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| -rw-r--r-- | doc/database.org | 22 |
1 files changed, 12 insertions, 10 deletions
diff --git a/doc/database.org b/doc/database.org index 32f1f8e0..315ee2b6 100644 --- a/doc/database.org +++ b/doc/database.org @@ -1327,16 +1327,18 @@ we list the Published entries. The SNP count info for the BXD is calculated like this #+begin_src python - while startMb<endMb: - snp_count = g.db.execute(""" - select - count(*) from BXDSnpPosition - where - Chr = '%s' AND Mb >= %2.6f AND Mb < %2.6f AND - StrainId1 = %d AND StrainId2 = %d - """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2)).fetchone()[0] - SNPCounts.append(snp_count) - startMb += stepMb + with database_connection() as conn, conn.cursor() as cursor: + while startMb < endMb: + # snp count + cursor.execute( + "SELECT COUNT(*) FROM BXDSnpPosition " + "WHERE CHr = %s AND Mb >= %s AND Mb < %s " + "AND StrainId1 = %s AND StrainId2 = %s", + (chrName, f"{startMb:2.6f}", f"{startMb+stepMb:2.6f}", + strainId1, strainId2,) + ) + SNPCounts.append(cursor.fetchone()[0]) + startMB += stepMb #+end_src : select * from BXDSnpPosition limit 5; |