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-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py207
1 files changed, 102 insertions, 105 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 43bb55b5..cd47f293 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,5 +1,3 @@
-from flask import Flask, g, url_for
-
import string
from PIL import (Image)
@@ -152,112 +150,111 @@ class SnpBrowser:
def get_browser_results(self):
self.snp_list = None
+ __query = ""
+ __vars = None
+ with database_connection() as conn, conn.cursor() as cursor:
+ if self.gene_name != "":
+ if self.species_id != 0:
+ __query = ("SELECT geneSymbol, chromosome, txStart, "
+ "txEnd FROM GeneList WHERE SpeciesId = %s "
+ "AND geneSymbol = %s")
+ __vars = (self.species_id, self.gene_name,)
+ else:
+ __query = ("SELECT geneSymbol, chromosome, txStart, "
+ "txEnd FROM GeneList WHERE geneSymbol = %s")
+ __vars = (self.gene_name,)
+ cursor.execute(__query, __vars)
- if self.gene_name != "":
- if self.species_id != 0:
- query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (
- self.species_id, self.gene_name)
- else:
- query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (
- self.gene_name)
- result = g.db.execute(query).fetchone()
- if result:
- self.gene_name, self.chr, self.start_mb, self.end_mb = result
- else:
- result_snp = None
- if self.variant_type == "SNP":
- if self.gene_name[:2] == "rs":
- query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name
- else:
- if self.species_id != 0:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (
- self.species_id, self.gene_name)
- else:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (
- self.gene_name)
- result_snp = g.db.execute(query).fetchall()
- if result_snp:
- self.snp_list = [item[0] for item in result_snp]
- self.chr = result_snp[0][1]
- self.start_mb = result_snp[0][2]
- self.end_mb = result_snp[0][3]
- else:
- return []
- elif self.variant_type == "InDel":
- if self.gene_name[0] == "I":
- if self.species_id != 0:
- query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (
- self.species_id, self.gene_name)
+ if result := cursor.fetchone():
+ self.gene_name, self.chr, self.start_mb, self.end_mb = result
+ else:
+ if self.variant_type in ["SNP", "InDel"]:
+ result_snp = None
+ __vars = (self.gene_name,)
+ if self.variant_type == "SNP":
+ if self.gene_name[:2] == "rs":
+ __query = ("SELECT Id, Chromosome, Position, "
+ "Position+0.000001 FROM SnpAll "
+ "WHERE Rs = %s")
+ else:
+ if self.species_id != 0:
+ __query = (
+ "SELECT Id, Chromosome, Position, "
+ "Position+0.000001 FROM SnpAll WHERE "
+ "SpeciesId = %s AND SnpName = %s")
+ __vars = (self.species_id, self.gene_name,)
+ else:
+ __query = (
+ "SELECT Id, Chromosome, Position, "
+ "Position+0.000001 FROM SnpAll "
+ "WHERE SnpName = %s")
+ cursor.execute(__query, __vars)
+ result_snp = cursor.fetchall()
+ else: # variant_type == InDel
+ if self.gene_name[0] == "I":
+ if self.species_id != 0:
+ __query = (
+ "SELECT Id, Chromosome, Mb_start, "
+ "Mb_end FROM IndelAll WHERE "
+ "SpeciesId = %s AND Name = %s")
+ __vars = (self.species_id, self.gene_name,)
+ else:
+ __query = (
+ "SELECT Id, Chromosome, Mb_start, "
+ "Mb_end FROM IndelAll WHERE Name = %s",)
+ __vars = (self.gene_name,)
+ cursor.execute(__query, __vars)
+ result_snp = cursor.fetchall()
+ if result_snp:
+ self.snp_list = [item[0] for item in result_snp]
+ self.chr = result_snp[0][1]
+ self.start_mb = result_snp[0][2]
+ self.end_mb = result_snp[0][3]
else:
- query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (
- self.gene_name)
- result_snp = g.db.execute(query).fetchall()
- if result_snp:
- self.snp_list = [item[0] for item in result_snp]
- self.chr = result_snp[0][1]
- self.start_mb = result_snp[0][2]
- self.end_mb = result_snp[0][3]
- else:
- return []
+ return []
- if self.variant_type == "SNP":
- mouse_query = """
- SELECT
- a.*, b.*
- FROM
- SnpAll a, SnpPattern b
- WHERE
- a.SpeciesId = %s AND a.Chromosome = '%s' AND
- a.Position >= %.6f AND a.Position < %.6f AND
- a.Id = b.SnpId
- ORDER BY a.Position
- """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
-
- rat_query = """
- SELECT
- a.*, b.*
- FROM
- SnpAll a, RatSnpPattern b
- WHERE
- a.SpeciesId = %s AND a.Chromosome = '%s' AND
- a.Position >= %.6f AND a.Position < %.6f AND
- a.Id = b.SnpId
- ORDER BY a.Position
- """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
- if self.species_id == 1:
- query = mouse_query
- elif self.species_id == 2:
- query = rat_query
-
- elif self.variant_type == "InDel":
- if self.species_id != 0:
- query = """
- SELECT
- DISTINCT a.Name, a.Chromosome, a.SourceId, a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, a.InDelSequence, b.Name
- FROM
- IndelAll a, SnpSource b
- WHERE
- a.SpeciesId = '%s' AND a.Chromosome = '%s' AND
- a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) AND
- b.Id = a.SourceId
- ORDER BY a.Mb_start
- """ % (self.species_id, self.chr, self.start_mb, self.end_mb)
- else:
- query = """
- SELECT
- DISTINCT a.Name, a.Chromosome, a.SourceId, a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, a.InDelSequence, b.Name
- FROM
- IndelAll a, SnpSource b
- WHERE
- a.Chromosome = '%s' AND
- a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) AND
- b.Id = a.SourceId
- ORDER BY a.Mb_start
- """ % (self.chr, self.start_mb, self.end_mb)
-
- results_all = g.db.execute(query).fetchall()
-
- return self.filter_results(results_all)
+ if self.variant_type == "SNP":
+ __vars = (self.species_id, self.chr,
+ f"{self.start_mb:.6f}",
+ f"{self.end_mb:.6f}",)
+ if self.species_id == 1: # Mouse
+ __query = ("SELECT a.*, b.* FROM SnpAll a, SnpPattern b "
+ "WHERE a.SpeciesId = %s AND a.Chromosome = %s "
+ "AND a.Position >= %s AND a.Position < %s "
+ "AND a.Id = b.SnpId ORDER BY a.Position")
+ elif self.species_id == 2: # Rat
+ __query = (
+ "SELECT a.*, b.* FROM SnpAll a, RatSnpPattern b "
+ "WHERE a.SpeciesId = %s AND a.Chromosome = %s "
+ "AND a.Position >= %s AND a.Position < %s "
+ "AND a.Id = b.SnpId ORDER BY a.Position")
+
+ elif self.variant_type == "InDel":
+ if self.species_id != 0:
+ __query = (
+ "SELECT DISTINCT a.Name, a.Chromosome, a.SourceId, "
+ "a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, "
+ "a.InDelSequence, b.Name FROM IndelAll a, "
+ "SnpSource b WHERE a.SpeciesId = %s AND "
+ "a.Chromosome = %s AND a.Mb_start >= %s "
+ "AND a.Mb_start < %s AND b.Id = a.SourceId "
+ "ORDER BY a.Mb_start")
+ __vars = (self.species_id,
+ self.chr, f"{self.start_mb:2.6f}",
+ f"{self.end_mb+0.0010:2.6f}",)
+ cursor.execute(__query, __vars)
+ else:
+ __query = (
+ "SELECT DISTINCT a.Name, a.Chromosome, a.SourceId, "
+ "a.Mb_start, a.Mb_end, a.Strand, a.Type, a.Size, "
+ "a.InDelSequence, b.Name FROM IndelAll a, "
+ "SnpSource b WHERE a.Chromosome = %s AND "
+ "a.Mb_start >= %2.6f AND a.Mb_start < (%2.6f+.0010) "
+ "AND b.Id = a.SourceId ORDER BY a.Mb_start")
+ __vars = (self.chr, f"{self.start_mb:2.6f}",
+ f"{self.end_mb+0.0010:2.6f}",)
+ cursor.execute(__query, __vars)
+ return self.filter_results(cursor.fetchall())
def filter_results(self, results):
filtered_results = []
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 17:57:48 +0000