def get_all_gene_ids(self):
"""
List of all gene IDs (arbitrary order) that we consider in xbrowse
This does *not* include genes are:
- not ensembl genes
- not on a standard chromosome (in genomeloc)
"""
cursor = self.db_conn.cursor()
cursor.execute("select gene.stable_id, seq_region.name from gene "
"join seq_region on gene.seq_region_id=seq_region.seq_region_id")
return [row[0] for row in cursor if ensembl_parsing_utils.get_chr_from_seq_region_name(row[1]) is not None]
def get_all_gene_ids(self):
"""
List of all gene IDs (arbitrary order) that we consider in xbrowse
This does *not* include genes are:
- not ensembl genes
- not on a standard chromosome (in genomeloc)
"""
cursor = self.db_conn.cursor()
cursor.execute("select gene.stable_id, seq_region.name from gene "
"join seq_region on gene.seq_region_id=seq_region.seq_region_id")
return [row[0] for row in cursor if ensembl_parsing_utils.get_chr_from_seq_region_name(row[1]) is not None]
def get_all_exons(self):
"""
Get a list of all exons (order not guaranteed) from ensembl
Fetched from database, not REST
"""
cursor = self.db_conn.cursor()
cursor.execute("select exon.stable_id, seq_region.name, exon.seq_region_start, exon.seq_region_end from exon "
"join seq_region on exon.seq_region_id=seq_region.seq_region_id")
exons = []
for row in cursor:
chr = ensembl_parsing_utils.get_chr_from_seq_region_name(row[1])
start = row[2]
stop = row[3]
if chr is None:
continue
exon = dict(exon_id=row[0])
exon['xstart'] = genomeloc.get_single_location(chr, start)
exon['xstop'] = genomeloc.get_single_location(chr, stop)
exons.append(exon)
return exons
def get_all_exons(self):
"""
Get a list of all exons (order not guaranteed) from ensembl
Fetched from database, not REST
"""
cursor = self.db_conn.cursor()
cursor.execute("select exon.stable_id, seq_region.name, exon.seq_region_start, exon.seq_region_end from exon "
"join seq_region on exon.seq_region_id=seq_region.seq_region_id")
exons = []
for row in cursor:
chr = ensembl_parsing_utils.get_chr_from_seq_region_name(row[1])
start = row[2]
stop = row[3]
if chr is None:
continue
exon = dict(exon_id=row[0])
exon['xstart'] = genomeloc.get_single_location(chr, start)
exon['xstop'] = genomeloc.get_single_location(chr, stop)
exons.append(exon)
return exons
def get_gene_structure(self, gene_id):
"""
Query ensembl API for the transcript/exon structure of a gene
This is the foundation of the elements in db.genes
Exception if can't process gene
"""
gene = {}
# gene basics
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'gene'}
gene_list_json = requests.get(url, params=params).json()
gene_list_json = [
item for item in gene_list_json if item['ID'] == gene_id
]
if len(gene_list_json) == 0:
raise Exception("No genes with ID %s" % gene_id)
if len(gene_list_json) > 1:
raise Exception(">1 ensembl genes with ID %s" % gene_id)
gene_json = gene_list_json[0]
chr = ensembl_parsing_utils.get_chr_from_seq_region_name(
gene_json['seq_region_name'])
if chr is None:
raise Exception("Gene %s is on a nonstandard chromosome: %s" %
(gene_id, chr))
gene['chr'] = chr
gene['start'] = gene_json['start']
gene['stop'] = gene_json['end']
gene['xstart'] = genomeloc.get_single_location(chr, gene['start'])
gene['xstop'] = genomeloc.get_single_location(chr, gene['stop'])
gene['gene_id'] = gene_json['ID']
gene['symbol'] = gene_json['external_name']
gene['description'] = gene_json['description']
gene['biotype'] = gene_json['biotype']
# transcripts
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'transcript'}
transcript_json = [
t for t in requests.get(url, params=params).json()
if t['Parent'] == gene_id
]
gene['transcripts'] = []
for t in transcript_json:
transcript_id = t['ID']
transcript = dict(transcript_id=transcript_id,
biotype=t['biotype'],
start=t['start'],
stop=t['end'])
transcript['xstart'] = genomeloc.get_single_location(
chr, transcript['start'])
transcript['xstop'] = genomeloc.get_single_location(
chr, transcript['stop'])
# exons_for_transcript
url = self._get_rest_url() + '/feature/id/%s' % transcript_id
params = {'content-type': 'application/json', 'feature': 'exon'}
transcript_exon_json = requests.get(url, params=params).json()
transcript['exons'] = [
e['ID']
for e in sorted(transcript_exon_json, key=lambda x: x['start'])
if e['Parent'] == transcript_id
]
gene['transcripts'].append(transcript)
# exons
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'exon'}
exon_json = requests.get(url, params=params).json()
transcript_ids = {t['transcript_id'] for t in gene['transcripts']}
exon_ids_seen = set()
gene['exons'] = []
for e in exon_json:
exon_id = e['ID']
# skip exons that aren't actually in one of this gene's transcripts
if e['Parent'] not in transcript_ids:
continue
if exon_id in exon_ids_seen:
continue
exon = {
'exon_id': exon_id,
'start': e['start'],
'stop': e['end'],
}
exon['xstart'] = genomeloc.get_single_location(chr, exon['start'])
exon['xstop'] = genomeloc.get_single_location(chr, exon['stop'])
gene['exons'].append(exon)
exon_ids_seen.add(e['ID'])
# cds
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'cds'}
cds_json = requests.get(url, params=params).json()
cds_map = {} # map from (start, stop) -> {start, stop, transcripts}
for c in cds_json:
# skip exons that aren't actually in one of this gene's transcripts
if c['Parent'] not in transcript_ids:
continue
cds_t = (c['start'], c['end'])
if cds_t not in cds_map:
cds_map[cds_t] = {
'start': c['start'],
'stop': c['end'],
'xstart': genomeloc.get_single_location(chr, c['start']),
'xstop': genomeloc.get_single_location(chr, c['end']),
'transcripts': [],
}
cds_map[cds_t]['transcripts'].append(c['Parent'])
gene['cds'] = sorted(cds_map.values(),
key=lambda x: (x['start'], x['stop']))
for i, cds in enumerate(gene['cds']):
cds['cds_id'] = '%s-%i' % (gene['gene_id'], i + 1)
return gene
def get_gene_structure(self, gene_id):
"""
Query ensembl API for the transcript/exon structure of a gene
This is the foundation of the elements in db.genes
Exception if can't process gene
"""
gene = {}
# gene basics
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'gene'}
gene_list_json = requests.get(url, params=params).json()
gene_list_json = [item for item in gene_list_json if item['ID'] == gene_id]
if len(gene_list_json) == 0:
raise Exception("No genes with ID %s" % gene_id)
if len(gene_list_json) > 1:
raise Exception(">1 ensembl genes with ID %s" % gene_id)
gene_json = gene_list_json[0]
chr = ensembl_parsing_utils.get_chr_from_seq_region_name(gene_json['seq_region_name'])
if chr is None:
raise Exception("Gene %s is on a nonstandard chromosome: %s" % (gene_id, chr) )
gene['chr'] = chr
gene['start'] = gene_json['start']
gene['stop'] = gene_json['end']
gene['xstart'] = genomeloc.get_single_location(chr, gene['start'])
gene['xstop'] = genomeloc.get_single_location(chr, gene['stop'])
gene['gene_id'] = gene_json['ID']
gene['symbol'] = gene_json['external_name']
gene['description'] = gene_json['description']
gene['biotype'] = gene_json['biotype']
# transcripts
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'transcript'}
transcript_json = [t for t in requests.get(url, params=params).json() if t['Parent'] == gene_id]
gene['transcripts'] = []
for t in transcript_json:
transcript_id = t['ID']
transcript = dict(
transcript_id=transcript_id,
biotype=t['biotype'],
start=t['start'],
stop=t['end']
)
transcript['xstart'] = genomeloc.get_single_location(chr, transcript['start'])
transcript['xstop'] = genomeloc.get_single_location(chr, transcript['stop'])
# exons_for_transcript
url = self._get_rest_url() + '/feature/id/%s' % transcript_id
params = {'content-type': 'application/json', 'feature': 'exon'}
transcript_exon_json = requests.get(url, params=params).json()
transcript['exons'] = [
e['ID'] for e in sorted(transcript_exon_json, key=lambda x: x['start']) if e['Parent'] == transcript_id
]
gene['transcripts'].append(transcript)
# exons
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'exon'}
exon_json = requests.get(url, params=params).json()
transcript_ids = {t['transcript_id'] for t in gene['transcripts']}
exon_ids_seen = set()
gene['exons'] = []
for e in exon_json:
exon_id = e['ID']
# skip exons that aren't actually in one of this gene's transcripts
if e['Parent'] not in transcript_ids:
continue
if exon_id in exon_ids_seen:
continue
exon = {
'exon_id': exon_id,
'start': e['start'],
'stop': e['end'],
}
exon['xstart'] = genomeloc.get_single_location(chr, exon['start'])
exon['xstop'] = genomeloc.get_single_location(chr, exon['stop'])
gene['exons'].append(exon)
exon_ids_seen.add(e['ID'])
# cds
url = self._get_rest_url() + '/feature/id/%s' % gene_id
params = {'content-type': 'application/json', 'feature': 'cds'}
cds_json = requests.get(url, params=params).json()
cds_map = {} # map from (start, stop) -> {start, stop, transcripts}
for c in cds_json:
# skip exons that aren't actually in one of this gene's transcripts
if c['Parent'] not in transcript_ids:
continue
cds_t = (c['start'], c['end'])
if cds_t not in cds_map:
cds_map[cds_t] = {
'start': c['start'],
'stop': c['end'],
'xstart': genomeloc.get_single_location(chr, c['start']),
'xstop': genomeloc.get_single_location(chr, c['end']),
'transcripts': [],
}
cds_map[cds_t]['transcripts'].append(c['Parent'])
gene['cds'] = sorted(cds_map.values(), key=lambda x: (x['start'], x['stop']))
for i, cds in enumerate(gene['cds']):
cds['cds_id'] = '%s-%i' % (gene['gene_id'], i+1)
return gene
