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Copy pathDB_OPS.py
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DB_OPS.py
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#!/usr/bin/env python3
import sqlite3
from sqlite3 import Error
import os
import re
def create_connection(db_file):
""" create a database connection to the SQLite database
specified by the db_file
:param db_file: database file
:return: Connection object or None
"""
conn = None
try:
conn = sqlite3.connect(db_file)
except Error as e:
print(e)
return conn
# Replace the other functions with this one
def extract_value(conn, table, sample, column):
cur = conn.cursor()
cur.row_factory = lambda cursor, row: row[0]
cur.execute(f"SELECT {column} FROM {table} WHERE Sample='{sample}'")
result = cur.fetchone()
if result:
return result
else:
return "NA"
cur.row_factory = None
def extract_patient_status(conn, patient, column):
cur = conn.cursor()
cur.row_factory = lambda cursor, row: row[0]
cur.execute(f"SELECT {column} FROM status WHERE patient='{patient}'")
result = cur.fetchone()
if result:
return result
else:
return "NA"
cur.row_factory = None
def extract_sample_metrics(conn, sample, column):
cur = conn.cursor()
cur.row_factory = lambda cursor, row: row[0]
cur.execute(f"SELECT {column} FROM KEY_METRICS WHERE Sample='{sample}'")
result = cur.fetchone()
if result:
return result
else:
return "NA"
cur.row_factory = None
def extract_sample_field(conn,sample,column):
cur = conn.cursor()
cur.row_factory = lambda cursor, row: row[0]
cur.execute(f"SELECT {column} FROM Samples WHERE Sample='{sample}'")
result = cur.fetchone()
if result:
return result
else:
return "NA"
cur.row_factory = None
def extract_fileloc_field(conn, sample, column):
cur = conn.cursor()
cur.row_factory = lambda cursor, row: row[0]
cur.execute(f"SELECT {column} FROM File_Locations WHERE Sample='{sample}'")
result = cur.fetchone()
if result:
return result
else:
return "NA"
cur.row_factory = None
def update_metrics_db(
conn,
sample,
WGS_Bases_Over_Q30,
WGS_Min_Aligned_Reads_Delivered,
Raw_Mean_Coverage,
WGS_Dedup_Coverage,
Median_Insert_Size,
Mean_Insert_Size,
Raw_Duplication_Rate,
WGS_Contamination,
Raw_Reads_Count,
WTS_Aligned_Reads,
WTS_rRNA_contamination,
WTS_Expression_Profiling_Efficiency,
Concordance,
Purity,
Flags,
Fails,
Raw_Median_Insert_Size,
Raw_Mean_Insert_Size
):
# Create cursor object
cur = conn.cursor()
#Test to see if it exists and if so extract the current data
cur.execute(f"""SELECT * FROM KEY_METRICS WHERE Sample='{sample}'""")
result = cur.fetchone()
if result:
cur.execute("""
UPDATE KEY_METRICS
SET WGS_Bases_Over_Q30 = :WGS_Bases_Over_Q30,
WGS_Min_Aligned_Reads_Delivered = :WGS_Min_Aligned_Reads_Delivered,
Raw_Mean_Coverage = :Raw_Mean_Coverage,
WGS_Dedup_Coverage = :WGS_Dedup_Coverage,
Raw_Duplication_Rate = :Raw_Duplication_Rate,
Raw_Median_Insert_Size = :Raw_Median_Insert_Size,
Raw_Mean_Insert_Size = :Raw_Mean_Insert_Size,
Median_Insert_Size = :Median_Insert_Size,
Mean_Insert_Size = :Mean_Insert_Size,
WGS_Contamination = :WGS_Contamination,
Concordance = :Concordance,
Purity = :Purity,
Raw_Reads_Count = :Raw_Reads_Count,
WTS_Aligned_Reads = :WTS_Aligned_Reads,
WTS_rRNA_contamination = :WTS_rRNA_contamination,
WTS_Expression_Profiling_Efficiency = :WTS_Expression_Profiling_Efficiency,
Flags = :Flags,
Fails = :Fails
WHERE
Sample = :sample
;
""",
{
"WGS_Bases_Over_Q30": WGS_Bases_Over_Q30,
"WGS_Min_Aligned_Reads_Delivered": WGS_Min_Aligned_Reads_Delivered,
"Raw_Mean_Coverage": Raw_Mean_Coverage,
"WGS_Dedup_Coverage": WGS_Dedup_Coverage,
"Raw_Duplication_Rate": Raw_Duplication_Rate,
"Raw_Median_Insert_Size": Raw_Median_Insert_Size,
"Raw_Mean_Insert_Size": Raw_Mean_Insert_Size,
"Median_Insert_Size": Median_Insert_Size,
"Mean_Insert_Size": Mean_Insert_Size,
"WGS_Contamination": WGS_Contamination,
"Concordance": Concordance,
"Purity": Purity,
"Raw_Reads_Count": Raw_Reads_Count,
"WTS_Aligned_Reads": WTS_Aligned_Reads,
"WTS_rRNA_contamination": WTS_rRNA_contamination,
"WTS_Expression_Profiling_Efficiency": WTS_Expression_Profiling_Efficiency,
"Flags": Flags,
"Fails": Fails,
"sample": sample
}
)
else:
cur.execute("""
INSERT INTO KEY_METRICS (
Sample,
WGS_Bases_Over_Q30,
WGS_Min_Aligned_Reads_Delivered,
Raw_Mean_Coverage,
WGS_Dedup_Coverage,
Raw_Duplication_Rate,
Raw_Median_Insert_Size,
Raw_Mean_Insert_Size,
Median_Insert_Size,
Mean_Insert_Size,
WGS_Contamination,
Concordance,
Purity,
Raw_Reads_Count,
WTS_Aligned_Reads,
WTS_rRNA_contamination,
WTS_Expression_Profiling_Efficiency,
Flags,
Fails
)
VALUES (
:sample,
:WGS_Bases_Over_Q30,
:WGS_Min_Aligned_Reads_Delivered,
:Raw_Mean_Coverage,
:WGS_Dedup_Coverage,
:Raw_Duplication_Rate,
:Raw_Median_Insert_Size,
:Raw_Mean_Insert_Size,
:Median_Insert_Size,
:Mean_Insert_Size,
:WGS_Contamination,
:Concordance,
:Purity,
:Raw_Reads_Count,
:WTS_Aligned_Reads,
:WTS_rRNA_contamination,
:WTS_Expression_Profiling_Efficiency,
:Flags,
:Fails
)
;
""",
{
"WGS_Bases_Over_Q30": WGS_Bases_Over_Q30,
"WGS_Min_Aligned_Reads_Delivered": WGS_Min_Aligned_Reads_Delivered,
"Raw_Mean_Coverage": Raw_Mean_Coverage,
"WGS_Dedup_Coverage": WGS_Dedup_Coverage,
"Raw_Duplication_Rate": Raw_Duplication_Rate,
"Raw_Median_Insert_Size": Raw_Median_Insert_Size,
"Raw_Mean_Insert_Size": Raw_Mean_Insert_Size,
"Median_Insert_Size": Median_Insert_Size,
"Mean_Insert_Size": Mean_Insert_Size,
"WGS_Contamination": WGS_Contamination,
"Concordance": Concordance,
"Purity": Purity,
"Raw_Reads_Count": Raw_Reads_Count,
"WTS_Aligned_Reads": WTS_Aligned_Reads,
"WTS_rRNA_contamination": WTS_rRNA_contamination,
"WTS_Expression_Profiling_Efficiency": WTS_Expression_Profiling_Efficiency,
"Flags": Flags,
"Fails": Fails,
"sample": sample
}
)
# if result:
# cur.execute(f"DELETE FROM KEY_METRICS WHERE Sample='{sample}'")
# cur.execute(f"INSERT INTO KEY_METRICS (Sample,WGS_Bases_Over_Q30,WGS_Min_Aligned_Reads_Delivered,Raw_Mean_Coverage,WGS_Dedup_Coverage,Median_Insert_Size,Mean_Insert_Size,Raw_Duplication_Rate,WGS_Contamination,Raw_Reads_Count,WTS_Exonic_Rate,WTS_Aligned_Reads,WTS_rRNA_contamination,Concordance,Purity,Flags,Fails,Raw_Median_Insert_Size,Raw_Mean_Insert_Size) VALUES ('{sample}','{WGS_Bases_Over_Q30}','{WGS_Min_Aligned_Reads_Delivered}','{Raw_Mean_Coverage}','{WGS_Dedup_Coverage}','{Median_Insert_Size}','{Mean_Insert_Size}','{Raw_Duplication_Rate}','{WGS_Contamination}','{Raw_Reads_Count}','{WTS_Exonic_Rate}','{WTS_Aligned_Reads}','{WTS_rRNA_contamination}','{Concordance}','{Purity}','{Flags}','{Fails}','{Raw_Median_Insert_Size}','{Raw_Mean_Insert_Size}')")
# else:
# cur.execute(f"INSERT INTO KEY_METRICS (Sample,WGS_Bases_Over_Q30,WGS_Min_Aligned_Reads_Delivered,Raw_Mean_Coverage,WGS_Dedup_Coverage,Median_Insert_Size,Mean_Insert_Size,Raw_Duplication_Rate,WGS_Contamination,Raw_Reads_Count,WTS_Exonic_Rate,WTS_Aligned_Reads,WTS_rRNA_contamination,Concordance,Purity,Flags,Fails,Raw_Median_Insert_Size,Raw_Mean_Insert_Size) VALUES ('{sample}','{WGS_Bases_Over_Q30}','{WGS_Min_Aligned_Reads_Delivered}','{Raw_Mean_Coverage}','{WGS_Dedup_Coverage}','{Median_Insert_Size}','{Mean_Insert_Size}','{Raw_Duplication_Rate}','{WGS_Contamination}','{Raw_Reads_Count}','{WTS_Exonic_Rate}','{WTS_Aligned_Reads}','{WTS_rRNA_contamination}','{Concordance}','{Purity}','{Flags}','{Fails}','{Raw_Median_Insert_Size}','{Raw_Mean_Insert_Size}')")
def Update_Samples_Table(conn, sample, sample_True, Instituion, Cohort, DNA_N, DNA_N_True, DNA_T, DNA_T_True, RNA, RNA_True):
# Create cursor object
cur = conn.cursor()
#Test to see if it exists and if so extract the current data
cur.execute(f"""SELECT * FROM Samples WHERE Sample='{sample}'""")
result = cur.fetchone()
if result:
if result[4].startswith('MoH') and DNA_N == 'NA':
DNA_N = result[4]
DNA_N_True = result[4]
if result[6].startswith('MoH') and DNA_T == 'NA':
DNA_T = result[6]
DNA_T_True = result[6]
if result[8].startswith('MoH') and RNA == 'NA':
RNA = result[8]
RNA_True = result[8]
cur.execute(f"DELETE FROM Samples WHERE Sample='{sample}'")
cur.execute(f"INSERT INTO Samples (Sample,Sample_True,Instituion,Cohort,DNA_N,DNA_N_True,DNA_T,DNA_T_True,RNA,RNA_True) VALUES ('{sample}','{sample}','{Instituion}','{Cohort}','{DNA_N}','{DNA_N_True}','{DNA_T}','{DNA_T_True}','{RNA}','{RNA_True}')")
else:
cur.execute(f"INSERT INTO Samples (Sample,Sample_True,Instituion,Cohort,DNA_N,DNA_N_True,DNA_T,DNA_T_True,RNA,RNA_True) VALUES ('{sample}','{sample}','{Instituion}','{Cohort}','{DNA_N}','{DNA_N_True}','{DNA_T}','{DNA_T_True}','{RNA}','{RNA_True}')")
#Grabs all fields from Sample table and outputs an array of the data
def extract_sample_details(conn, sample_true):
ret = {
"Sample": "NA",
"Sample_True": "NA",
"Instituion": "NA",
"Cohort": "NA",
"DNA_N": "NA",
"DNA_N_True": "NA",
"DNA_T": "NA",
"DNA_T_True": "NA",
"RNA": "NA",
"RNA_True": "NA"
}
conn.row_factory = sqlite3.Row
cur = conn.cursor()
#Test to see if it exists and if so extract the current data
cur.execute(f"""SELECT * FROM Samples WHERE Sample='{sample_true}'""")
result = cur.fetchone()
ret.update(result)
return ret
def extract_sample_names(conn):
# Create cursor object
cur = conn.cursor()
cur.execute(f"""SELECT Sample FROM Samples""")
cur.row_factory = lambda cursor, row: row[0]
result = cur.fetchall()
cur.row_factory = None
if result:
return result
else:
return []
def extract_fileloc_details(conn, sample):
ret = {
"Sample": "NA",
"Run_Proc_BAM_DNA_T": "NA",
"Run_Proc_BAM_DNA_N": "NA",
"Beluga_BAM_DNA_T": "NA",
"Beluga_BAM_DNA_N": "NA",
"DNA_VCF_G": "NA",
"DNA_VCF_S": "NA",
"Mutect2_Somatic_vcf": "NA",
"Mutect2_Germline_vcf": "NA",
"strelka2_Germline_vcf": "NA",
"strelka2_Somatic_vcf": "NA",
"vardict_Germline_vcf": "NA",
"vardict_Somatic_vcf": "NA",
"varscan2_Germline_vcf": "NA",
"varscan2_Somatic_vcf": "NA",
"GRIDSS": "NA",
"gripss_somatic": "NA",
"gripss_germline": "NA",
"purple_somatic": "NA",
"purple_germline": "NA",
"purple_circos": "NA",
"cnvkit_vcf": "NA",
"Final_VCF": "NA",
"Final_DNA_BAM_T": "NA",
"Final_DNA_BAM_N": "NA",
"DNA_MultiQC": "NA",
"pcgr_report": "NA",
"pcgr_maf": "NA",
"pcgr_snvs_indels": "NA",
"pcgr_cna_segments": "NA",
"TP_ini": "NA",
"Run_Proc_fastq_1_RNA": "NA",
"Run_Proc_fastq_2_RNA": "NA",
"Beluga_fastq_1_RNA": "NA",
"Beluga_fastq_2_RNA": "NA",
"RNA_VCF": "NA",
"RNA_VCF_filt": "NA",
"Final_RNA_BAM": "NA",
"RNA_MultiQC": "NA",
"rna_pcgr_report": "NA",
"rna_pcgr_maf": "NA",
"rna_pcgr_snvs_indels": "NA",
"AnnoFuse": "NA",
"RNA_Abundance": "NA",
"big_wig_tracks_F": "NA",
"big_wig_tracks_R": "NA",
"RNA_Abundance_ini": "NA",
"RNA_Variants_ini": "NA"
}
conn.row_factory = sqlite3.Row
cur = conn.cursor()
cur.execute(f"""SELECT * FROM File_Locations WHERE Sample='{sample}'""")
result = cur.fetchone()
if result:
ret.update(result)
return ret
def extract_timestamp_details(conn, sample):
ret = {
"Sample": "NA",
"Run_Proc_BAM_DNA_T": "NA",
"Run_Proc_BAM_DNA_N": "NA",
"Beluga_BAM_DNA_T": "NA",
"Beluga_BAM_DNA_N": "NA",
"DNA_VCF_G": "NA",
"DNA_VCF_S": "NA",
"Mutect2_Somatic_vcf": "NA",
"Mutect2_Germline_vcf": "NA",
"strelka2_Germline_vcf": "NA",
"strelka2_Somatic_vcf": "NA",
"vardict_Germline_vcf": "NA",
"vardict_Somatic_vcf": "NA",
"varscan2_Germline_vcf": "NA",
"varscan2_Somatic_vcf": "NA",
"GRIDSS": "NA",
"gripss_somatic": "NA",
"gripss_germline": "NA",
"purple_somatic": "NA",
"purple_germline": "NA",
"purple_circos": "NA",
"cnvkit_vcf": "NA",
"Final_VCF": "NA",
"Final_DNA_BAM_T": "NA",
"Final_DNA_BAM_N": "NA",
"DNA_MultiQC": "NA",
"pcgr_report": "NA",
"pcgr_maf": "NA",
"pcgr_snvs_indels": "NA",
"pcgr_cna_segments": "NA",
"TP_ini": "NA",
"Run_Proc_fastq_1_RNA": "NA",
"Run_Proc_fastq_2_RNA": "NA",
"Beluga_fastq_1_RNA": "NA",
"Beluga_fastq_2_RNA": "NA",
"RNA_VCF": "NA",
"RNA_VCF_filt": "NA",
"Final_RNA_BAM": "NA",
"RNA_MultiQC": "NA",
"rna_pcgr_report": "NA",
"rna_pcgr_maf": "NA",
"rna_pcgr_snvs_indels": "NA",
"AnnoFuse": "NA",
"RNA_Abundance": "NA",
"big_wig_tracks_F": "NA",
"big_wig_tracks_R": "NA",
"RNA_Abundance_ini": "NA",
"RNA_Variants_ini": "NA"
}
conn.row_factory = sqlite3.Row
cur = conn.cursor()
cur.execute(f"""SELECT * FROM Timestamps WHERE Sample='{sample}'""")
result = cur.fetchone()
if result:
ret.update(result)
return ret
def update_timestamp_details(sample):
cur = sample.conn.cursor()
cur.execute(f"""SELECT * FROM Timestamps WHERE Sample='{sample.sample}'""")
result = cur.fetchone()
result = cur.fetchone()
if result:
cur.execute("""
UPDATE Timestamps
SET Run_Proc_BAM_DNA_T = :run_proc_bam_dna_t,
Run_Proc_BAM_DNA_N = :run_proc_bam_dna_n,
Beluga_BAM_DNA_T = :beluga_bam_dna_t,
Beluga_BAM_DNA_N = :beluga_bam_dna_n,
DNA_VCF_G = :dna_vcf_g,
DNA_VCF_S = :dna_vcf_s,
Mutect2_Somatic_vcf = :mutect2_somatic_vcf,
strelka2_Germline_vcf = :strelka2_germline_vcf,
strelka2_Somatic_vcf = :strelka2_somatic_vcf,
vardict_Germline_vcf = :vardict_germline_vcf,
vardict_Somatic_vcf = :vardict_somatic_vcf,
varscan2_Germline_vcf = :varscan2_germline_vcf,
varscan2_Somatic_vcf = :varscan2_somatic_vcf,
GRIDSS = :gridss,
gripss_somatic = :gripss_somatic,
gripss_germline = :gripss_germline,
purple_somatic = :purple_somatic,
purple_germline = :purple_germline,
purple_circos = :purple_circos,
cnvkit_vcf = :cnvkit_vcf,
Final_VCF = :final_vcf,
Final_DNA_BAM_T = :final_dna_bam_t,
Final_DNA_BAM_N = :final_dna_bam_n,
DNA_MultiQC = :dna_multiqc,
pcgr_report = :pcgr_report,
pcgr_maf = :pcgr_maf,
pcgr_snvs_indels = :pcgr_snvs_indels,
pcgr_cna_segments = :pcgr_cna_segments,
TP_ini = :tp_ini,
Run_Proc_fastq_1_RNA = :run_proc_fastq_1_rna,
Run_Proc_fastq_2_RNA = :run_proc_fastq_2_rna,
Beluga_fastq_1_RNA = :beluga_fastq_1_rna,
Beluga_fastq_2_RNA = :beluga_fastq_2_rna,
RNA_VCF = :rna_vcf,
RNA_VCF_filt = :rna_vcf_filt,
Final_RNA_BAM = :final_rna_bam,
RNA_MultiQC = :rna_multiqc,
rna_pcgr_report = :rna_pcgr_report,
rna_pcgr_maf = :rna_pcgr_maf,
rna_pcgr_snvs_indels = :rna_pcgr_snvs_indels,
AnnoFuse = :annofuse,
RNA_Abundance = :rna_abundance,
big_wig_tracks_F = :big_wig_tracks_f,
big_wig_tracks_R = :big_wig_tracks_r,
RNA_Abundance_ini = :rna_abundance_ini,
RNA_Variants_ini = :rna_variants_ini
WHERE
Sample = :sample
;
""",
{
"run_proc_bam_dna_t": sample.ts_run_proc_bam_dna_t,
"run_proc_bam_dna_n": sample.ts_run_proc_bam_dna_n,
"beluga_bam_dna_t": sample.ts_beluga_bam_dna_t,
"beluga_bam_dna_n": sample.ts_beluga_bam_dna_n,
"dna_vcf_g": sample.ts_dna_vcf_g,
"dna_vcf_s": sample.ts_dna_vcf_s,
"mutect2_somatic_vcf": sample.ts_mutect2_somatic_vcf,
"strelka2_germline_vcf": sample.ts_strelka2_germline_vcf,
"strelka2_somatic_vcf": sample.ts_strelka2_somatic_vcf,
"vardict_germline_vcf": sample.ts_vardict_germline_vcf,
"vardict_somatic_vcf": sample.ts_vardict_somatic_vcf,
"varscan2_germline_vcf": sample.ts_varscan2_germline_vcf,
"varscan2_somatic_vcf": sample.ts_varscan2_somatic_vcf,
"gridss": sample.ts_gridss,
"gripss_somatic": sample.ts_gripss_somatic,
"gripss_germline": sample.ts_gripss_germline,
"purple_somatic": sample.ts_purple_somatic,
"purple_germline": sample.ts_purple_germline,
"purple_circos": sample.ts_purple_circos,
"cnvkit_vcf": sample.ts_cnvkit_vcf,
"final_vcf": sample.ts_final_vcf,
"final_dna_bam_t": sample.ts_final_dna_bam_t,
"final_dna_bam_n": sample.ts_final_dna_bam_n,
"dna_multiqc": sample.ts_dna_multiqc,
"pcgr_report": sample.ts_pcgr_report,
"pcgr_maf": sample.ts_pcgr_maf,
"pcgr_snvs_indels": sample.ts_pcgr_snvs_indels,
"pcgr_cna_segments": sample.ts_pcgr_cna_segments,
"tp_ini": sample.ts_tp_ini,
"run_proc_fastq_1_rna": sample.ts_run_proc_fastq_1_rna,
"run_proc_fastq_2_rna": sample.ts_run_proc_fastq_2_rna,
"beluga_fastq_1_rna": sample.ts_beluga_fastq_1_rna,
"beluga_fastq_2_rna": sample.ts_beluga_fastq_2_rna,
"rna_vcf": sample.ts_rna_vcf,
"rna_vcf_filt": sample.ts_rna_vcf_filt,
"final_rna_bam": sample.ts_final_rna_bam,
"rna_multiqc": sample.ts_rna_multiqc,
"rna_pcgr_report": sample.ts_rna_pcgr_report,
"rna_pcgr_maf": sample.ts_rna_pcgr_maf,
"rna_pcgr_snvs_indels": sample.ts_rna_pcgr_snvs_indels,
"annofuse": sample.ts_annofuse,
"rna_abundance": sample.ts_rna_abundance,
"big_wig_tracks_f": sample.ts_big_wig_tracks_f,
"big_wig_tracks_r": sample.ts_big_wig_tracks_r,
"rna_abundance_ini": sample.ts_rna_abundance_ini,
"rna_variants_ini": sample.ts_rna_variants_ini,
"sample": sample.sample
}
)
else:
cur.execute("""
INSERT INTO Timestamps (
Sample,
Run_Proc_BAM_DNA_T,
Run_Proc_BAM_DNA_N,
Beluga_BAM_DNA_T,
Beluga_BAM_DNA_N,
DNA_VCF_G,
DNA_VCF_S,
Mutect2_Somatic_vcf,
strelka2_Germline_vcf,
strelka2_Somatic_vcf,
vardict_Germline_vcf,
vardict_Somatic_vcf,
varscan2_Germline_vcf,
varscan2_Somatic_vcf,
GRIDSS,
gripss_somatic,
gripss_germline,
purple_somatic,
purple_germline,
purple_circos,
cnvkit_vcf,
Final_VCF,
Final_DNA_BAM_T,
Final_DNA_BAM_N,
DNA_MultiQC,
pcgr_report,
pcgr_maf,
pcgr_snvs_indels,
pcgr_cna_segments,
TP_ini,
Run_Proc_fastq_1_RNA,
Run_Proc_fastq_2_RNA,
Beluga_fastq_1_RNA,
Beluga_fastq_2_RNA,
RNA_VCF,
RNA_VCF_filt,
Final_RNA_BAM,
RNA_MultiQC,
rna_pcgr_report,
rna_pcgr_maf,
rna_pcgr_snvs_indels,
AnnoFuse,
RNA_Abundance,
big_wig_tracks_F,
big_wig_tracks_R,
RNA_Abundance_ini,
RNA_Variants_ini
)
VALUES (
:sample,
:run_proc_bam_dna_t,
:run_proc_bam_dna_n,
:beluga_bam_dna_t,
:beluga_bam_dna_n,
:dna_vcf_g,
:dna_vcf_s,
:mutect2_somatic_vcf,
:strelka2_germline_vcf,
:strelka2_somatic_vcf,
:vardict_germline_vcf,
:vardict_somatic_vcf,
:varscan2_germline_vcf,
:varscan2_somatic_vcf,
:gridss,
:gripss_somatic,
:gripss_germline,
:purple_somatic,
:purple_germline,
:purple_circos,
:cnvkit_vcf,
:final_vcf,
:final_dna_bam_t,
:final_dna_bam_n,
:dna_multiqc,
:pcgr_report,
:pcgr_maf,
:pcgr_snvs_indels,
:pcgr_cna_segments,
:tp_ini,
:run_proc_fastq_1_rna,
:run_proc_fastq_2_rna,
:beluga_fastq_1_rna,
:beluga_fastq_2_rna,
:rna_vcf,
:rna_vcf_filt,
:final_rna_bam,
:rna_multiqc,
:rna_pcgr_report,
:rna_pcgr_maf,
:rna_pcgr_snvs_indels,
:annofuse,
:rna_abundance,
:big_wig_tracks_f,
:big_wig_tracks_r,
:rna_abundance_ini,
:rna_variants_ini
)
;
""",
{
"run_proc_bam_dna_t": sample.ts_run_proc_bam_dna_t,
"run_proc_bam_dna_n": sample.ts_run_proc_bam_dna_n,
"beluga_bam_dna_t": sample.ts_beluga_bam_dna_t,
"beluga_bam_dna_n": sample.ts_beluga_bam_dna_n,
"dna_vcf_g": sample.ts_dna_vcf_g,
"dna_vcf_s": sample.ts_dna_vcf_s,
"mutect2_somatic_vcf": sample.ts_mutect2_somatic_vcf,
"strelka2_germline_vcf": sample.ts_strelka2_germline_vcf,
"strelka2_somatic_vcf": sample.ts_strelka2_somatic_vcf,
"vardict_germline_vcf": sample.ts_vardict_germline_vcf,
"vardict_somatic_vcf": sample.ts_vardict_somatic_vcf,
"varscan2_germline_vcf": sample.ts_varscan2_germline_vcf,
"varscan2_somatic_vcf": sample.ts_varscan2_somatic_vcf,
"gridss": sample.ts_gridss,
"gripss_somatic": sample.ts_gripss_somatic,
"gripss_germline": sample.ts_gripss_germline,
"purple_somatic": sample.ts_purple_somatic,
"purple_germline": sample.ts_purple_germline,
"purple_circos": sample.ts_purple_circos,
"cnvkit_vcf": sample.ts_cnvkit_vcf,
"final_vcf": sample.ts_final_vcf,
"final_dna_bam_t": sample.ts_final_dna_bam_t,
"final_dna_bam_n": sample.ts_final_dna_bam_n,
"dna_multiqc": sample.ts_dna_multiqc,
"pcgr_report": sample.ts_pcgr_report,
"pcgr_maf": sample.ts_pcgr_maf,
"pcgr_snvs_indels": sample.ts_pcgr_snvs_indels,
"pcgr_cna_segments": sample.ts_pcgr_cna_segments,
"tp_ini": sample.ts_tp_ini,
"run_proc_fastq_1_rna": sample.ts_run_proc_fastq_1_rna,
"run_proc_fastq_2_rna": sample.ts_run_proc_fastq_2_rna,
"beluga_fastq_1_rna": sample.ts_beluga_fastq_1_rna,
"beluga_fastq_2_rna": sample.ts_beluga_fastq_2_rna,
"rna_vcf": sample.ts_rna_vcf,
"rna_vcf_filt": sample.ts_rna_vcf_filt,
"final_rna_bam": sample.ts_final_rna_bam,
"rna_multiqc": sample.ts_rna_multiqc,
"rna_pcgr_report": sample.ts_rna_pcgr_report,
"rna_pcgr_maf": sample.ts_rna_pcgr_maf,
"rna_pcgr_snvs_indels": sample.ts_rna_pcgr_snvs_indels,
"annofuse": sample.ts_annofuse,
"rna_abundance": sample.ts_rna_abundance,
"big_wig_tracks_f": sample.ts_big_wig_tracks_f,
"big_wig_tracks_r": sample.ts_big_wig_tracks_r,
"rna_abundance_ini": sample.ts_rna_abundance_ini,
"rna_variants_ini": sample.ts_rna_variants_ini,
"sample": sample.sample
}
)
# if result:
# cur.execute(f"DELETE FROM Timestamps WHERE Sample='{sample.sample}'")
# cur.execute(f"INSERT INTO Timestamps (Sample,Run_Proc_BAM_DNA_T,Run_Proc_BAM_DNA_N,Beluga_BAM_DNA_T,Beluga_BAM_DNA_N,DNA_VCF_G,DNA_VCF_S,Mutect2_Somatic_vcf,strelka2_Germline_vcf,strelka2_Somatic_vcf,vardict_Germline_vcf,vardict_Somatic_vcf,varscan2_Germline_vcf,varscan2_Somatic_vcf,GRIDSS,gripss_somatic,gripss_germline,purple_somatic,purple_germline,purple_circos,cnvkit_vcf,Final_VCF,Final_DNA_BAM_T,Final_DNA_BAM_N,DNA_MultiQC,pcgr_report,pcgr_maf,pcgr_snvs_indels,pcgr_cna_segments,TP_ini,Run_Proc_fastq_1_RNA,Run_Proc_fastq_2_RNA,Beluga_fastq_1_RNA,Beluga_fastq_2_RNA,RNA_VCF,Final_RNA_BAM_variants,RNA_MultiQC,AnnoFuse,RNA_Abundance,big_wig_tracks_F,big_wig_tracks_R,RNA_Abundance_ini,RNA_Variants_ini) VALUES ('{sample.sample}','{sample.ts_run_proc_bam_dna_t}','{sample.ts_run_proc_bam_dna_n}','{sample.ts_beluga_bam_dna_t}','{sample.ts_beluga_bam_dna_n}','{sample.ts_dna_vcf_g}','{sample.ts_dna_vcf_s}','{sample.ts_mutect2_somatic_vcf}','{sample.ts_strelka2_germline_vcf}','{sample.ts_strelka2_somatic_vcf}','{sample.ts_vardict_germline_vcf}','{sample.ts_vardict_somatic_vcf}','{sample.ts_varscan2_germline_vcf}','{sample.ts_varscan2_somatic_vcf}','{sample.ts_cnvkit_vcf}','{sample.ts_final_vcf}','{sample.ts_final_dna_bam_t}','{sample.ts_final_dna_bam_n}','{sample.ts_dna_multiqc}','{sample.ts_pcgr_report}','{sample.ts_pcgr_maf}','{sample.ts_pcgr_snvs_indels}','{sample.ts_pcgr_cna_segments}','{sample.ts_tp_ini}','{sample.ts_run_proc_fastq_1_rna}','{sample.ts_run_proc_fastq_2_rna}','{sample.ts_beluga_fastq_1_rna}','{sample.ts_beluga_fastq_2_rna}','{sample.ts_rna_vcf}','{sample.ts_final_rna_bam}','{sample.ts_rna_multiqc}','{sample.ts_annofuse}','{sample.ts_gridss}','{sample.ts_rna_abundance}','{sample.ts_big_wig_tracks_f}','{sample.ts_big_wig_tracks_r}','{sample.ts_rna_abundance_ini}','{sample.ts_rna_variants_ini}')")
# else:
# cur.execute(f"INSERT INTO Timestamps (Sample,Run_Proc_BAM_DNA_T,Run_Proc_BAM_DNA_N,Beluga_BAM_DNA_T,Beluga_BAM_DNA_N,DNA_VCF_G,DNA_VCF_S,Mutect2_Somatic_vcf,strelka2_Germline_vcf,strelka2_Somatic_vcf,vardict_Germline_vcf,vardict_Somatic_vcf,varscan2_Germline_vcf,varscan2_Somatic_vcf,GRIDSS,gripss_somatic,gripss_germline,purple_somatic,purple_germline,purple_circos,cnvkit_vcf,Final_VCF,Final_DNA_BAM_T,Final_DNA_BAM_N,DNA_MultiQC,pcgr_report,pcgr_maf,pcgr_snvs_indels,pcgr_cna_segments,TP_ini,Run_Proc_fastq_1_RNA,Run_Proc_fastq_2_RNA,Beluga_fastq_1_RNA,Beluga_fastq_2_RNA,RNA_VCF,Final_RNA_BAM_variants,RNA_MultiQC,AnnoFuse,RNA_Abundance,big_wig_tracks_F,big_wig_tracks_R,RNA_Abundance_ini,RNA_Variants_ini) VALUES ('{sample.sample}','{sample.ts_run_proc_bam_dna_t}','{sample.ts_run_proc_bam_dna_n}','{sample.ts_beluga_bam_dna_t}','{sample.ts_beluga_bam_dna_n}','{sample.ts_dna_vcf_g}','{sample.ts_dna_vcf_s}','{sample.ts_mutect2_somatic_vcf}','{sample.ts_strelka2_germline_vcf}','{sample.ts_strelka2_somatic_vcf}','{sample.ts_vardict_germline_vcf}','{sample.ts_vardict_somatic_vcf}','{sample.ts_varscan2_germline_vcf}','{sample.ts_varscan2_somatic_vcf}','{sample.ts_cnvkit_vcf}','{sample.ts_final_vcf}','{sample.ts_final_dna_bam_t}','{sample.ts_final_dna_bam_n}','{sample.ts_dna_multiqc}','{sample.ts_pcgr_report}','{sample.ts_pcgr_maf}','{sample.ts_pcgr_snvs_indels}','{sample.ts_pcgr_cna_segments}','{sample.ts_tp_ini}','{sample.ts_run_proc_fastq_1_rna}','{sample.ts_run_proc_fastq_2_rna}','{sample.ts_beluga_fastq_1_rna}','{sample.ts_beluga_fastq_2_rna}','{sample.ts_rna_vcf}','{sample.ts_final_rna_bam}','{sample.ts_rna_multiqc}','{sample.ts_annofuse}','{sample.ts_gridss}','{sample.ts_rna_abundance}','{sample.ts_big_wig_tracks_f}','{sample.ts_big_wig_tracks_r}','{sample.ts_rna_abundance_ini}','{sample.ts_rna_variants_ini}')")
def update_fileloc_details(sample):
cur = sample.conn.cursor()
cur.execute(f"""SELECT * FROM File_Locations WHERE Sample='{sample.sample}'""")
result = cur.fetchone()
if result:
cur.execute("""
UPDATE File_Locations
SET Run_Proc_BAM_DNA_T = :run_proc_bam_dna_t,
Run_Proc_BAM_DNA_N = :run_proc_bam_dna_n,
Beluga_BAM_DNA_T = :beluga_bam_dna_t,
Beluga_BAM_DNA_N = :beluga_bam_dna_n,
DNA_VCF_G = :dna_vcf_g,
DNA_VCF_S = :dna_vcf_s,
Mutect2_Somatic_vcf = :mutect2_somatic_vcf,
strelka2_Germline_vcf = :strelka2_germline_vcf,
strelka2_Somatic_vcf = :strelka2_somatic_vcf,
vardict_Germline_vcf = :vardict_germline_vcf,
vardict_Somatic_vcf = :vardict_somatic_vcf,
varscan2_Germline_vcf = :varscan2_germline_vcf,
varscan2_Somatic_vcf = :varscan2_somatic_vcf,
GRIDSS = :gridss,
gripss_somatic = :gripss_somatic,
gripss_germline = :gripss_germline,
purple_somatic = :purple_somatic,
purple_germline = :purple_germline,
purple_circos = :purple_circos,
cnvkit_vcf = :cnvkit_vcf,
Final_VCF = :final_vcf,
Final_DNA_BAM_T = :final_dna_bam_t,
Final_DNA_BAM_N = :final_dna_bam_n,
DNA_MultiQC = :dna_multiqc,
pcgr_report = :pcgr_report,
pcgr_maf = :pcgr_maf,
pcgr_snvs_indels = :pcgr_snvs_indels,
pcgr_cna_segments = :pcgr_cna_segments,
TP_ini = :tp_ini,
Run_Proc_fastq_1_RNA = :run_proc_fastq_1_rna,
Run_Proc_fastq_2_RNA = :run_proc_fastq_2_rna,
Beluga_fastq_1_RNA = :beluga_fastq_1_rna,
Beluga_fastq_2_RNA = :beluga_fastq_2_rna,
RNA_VCF = :rna_vcf,
RNA_VCF_filt = :rna_vcf_filt,
Final_RNA_BAM = :final_rna_bam,
RNA_MultiQC = :rna_multiqc,
rna_pcgr_report = :rna_pcgr_report,
rna_pcgr_maf = :rna_pcgr_maf,
rna_pcgr_snvs_indels = :rna_pcgr_snvs_indels,
AnnoFuse = :annofuse,
RNA_Abundance = :rna_abundance,
big_wig_tracks_F = :big_wig_tracks_f,
big_wig_tracks_R = :big_wig_tracks_r,
RNA_Abundance_ini = :rna_abundance_ini,
RNA_Variants_ini = :rna_variants_ini
WHERE
sample = :sample
;
""",
{
"run_proc_bam_dna_t": sample.run_proc_bam_dna_t,
"run_proc_bam_dna_n": sample.run_proc_bam_dna_n,
"beluga_bam_dna_t": sample.beluga_bam_dna_t,
"beluga_bam_dna_n": sample.beluga_bam_dna_n,
"dna_vcf_g": sample.dna_vcf_g,
"dna_vcf_s": sample.dna_vcf_s,
"mutect2_somatic_vcf": sample.mutect2_somatic_vcf,
"strelka2_germline_vcf": sample.strelka2_germline_vcf,
"strelka2_somatic_vcf": sample.strelka2_somatic_vcf,
"vardict_germline_vcf": sample.vardict_germline_vcf,
"vardict_somatic_vcf": sample.vardict_somatic_vcf,
"varscan2_germline_vcf": sample.varscan2_germline_vcf,
"varscan2_somatic_vcf": sample.varscan2_somatic_vcf,
"gridss": sample.gridss,
"gripss_somatic": sample.gripss_somatic,
"gripss_germline": sample.gripss_germline,
"purple_somatic": sample.purple_somatic,
"purple_germline": sample.purple_germline,
"purple_circos": sample.purple_circos,
"cnvkit_vcf": sample.cnvkit_vcf,
"final_vcf": sample.final_vcf,
"final_dna_bam_t": sample.final_dna_bam_t,
"final_dna_bam_n": sample.final_dna_bam_n,
"dna_multiqc": sample.dna_multiqc,
"pcgr_report": sample.pcgr_report,
"pcgr_maf": sample.pcgr_maf,
"pcgr_snvs_indels": sample.pcgr_snvs_indels,
"pcgr_cna_segments": sample.pcgr_cna_segments,
"tp_ini": sample.tp_ini,
"run_proc_fastq_1_rna": sample.run_proc_fastq_1_rna,
"run_proc_fastq_2_rna": sample.run_proc_fastq_2_rna,
"beluga_fastq_1_rna": sample.beluga_fastq_1_rna,
"beluga_fastq_2_rna": sample.beluga_fastq_2_rna,
"rna_vcf": sample.rna_vcf,
"rna_vcf_filt": sample.rna_vcf_filt,
"final_rna_bam": sample.final_rna_bam,
"rna_multiqc": sample.rna_multiqc,
"rna_pcgr_report": sample.rna_pcgr_report,
"rna_pcgr_maf": sample.rna_pcgr_maf,
"rna_pcgr_snvs_indels": sample.rna_pcgr_snvs_indels,
"annofuse": sample.annofuse,
"rna_abundance": sample.rna_abundance,
"big_wig_tracks_f": sample.big_wig_tracks_f,
"big_wig_tracks_r": sample.big_wig_tracks_r,
"rna_abundance_ini": sample.rna_abundance_ini,
"rna_variants_ini": sample.rna_variants_ini,
"sample": sample.sample
}
)
else:
cur.execute("""
INSERT INTO File_Locations (
Sample,
Run_Proc_BAM_DNA_T,
Run_Proc_BAM_DNA_N,
Beluga_BAM_DNA_T,
Beluga_BAM_DNA_N,
DNA_VCF_G,
DNA_VCF_S,
Mutect2_Somatic_vcf,
strelka2_Germline_vcf,
strelka2_Somatic_vcf,
vardict_Germline_vcf,
vardict_Somatic_vcf,
varscan2_Germline_vcf,
varscan2_Somatic_vcf,
GRIDSS,
gripss_somatic,
gripss_germline,
purple_somatic,
purple_germline,
purple_circos,
cnvkit_vcf,
Final_VCF,
Final_DNA_BAM_T,
Final_DNA_BAM_N,
DNA_MultiQC,
pcgr_report,
pcgr_maf,
pcgr_snvs_indels,
pcgr_cna_segments,
TP_ini,
Run_Proc_fastq_1_RNA,
Run_Proc_fastq_2_RNA,
Beluga_fastq_1_RNA,
Beluga_fastq_2_RNA,
RNA_VCF,
RNA_VCF_filt,
Final_RNA_BAM,
RNA_MultiQC,
rna_pcgr_report,
rna_pcgr_maf,
rna_pcgr_snvs_indels,
AnnoFuse,
RNA_Abundance,
big_wig_tracks_F,
big_wig_tracks_R,
RNA_Abundance_ini,
RNA_Variants_ini
)
VALUES (
:sample,
:run_proc_bam_dna_t,
:run_proc_bam_dna_n,
:beluga_bam_dna_t,
:beluga_bam_dna_n,
:dna_vcf_g,
:dna_vcf_s,
:mutect2_somatic_vcf,
:strelka2_germline_vcf,
:strelka2_somatic_vcf,
:vardict_germline_vcf,
:vardict_somatic_vcf,
:varscan2_germline_vcf,
:varscan2_somatic_vcf,
:gridss,
:gripss_somatic,
:gripss_germline,
:purple_somatic,
:purple_germline,
:purple_circos,
:cnvkit_vcf,
:final_vcf,
:final_dna_bam_t,
:final_dna_bam_n,
:dna_multiqc,
:pcgr_report,
:pcgr_maf,
:pcgr_snvs_indels,
:pcgr_cna_segments,
:tp_ini,
:run_proc_fastq_1_rna,
:run_proc_fastq_2_rna,
:beluga_fastq_1_rna,
:beluga_fastq_2_rna,
:rna_vcf,
:rna_vcf_filt,
:final_rna_bam,
:rna_multiqc,
:rna_pcgr_report,
:rna_pcgr_maf,
:rna_pcgr_snvs_indels,
:annofuse,
:rna_abundance,
:big_wig_tracks_f,
:big_wig_tracks_r,
:rna_abundance_ini,
:rna_variants_ini
)
;
""",
{
"run_proc_bam_dna_t": sample.run_proc_bam_dna_t,
"run_proc_bam_dna_n": sample.run_proc_bam_dna_n,
"beluga_bam_dna_t": sample.beluga_bam_dna_t,
"beluga_bam_dna_n": sample.beluga_bam_dna_n,
"dna_vcf_g": sample.dna_vcf_g,
"dna_vcf_s": sample.dna_vcf_s,
"mutect2_somatic_vcf": sample.mutect2_somatic_vcf,
"strelka2_germline_vcf": sample.strelka2_germline_vcf,
"strelka2_somatic_vcf": sample.strelka2_somatic_vcf,
"vardict_germline_vcf": sample.vardict_germline_vcf,
"vardict_somatic_vcf": sample.vardict_somatic_vcf,
"varscan2_germline_vcf": sample.varscan2_germline_vcf,
"varscan2_somatic_vcf": sample.varscan2_somatic_vcf,
"gridss": sample.gridss,
"gripss_somatic": sample.gripss_somatic,
"gripss_germline": sample.gripss_germline,
"purple_somatic": sample.purple_somatic,
"purple_germline": sample.purple_germline,
"purple_circos": sample.purple_circos,
"cnvkit_vcf": sample.cnvkit_vcf,
"final_vcf": sample.final_vcf,
"final_dna_bam_t": sample.final_dna_bam_t,
"final_dna_bam_n": sample.final_dna_bam_n,
"dna_multiqc": sample.dna_multiqc,
"pcgr_report": sample.pcgr_report,
"pcgr_maf": sample.pcgr_maf,
"pcgr_snvs_indels": sample.pcgr_snvs_indels,
"pcgr_cna_segments": sample.pcgr_cna_segments,
"tp_ini": sample.tp_ini,
"run_proc_fastq_1_rna": sample.run_proc_fastq_1_rna,
"run_proc_fastq_2_rna": sample.run_proc_fastq_2_rna,
"beluga_fastq_1_rna": sample.beluga_fastq_1_rna,
"beluga_fastq_2_rna": sample.beluga_fastq_2_rna,
"rna_vcf": sample.rna_vcf,
"rna_vcf_filt": sample.rna_vcf_filt,
"final_rna_bam": sample.final_rna_bam,
"rna_multiqc": sample.rna_multiqc,
"rna_pcgr_report": sample.rna_pcgr_report,
"rna_pcgr_maf": sample.rna_pcgr_maf,
"rna_pcgr_snvs_indels": sample.rna_pcgr_snvs_indels,
"annofuse": sample.annofuse,
"rna_abundance": sample.rna_abundance,
"big_wig_tracks_f": sample.big_wig_tracks_f,
"big_wig_tracks_r": sample.big_wig_tracks_r,
"rna_abundance_ini": sample.rna_abundance_ini,
"rna_variants_ini": sample.rna_variants_ini,
"sample": sample.sample
}
)
# if result:
# cur.execute(f"DELETE FROM File_Locations WHERE Sample='{sample.sample}'")
# cur.execute(f"INSERT INTO File_Locations (Sample,Run_Proc_BAM_DNA_T,Run_Proc_BAM_DNA_N,Beluga_BAM_DNA_T,Beluga_BAM_DNA_N,DNA_VCF_G,DNA_VCF_S,Mutect2_Somatic_vcf,strelka2_Germline_vcf,strelka2_Somatic_vcf,vardict_Germline_vcf,vardict_Somatic_vcf,varscan2_Germline_vcf,varscan2_Somatic_vcf,GRIDSS,gripss_somatic,gripss_germline,purple_somatic,purple_germline,purple_circos,cnvkit_vcf,Final_VCF,Final_DNA_BAM_T,Final_DNA_BAM_N,DNA_MultiQC,pcgr_report,pcgr_maf,pcgr_snvs_indels,pcgr_cna_segments,TP_ini,Run_Proc_fastq_1_RNA,Run_Proc_fastq_2_RNA,Beluga_fastq_1_RNA,Beluga_fastq_2_RNA,RNA_VCF,Final_RNA_BAM,RNA_MultiQC,AnnoFuse,RNA_Abundance,big_wig_tracks_F,big_wig_tracks_R,RNA_Abundance_ini,RNA_Variants_ini) VALUES ('{sample.sample}','{sample.run_proc_bam_dna_t}','{sample.run_proc_bam_dna_n}','{sample.beluga_bam_dna_t}','{sample.beluga_bam_dna_n}','{sample.dna_vcf_g}','{sample.dna_vcf_s}','{sample.mutect2_somatic_vcf}','{sample.strelka2_germline_vcf}','{sample.strelka2_somatic_vcf}','{sample.vardict_germline_vcf}','{sample.vardict_somatic_vcf}','{sample.varscan2_germline_vcf}','{sample.varscan2_somatic_vcf}','{sample.cnvkit_vcf}','{sample.final_vcf}','{sample.final_dna_bam_t}','{sample.final_dna_bam_n}','{sample.dna_multiqc}','{sample.pcgr_report}','{sample.pcgr_maf}','{sample.pcgr_snvs_indels}','{sample.pcgr_cna_segments}','{sample.tp_ini}','{sample.run_proc_fastq_1_rna}','{sample.run_proc_fastq_2_rna}','{sample.beluga_fastq_1_rna}','{sample.beluga_fastq_2_rna}','{sample.rna_vcf}','{sample.final_rna_bam_variants}','{sample.rna_multiqc}','{sample.annofuse}','{sample.gridss}','{sample.rna_abundance}','{sample.big_wig_tracks_f}','{sample.big_wig_tracks_r}','{sample.rna_abundance_ini}','{sample.rna_variants_ini}')")
# else:
# cur.execute(f"INSERT INTO File_Locations (Sample,Run_Proc_BAM_DNA_T,Run_Proc_BAM_DNA_N,Beluga_BAM_DNA_T,Beluga_BAM_DNA_N,DNA_VCF_G,DNA_VCF_S,Mutect2_Somatic_vcf,strelka2_Germline_vcf,strelka2_Somatic_vcf,vardict_Germline_vcf,vardict_Somatic_vcf,varscan2_Germline_vcf,varscan2_Somatic_vcf,GRIDSS,gripss_somatic,gripss_germline,purple_somatic,purple_germline,purple_circos,cnvkit_vcf,Final_VCF,Final_DNA_BAM_T,Final_DNA_BAM_N,DNA_MultiQC,pcgr_report,pcgr_maf,pcgr_snvs_indels,pcgr_cna_segments,TP_ini,Run_Proc_fastq_1_RNA,Run_Proc_fastq_2_RNA,Beluga_fastq_1_RNA,Beluga_fastq_2_RNA,RNA_VCF,Final_RNA_BAM,RNA_MultiQC,AnnoFuse,RNA_Abundance,big_wig_tracks_F,big_wig_tracks_R,RNA_Abundance_ini,RNA_Variants_ini) VALUES ('{sample.sample}','{sample.run_proc_bam_dna_t}','{sample.run_proc_bam_dna_n}','{sample.beluga_bam_dna_t}','{sample.beluga_bam_dna_n}','{sample.dna_vcf_g}','{sample.dna_vcf_s}','{sample.mutect2_somatic_vcf}','{sample.strelka2_germline_vcf}','{sample.strelka2_somatic_vcf}','{sample.vardict_germline_vcf}','{sample.vardict_somatic_vcf}','{sample.varscan2_germline_vcf}','{sample.varscan2_somatic_vcf}','{sample.cnvkit_vcf}','{sample.final_vcf}','{sample.final_dna_bam_t}','{sample.final_dna_bam_n}','{sample.dna_multiqc}','{sample.pcgr_report}','{sample.pcgr_maf}','{sample.pcgr_snvs_indels}','{sample.pcgr_cna_segments}','{sample.tp_ini}','{sample.run_proc_fastq_1_rna}','{sample.run_proc_fastq_2_rna}','{sample.beluga_fastq_1_rna}','{sample.beluga_fastq_2_rna}','{sample.rna_vcf}','{sample.final_rna_bam_variants}','{sample.rna_multiqc}','{sample.annofuse}','{sample.gridss}','{sample.rna_abundance}','{sample.big_wig_tracks_f}','{sample.big_wig_tracks_r}','{sample.rna_abundance_ini}','{sample.rna_variants_ini}')")
# def update_status_db(
# conn,
# sample,
# DNA_N_Transfered,
# DNA_T_Transfered,
# Alignment,
# Variants,
# Reports,
# Tumour_Pair_Complete,
# RNA_Transfrered,
# rna_abundance,
# RNA_Pseudoalign_expression,
# RNA_Alignment_Variant,
# RNA_Reports,
# RNA_Complete
# ):
# cur = conn.cursor()
# cur.execute(f"SELECT * FROM STATUS WHERE Sample='{sample}'")
# result = cur.fetchone()
# if result:
# cur.execute(f"DELETE FROM STATUS WHERE Sample='{sample}'")
# cur.execute(f"INSERT INTO STATUS (Sample,DNA_N_Transfered,DNA_T_Transfered,Alignment,Variants,Reports,Tumour_Pair_Complete,RNA_Transfrered,RNA_Abundance,RNA_Pseudoalign_expression,RNA_Alignment_Variant,RNA_Reports,RNA_Complete) VALUES ('{sample}','{DNA_N_Transfered}','{DNA_T_Transfered}','{Alignment}','{Variants}','{Reports}','{Tumour_Pair_Complete}','{RNA_Transfrered}','{rna_abundance}','{RNA_Pseudoalign_expression}','{RNA_Alignment_Variant}','{RNA_Reports}','{RNA_Complete}')")
# else:
# cur.execute(f"INSERT INTO STATUS (Sample,DNA_N_Transfered,DNA_T_Transfered,Alignment,Variants,Reports,Tumour_Pair_Complete,RNA_Transfrered,RNA_Abundance,RNA_Pseudoalign_expression,RNA_Alignment_Variant,RNA_Reports,RNA_Complete) VALUES ('{sample}','{DNA_N_Transfered}','{DNA_T_Transfered}','{Alignment}','{Variants}','{Reports}','{Tumour_Pair_Complete}','{RNA_Transfrered}','{rna_abundance}','{RNA_Pseudoalign_expression}','{RNA_Alignment_Variant}','{RNA_Reports}','{RNA_Complete}')")
def update_status_db(
conn,
patient,
dna_n_transferred,
dna_t_transferred,
dna_alignment,
dna_variant_call,
dna_report,
dna_pipeline_execution,
dna_delivered,
rna_transferred,
rna_pipeline_light_execution,
rna_light_delivered,
rna_alignment,
rna_variant_call,
rna_report,
rna_pipeline_execution,
rna_delivered
):
cur = conn.cursor()
cur.execute(f"SELECT * FROM status WHERE patient='{patient}'")
result = cur.fetchone()
if result:
cur.execute("""
UPDATE status
SET dna_n_transferred = :dna_n_transferred,
dna_t_transferred = :dna_t_transferred,
dna_alignment = :dna_alignment,
dna_variant_call = :dna_variant_call,
dna_report = :dna_report,
dna_pipeline_execution = :dna_pipeline_execution,
dna_delivered = :dna_delivered,
rna_transferred = :rna_transferred,
rna_pipeline_light_execution = :rna_pipeline_light_execution,
rna_light_delivered = :rna_light_delivered,
rna_alignment = :rna_alignment,
rna_variant_call = :rna_variant_call,
rna_report = :rna_report,
rna_pipeline_execution = :rna_pipeline_execution,
rna_delivered = :rna_delivered
WHERE
patient = :patient
;
""",
{
"dna_n_transferred": dna_n_transferred,