib/sequenceserver/links.rb

Overview

Module to contain methods for generating sequence retrieval links.

Constant Summary collapse

NCBI_ID_PATTERN = 
/gi\|(\d+)\|/
UNIPROT_ID_PATTERN = 
/sp\|(\w+)\|/
PFAM_ID_PATTERN = 
/(PF\d{5}\.?\d*)/
RFAM_ID_PATTERN = 
/(RF\d{5})/

Instance Method Summary collapse

Instance Method Details

#ncbi ⇒ Object

Link generators are methods that return a Hash as defined below.

# Required. Display title.
:title => "title",

# Required. Generated url.
:url => url,

# Optional. Left-right order in which the link should appear.
:order => num,

# Optional. Classes, if any, to apply to the link.
:class => "class1 class2",

# Optional. Class name of a FontAwesome icon to use.
:icon => "fa-icon-class"

If no url could be generated, return nil.

Helper methods

Following helper methods are available to help with link generation.

encode:
  URL encode query params.

  Don't use this function to encode the entire URL. Only params.

  e.g:
      sequence_id = encode sequence_id
      url = "http://www.ncbi.nlm.nih.gov/nucleotide/#{sequence_id}"

dbtype:
  Returns the database type (nucleotide or protein) that was used for
  BLAST search.

whichdb:
  Returns the databases from which the hit could have originated. To
  ensure that one and the correct database is returned, ensure that
  your sequence ids are unique across different FASTA files.
  NOTE: This method is slow.

coordinates:
  Returns min alignment start and max alignment end coordinates for
  query and hit sequences.

  e.g.,
  query_coords = coordinates[0]
  hit_coords = coordinates[1]



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# File 'lib/sequenceserver/links.rb', line 68

def ncbi
  return nil unless id.match(NCBI_ID_PATTERN) or title.match(NCBI_ID_PATTERN)
  ncbi_id = Regexp.last_match[1]
  ncbi_id = encode ncbi_id
  url = "https://www.ncbi.nlm.nih.gov/#{dbtype}/#{ncbi_id}"
  {
    order: 2,
    title: 'NCBI',
    url:   url,
    icon:  'fa-external-link'
  }
end

#pfam ⇒ Object 



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# File 'lib/sequenceserver/links.rb', line 94

def pfam
  return nil unless id.match(PFAM_ID_PATTERN) or title.match(PFAM_ID_PATTERN)
  pfam_id = Regexp.last_match[1]
  pfam_id = encode pfam_id
  url = "https://pfam.xfam.org/family/#{pfam_id}"
  {
    order: 2,
    title: 'Pfam',
    url:   url,
    icon:  'fa-external-link'
  }
end

#rfam ⇒ Object 



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# File 'lib/sequenceserver/links.rb', line 107

def rfam
  return nil unless id.match(RFAM_ID_PATTERN) or title.match(RFAM_ID_PATTERN)
  rfam_id = Regexp.last_match[1]
  rfam_id = encode rfam_id
  url = "https://rfam.xfam.org/family/#{rfam_id}"
  {
    order: 2,
    title: 'Rfam',
    url:   url,
    icon:  'fa-external-link'
  }
end

#uniprot ⇒ Object 



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# File 'lib/sequenceserver/links.rb', line 81

def uniprot
  return nil unless id.match(UNIPROT_ID_PATTERN) or title.match(UNIPROT_ID_PATTERN)
  uniprot_id = Regexp.last_match[1]
  uniprot_id = encode uniprot_id
  url = "https://www.uniprot.org/uniprot/#{uniprot_id}"
  {
    order: 2,
    title: 'UniProt',
    url:   url,
    icon:  'fa-external-link'
  }
end