<commit_before>package XrefMapper::mus_musculus;

use  XrefMapper::BasicMapper;

use vars '@ISA';

@ISA = qw{ XrefMapper::BasicMapper };
use strict;

sub get_set_lists {

  return [["ExonerateGappedBest1", ["mus_musculus","*"]]];

}

sub consortium {

  return "MarkerSymbol";

}

sub gene_description_sources {

  return ("Uniprot/SPTREMBL", 
	  "RefSeq_dna", 
	  "RefSeq_peptide", 
	  "Uniprot/Varsplic", 
	  "Uniprot/SWISSPROT", 
	  "MarkerSymbol",
	  "RFAM", 
	  "miRNA_Registry");

}

sub special_filter {

  return ('\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
	  'RIKEN CDNA [0-9A-Z]{10} GENE',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
	  '\(*HYPOTHETICAL\s+.*',
	  '^UNKNOWN\s+.*',
	  'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
	  'CLONE MGC:\d+[ \.;]',
	  ' MGC:\s*\d+[ \.;]',
	  'HYPOTHETICAL PROTEIN,',
	  'HYPOTHETICAL PROTEIN \S+[\.;]',
	  'DNA SEGMENT, CHR.*',
	  'PROTEIN \S+ HOMOLOG\.?',
	  '^SIMILAR TO GENE.*',
	  'SIMILAR TO PUTATIVE[ \.]',
	  '^SIMILAR TO HYPOTHETICAL.*',
	  'SIMILAR TO (KIAA|LOC|RIKEN).*',
	  'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
	  'SIMILAR TO\s+$',
          'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
          'EST [A-Z]+\d+[ \.;]',
          '^\s*\(FRAGMENT\)\.?\s*$',<commit_msg>Added IMGT/GENE-DB to gene_description sources<commit_after>package XrefMapper::mus_musculus;

use  XrefMapper::BasicMapper;

use vars '@ISA';

@ISA = qw{ XrefMapper::BasicMapper };
use strict;

sub get_set_lists {

  return [["ExonerateGappedBest1", ["mus_musculus","*"]]];

}

sub consortium {

  return "MarkerSymbol";

}

sub gene_description_sources {

  return ("Uniprot/SPTREMBL", 
	  "RefSeq_dna", 
	  "RefSeq_peptide", 
	  "Uniprot/Varsplic", 
	  "Uniprot/SWISSPROT", 
	  "MarkerSymbol",
          "IMGT/GENE-DB",
	  "RFAM", 
	  "miRNA_Registry");

}

sub special_filter {

  return ('\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
	  'RIKEN CDNA [0-9A-Z]{10} GENE',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
	  '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
	  '\(*HYPOTHETICAL\s+.*',
	  '^UNKNOWN\s+.*',
	  'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
	  'CLONE MGC:\d+[ \.;]',
	  ' MGC:\s*\d+[ \.;]',
	  'HYPOTHETICAL PROTEIN,',
	  'HYPOTHETICAL PROTEIN \S+[\.;]',
	  'DNA SEGMENT, CHR.*',
	  'PROTEIN \S+ HOMOLOG\.?',
	  '^SIMILAR TO GENE.*',
	  'SIMILAR TO PUTATIVE[ \.]',
	  '^SIMILAR TO HYPOTHETICAL.*',
	  'SIMILAR TO (KIAA|LOC|RIKEN).*',
	  'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
	  'SIMILAR TO\s+$',
          'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
          'EST [A-Z]+\d+[ \.;]',
          '^\s*\(FRAGMENT\)\.?\s*$',
{'fraction_non_alphanumeric': 0.22935074913561276, 'fraction_numerical': 0.006915097963887821, 'mean_word_length': 3.1202531645569622, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3102952', 'n_tokens_mistral': 1306, 'n_tokens_neox': 1163, 'n_words': 190}