def clinvar_doc_feeder(input_file, hg19: bool):
"""
This function will split the xml file into `<ClinVarSet>...</ClinVarSet>` blocks, then parse each block into an
`PublicSetType` object (which is defined in the dynamically imported `clinvarlib`), and finally convert each
`PublicSetType` object into a clinvar document.
"""
"""
A ClinVarFullRelease_*.xml.gz file has the following structure:
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ReleaseSet Dated="2021-06-26" ...>
<ClinVarSet ID="38756179">
...
</ClinVarSet>
<ClinVarSet ID="38756180">
...
</ClinVarSet>
...
</ReleaseSet>
Therefore when splitting the xml into `<ClinVarSet>` blocks, the first 2 lines and the last 1 line should be
skipped.
However the `rec_handler` function cannot skip the last 1 line, and will return "\n</ReleaseSet>...</ClinVarSet>" as
the last block in this scenario. Therefore in the for-loop below, we will skip any block starting with
"\n</ReleaseSet>".
"""
clinvar_set_blocks = rec_handler(input_file,
block_end='</ClinVarSet>\n',
skip=2,
include_block_end=True)
for clinvar_set_block in clinvar_set_blocks:
# Skip any block starting with "\n</ReleaseSet>"
# Actually only the last block will be skipped. See comments above
if clinvar_set_block.startswith('\n</ReleaseSet>'):
continue
try:
# Parse each `<ClinVarSet>` block into a `clinvarlib.PublicSetType` object
public_set_obj = clinvarlib.parseString(clinvar_set_block,
silence=1)
except:
logging.debug(clinvar_set_block)
raise
# Convert each `clinvarlib.PublicSetType` object into a json document
for doc in _map_public_set_to_json(public_set_obj, hg19):
yield doc
def rcv_feeder(input_file, hg19):
# the first two line of clinvar_xml is not useful information
cv_data = rec_handler(input_file, block_end='</ClinVarSet>\n',
skip=2, include_block_end=True)
for record in cv_data:
# some exceptions
if record.startswith('\n</ReleaseSet>'):
continue
try:
record_parsed = clinvar.parseString(record, silence=1)
except:
logging.debug(record)
raise
for record_mapped in _map_line_to_json(record_parsed, hg19):
yield record_mapped