`COSMIC` data source class doesn't handle correctly cases with blank genomic mutation

[mtiberti]

this reproduces the problem:

from cancermuts.datasources import UniProt
from cancermuts.datasources import COSMIC

up = UniProt()
seq = up.get_sequence('RECQL4', upid='RECQ4_HUMAN', upac='O94761')

cosmic = COSMIC(targeted_database_file='/data/databases/cosmic-v102/Cosmic_CompleteTargetedScreensMutant_v102_GRCh38.tsv',
                                screen_mutant_database_file='/data/databases/cosmic-v102/Cosmic_GenomeScreensMutant_v102_GRCh38.tsv',
                                classification_database_file='/data/databases/cosmic-v102/Cosmic_Classification_v102_GRCh38.tsv',
                                database_encoding='latin1', lazy_load_db=True,
                )
cosmic.add_mutations(seq, genome_assembly_version='GRCh38', metadata=['genomic_coordinates', 'genomic_mutations',
                                                'cancer_site', 'cancer_histology'])

Traceroute:

      1 cosmic = COSMIC(targeted_database_file='/data/databases/cosmic-v102/Cosmic_CompleteTargetedScreensMutant_v102_GRCh38.tsv',
      2                                 screen_mutant_database_file='/data/databases/cosmic-v102/Cosmic_GenomeScreensMutant_v102_GRCh38.tsv',
      3                                 classification_database_file='/data/databases/cosmic-v102/Cosmic_Classification_v102_GRCh38.tsv',
      4                                 database_encoding='latin1', lazy_load_db=True,
      5                 )
----> 6 cosmic.add_mutations(seq, genome_assembly_version='GRCh38', metadata=['genomic_coordinates', 'genomic_mutations',
      7                                                 'cancer_site', 'cancer_histology'])

File /data/user/teo/devel/cancermuts/cancermuts/datasources.py:1808, in COSMIC.add_mutations(self, sequence, genome_assembly_version, cancer_types, cancer_histology_subtype_1, cancer_histology_subtype_2, cancer_histology_subtype_3, cancer_sites, cancer_site_subtype_1, cancer_site_subtype_2, cancer_site_subtype_3, use_alias, metadata)
   1806             tmp_md = [self] + out_metadata[md][mi]
   1807             print(mutation_obj, md, tmp_md)
-> 1808             this_md = metadata_classes[md](*tmp_md)
   1809             mutation_obj.metadata[md].append(this_md)
   1810 position.add_mutation(mutation_obj)

File /data/user/teo/devel/cancermuts/cancermuts/log.py:50, in logger_init.<locals>.wrapper(*args, **kwargs)
     48 this_self = args[0]
     49 this_self.log = logging.getLogger('.'.join([logger_name, this_self.__class__.__name__]))
---> 50 function(*args, **kwargs)

File /data/user/teo/devel/cancermuts/cancermuts/metadata.py:159, in GenomicMutation.__init__(self, source, genome_build, definition)
    156 self.genome_build = genome_build
    157 self.definition = definition
--> 159 if self._mut_snv_prog.match(definition):
    160     tokens = parse(self._mut_snv_parse, definition)
    162     if tokens['chr'] == '23':

TypeError: expected string or bytes-like object

this is due to the fact that the corresponding COSMIC mutation doesn't have a genomic mutation set and this case is not handled correctly by the class. See mutation with COSMIC ID COSM10510683 which triggers this issue

the genomic_coordinates metadata also probably needs some attention - from a quick look it seems that it's not initialized incorrectly