From f7f30893fefe3830dfeb735c8cd49de2cc18eb5a Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Fri, 16 Oct 2020 12:17:58 +0100 Subject: [PATCH 1/9] Clobber (and warn about) existing output directories instead of raising exception. --- python/clockwork/db.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/python/clockwork/db.py b/python/clockwork/db.py index 3a89ba1..c7f0d90 100644 --- a/python/clockwork/db.py +++ b/python/clockwork/db.py @@ -5,6 +5,7 @@ import re import sys import tempfile +import shutil from operator import itemgetter from clockwork import ( db_connection, @@ -558,7 +559,9 @@ def make_qc_jobs_tsv( output_dir = iso_dir.pipeline_dir( row["sequence_replicate_number"], "qc", pipeline_version ) - assert not os.path.exists(output_dir) + if os.path.exists(output_dir): + print("Warning:", output_dir, "already exists. Removing.", file=sys.stderr) + shutil.rmtree(output_dir) try: os.makedirs(output_dir) except: From d6e9ac80bb46ec806acd7db85ed5c3430c3f2438 Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Fri, 16 Oct 2020 12:19:07 +0100 Subject: [PATCH 2/9] pin openpyxl to 2.5.0, newer versions break tests --- python/setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/setup.py b/python/setup.py index e346b74..0eff21d 100644 --- a/python/setup.py +++ b/python/setup.py @@ -16,7 +16,7 @@ install_requires=[ "cluster_vcf_records >= 0.11.1", "python-dateutil >= 2.6.1", - "openpyxl >= 2.4.7", + "openpyxl == 2.5.0", "pyfastaq >= 3.14.0", "pymysql >= 0.7.11", "pysam >= 0.11.2.1", From dc64166eb89a112bd2cd0a8f7628ae88f74623ba Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Fri, 16 Oct 2020 14:59:08 +0100 Subject: [PATCH 3/9] QC: database migrations and function stubs for counting coverage at depth thresholds --- db_schema_patches/3_to_4.sql | 5 +++++ python/clockwork/db.py | 6 ++++++ python/clockwork/db_schema.py | 5 ++++- python/clockwork/samtools_qc.py | 13 +++++++++++++ 4 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 db_schema_patches/3_to_4.sql diff --git a/db_schema_patches/3_to_4.sql b/db_schema_patches/3_to_4.sql new file mode 100644 index 0000000..1d43755 --- /dev/null +++ b/db_schema_patches/3_to_4.sql @@ -0,0 +1,5 @@ +# Updates schema from version 3 to version 4 +ALTER TABLE QC ADD samtools_positions_with_depth_over_0 INT UNSIGNED, samtools_positions_with_depth_over_10 INT UNSIGNED, samtools_positions_with_depth_over_100 INT UNSIGNED; + +UPDATE Version SET version=4 WHERE version=3; + diff --git a/python/clockwork/db.py b/python/clockwork/db.py index 3a89ba1..cb96d72 100644 --- a/python/clockwork/db.py +++ b/python/clockwork/db.py @@ -1163,6 +1163,12 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root): samtools_stats = samtools_qc.SamtoolsQc.stats_from_report( os.path.join(qc_dir, "samtools_qc", "samtools_qc.stats") ) + depth_stats = samtools_qc.SamtoolsQc.depth_stats() + + new_row["samtools_positions_with_depth_over_0"] = depth_stats["over_0"] + new_row["samtools_positions_with_depth_over_10"] = depth_stats["over_10"] + new_row["samtools_positions_with_depth_over_100"] = depth_stats["over_100"] + fastqc_stats = fastqc.Fastqc.gather_all_stats(os.path.join(qc_dir, "fastqc")) assert len(fastqc_stats) == 2 new_row = {"seqrep_id": seqrep_id, "pipeline_version": pipeline_version} diff --git a/python/clockwork/db_schema.py b/python/clockwork/db_schema.py index 9407415..fe4a8bb 100644 --- a/python/clockwork/db_schema.py +++ b/python/clockwork/db_schema.py @@ -1,4 +1,4 @@ -version = 3 +version = 4 tables = { "Isolate": [ @@ -67,6 +67,9 @@ ("het_snp_positions", "integer unsigned"), ("het_snp_total_snps", "integer unsigned"), ("het_snp_het_calls", "integer unsigned"), + ("samtools_positions_with_depth_over_0", "integer unsigned"), + ("samtools_positions_with_depth_over_10", "integer unsigned"), + ("samtools_positions_with_depth_over_100", "integer unsigned"), ], "Read_counts": [ ("seqrep_id", "integer"), diff --git a/python/clockwork/samtools_qc.py b/python/clockwork/samtools_qc.py index 0c4bf19..da14425 100644 --- a/python/clockwork/samtools_qc.py +++ b/python/clockwork/samtools_qc.py @@ -21,6 +21,18 @@ def __init__(self, ref_fasta, reads1, reads2, outdir): def _map_reads(cls, ref_fasta, reads1, reads2, outfile): read_map.map_reads(ref_fasta, reads1, reads2, outfile, markdup=True) + @classmethod + def _make_depth_stats(cls, samfile): + """TODO either process samfile with pysam or samtools depth and + create report for number of positions covered at various thresholds + """ + pass + + @classmethod + def depth_stats(cls): + raise NotImplementedError + return {"over_0": 0, "over_10": 10, "over_100": 0} + @classmethod def _make_stats_and_plots(cls, samfile, ref_fasta, outprefix): stats_file = outprefix + ".stats" @@ -101,6 +113,7 @@ def run(self): outprefix = os.path.join(self.outdir, "samtools_qc") samfile = os.path.join(self.outdir, "tmp.sam") SamtoolsQc._map_reads(self.ref_fasta, self.reads1, self.reads2, samfile) + SamtoolsQc._make_depth_stats(samfile) SamtoolsQc._make_stats_and_plots(samfile, self.ref_fasta, outprefix) hsc = het_snp_caller.HetSnpCaller( samfile, self.ref_fasta, os.path.join(self.outdir, "het_snps") From 10059a344cca1874f453f9c0245758ab37f3db98 Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Fri, 16 Oct 2020 17:33:20 +0100 Subject: [PATCH 4/9] measure coverage for lower thresholds, implement samtools depth stats collection --- db_schema_patches/3_to_4.sql | 7 +++- python/clockwork/db.py | 13 ++++--- python/clockwork/db_schema.py | 11 +++--- python/clockwork/samtools_qc.py | 41 +++++++++++++++++----- python/clockwork/tests/nextflow_qc_test.py | 6 ++++ 5 files changed, 60 insertions(+), 18 deletions(-) diff --git a/db_schema_patches/3_to_4.sql b/db_schema_patches/3_to_4.sql index 1d43755..da9c4f1 100644 --- a/db_schema_patches/3_to_4.sql +++ b/db_schema_patches/3_to_4.sql @@ -1,5 +1,10 @@ # Updates schema from version 3 to version 4 -ALTER TABLE QC ADD samtools_positions_with_depth_over_0 INT UNSIGNED, samtools_positions_with_depth_over_10 INT UNSIGNED, samtools_positions_with_depth_over_100 INT UNSIGNED; +ALTER TABLE QC ADD samtools_positions_with_depth_of_0 INT UNSIGNED, + samtools_positions_with_depth_atleast_2 INT UNSIGNED, + samtools_positions_with_depth_atleast_5 INT UNSIGNED; + samtools_positions_with_depth_atleast_10 INT UNSIGNED, + samtools_positions_with_depth_atleast_20 INT UNSIGNED; + samtools_positions_with_depth_atleast_100 INT UNSIGNED, UPDATE Version SET version=4 WHERE version=3; diff --git a/python/clockwork/db.py b/python/clockwork/db.py index cb96d72..66622ec 100644 --- a/python/clockwork/db.py +++ b/python/clockwork/db.py @@ -1163,11 +1163,16 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root): samtools_stats = samtools_qc.SamtoolsQc.stats_from_report( os.path.join(qc_dir, "samtools_qc", "samtools_qc.stats") ) - depth_stats = samtools_qc.SamtoolsQc.depth_stats() + depth_stats = samtools_qc.SamtoolsQc.depth_stats( + os.path.join(qc_dir, "samtools_qc", "samtools_qc.depths") + ) - new_row["samtools_positions_with_depth_over_0"] = depth_stats["over_0"] - new_row["samtools_positions_with_depth_over_10"] = depth_stats["over_10"] - new_row["samtools_positions_with_depth_over_100"] = depth_stats["over_100"] + new_row["samtools_positions_with_depth_of_0"] = depth_stats["eq_0"] + new_row["samtools_positions_with_depth_atleast_2"] = depth_stats["atleast_2"] + new_row["samtools_positions_with_depth_atleast_5"] = depth_stats["atleast_5"] + new_row["samtools_positions_with_depth_atleast_10"] = depth_stats["atleast_10"] + new_row["samtools_positions_with_depth_atleast_20"] = depth_stats["atleast_20"] + new_row["samtools_positions_with_depth_atleast_100"] = depth_stats["atleast_100"] fastqc_stats = fastqc.Fastqc.gather_all_stats(os.path.join(qc_dir, "fastqc")) assert len(fastqc_stats) == 2 diff --git a/python/clockwork/db_schema.py b/python/clockwork/db_schema.py index fe4a8bb..827f7a5 100644 --- a/python/clockwork/db_schema.py +++ b/python/clockwork/db_schema.py @@ -67,10 +67,13 @@ ("het_snp_positions", "integer unsigned"), ("het_snp_total_snps", "integer unsigned"), ("het_snp_het_calls", "integer unsigned"), - ("samtools_positions_with_depth_over_0", "integer unsigned"), - ("samtools_positions_with_depth_over_10", "integer unsigned"), - ("samtools_positions_with_depth_over_100", "integer unsigned"), - ], + ("samtools_positions_with_depth_of_0", "integer unsigned"), + ("samtools_positions_with_depth_atleast_2", "integer unsigned"), + ("samtools_positions_with_depth_atleast_5", "integer unsigned"), + ("samtools_positions_with_depth_atleast_10", "integer unsigned"), + ("samtools_positions_with_depth_atleast_20", "integer unsigned"), + ("samtools_positions_with_depth_atleast_100", "integer unsigned"), + ], "Read_counts": [ ("seqrep_id", "integer"), ("original_total", "integer unsigned"), diff --git a/python/clockwork/samtools_qc.py b/python/clockwork/samtools_qc.py index da14425..626e90f 100644 --- a/python/clockwork/samtools_qc.py +++ b/python/clockwork/samtools_qc.py @@ -22,16 +22,39 @@ def _map_reads(cls, ref_fasta, reads1, reads2, outfile): read_map.map_reads(ref_fasta, reads1, reads2, outfile, markdup=True) @classmethod - def _make_depth_stats(cls, samfile): - """TODO either process samfile with pysam or samtools depth and - create report for number of positions covered at various thresholds - """ - pass + def _make_depth_stats(cls, samfile, outprefix): + depth_file = outprefix + ".depths" + cmd = " ".join(["samtools depth", "-a", samfile, ">", depth_file]) + utils.syscall(cmd) @classmethod - def depth_stats(cls): - raise NotImplementedError - return {"over_0": 0, "over_10": 10, "over_100": 0} + def depth_stats(cls, filename): + depths = { + "eq_0": 0, + "atleast_2": 0, + "atleast_5": 0, + "atleast_10": 0, + "atleast_20": 0, + "atleast_100": 0, + } + + with open(filename) as f: + for line in f: + _, _, depth = strip().split() + depth = int(depth) + if depth == 0: + depths["eq_0"] += 1 + if depth >= 2: + depths["atleast_2"] += 1 + if depth >= 5: + depths["atleast_5"] += 1 + if depth >= 10: + depths["atleast_10"] += 1 + if depth >= 20: + depths["atleast_20"] += 1 + if depth >= 100: + depths["atleast_100"] += 1 + return depths @classmethod def _make_stats_and_plots(cls, samfile, ref_fasta, outprefix): @@ -113,7 +136,7 @@ def run(self): outprefix = os.path.join(self.outdir, "samtools_qc") samfile = os.path.join(self.outdir, "tmp.sam") SamtoolsQc._map_reads(self.ref_fasta, self.reads1, self.reads2, samfile) - SamtoolsQc._make_depth_stats(samfile) + SamtoolsQc._make_depth_stats(samfile, outprefix) SamtoolsQc._make_stats_and_plots(samfile, self.ref_fasta, outprefix) hsc = het_snp_caller.HetSnpCaller( samfile, self.ref_fasta, os.path.join(self.outdir, "het_snps") diff --git a/python/clockwork/tests/nextflow_qc_test.py b/python/clockwork/tests/nextflow_qc_test.py index 343baca..c074e2d 100644 --- a/python/clockwork/tests/nextflow_qc_test.py +++ b/python/clockwork/tests/nextflow_qc_test.py @@ -254,6 +254,12 @@ def test_nextflow_qc_using_database(self): "het_snp_het_calls": 0, "het_snp_positions": 983, "het_snp_total_snps": 0, + "samtools_positions_with_depth_of_0": 0, #TODO + "samtools_positions_with_depth_atleast_2": 0, #TODO + "samtools_positions_with_depth_atleast_5": 0, #TODO + "samtools_positions_with_depth_atleast_10": 0, #TODO + "samtools_positions_with_depth_atleast_20": 0, #TODO + "samtools_positions_with_depth_atleast_100": 0, #TODO }, ] self.assertEqual(expected_qc_rows, got_qc_rows) From 4559160a347abc3010114bb6896671facd7087d8 Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Wed, 21 Oct 2020 16:30:56 +0100 Subject: [PATCH 5/9] Fixes for depth stats, additional test --- python/clockwork/db.py | 14 +++++++------- python/clockwork/samtools_qc.py | 2 +- python/clockwork/tests/samtools_qc_test.py | 19 +++++++++++++++++++ vagrant/Vagrantfile | 4 ++-- 4 files changed, 29 insertions(+), 10 deletions(-) diff --git a/python/clockwork/db.py b/python/clockwork/db.py index 66622ec..bc0daef 100644 --- a/python/clockwork/db.py +++ b/python/clockwork/db.py @@ -1167,13 +1167,6 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root): os.path.join(qc_dir, "samtools_qc", "samtools_qc.depths") ) - new_row["samtools_positions_with_depth_of_0"] = depth_stats["eq_0"] - new_row["samtools_positions_with_depth_atleast_2"] = depth_stats["atleast_2"] - new_row["samtools_positions_with_depth_atleast_5"] = depth_stats["atleast_5"] - new_row["samtools_positions_with_depth_atleast_10"] = depth_stats["atleast_10"] - new_row["samtools_positions_with_depth_atleast_20"] = depth_stats["atleast_20"] - new_row["samtools_positions_with_depth_atleast_100"] = depth_stats["atleast_100"] - fastqc_stats = fastqc.Fastqc.gather_all_stats(os.path.join(qc_dir, "fastqc")) assert len(fastqc_stats) == 2 new_row = {"seqrep_id": seqrep_id, "pipeline_version": pipeline_version} @@ -1207,6 +1200,13 @@ def _update_qc_stats(self, seqrep_id, pipeline_version, pipeline_root): new_row["het_snp_positions"] = het_stats["Positions_used"] new_row["het_snp_total_snps"] = het_stats["Total_SNPs"] new_row["het_snp_het_calls"] = het_stats["Het_SNPs"] + new_row["samtools_positions_with_depth_of_0"] = depth_stats["eq_0"] + new_row["samtools_positions_with_depth_atleast_2"] = depth_stats["atleast_2"] + new_row["samtools_positions_with_depth_atleast_5"] = depth_stats["atleast_5"] + new_row["samtools_positions_with_depth_atleast_10"] = depth_stats["atleast_10"] + new_row["samtools_positions_with_depth_atleast_20"] = depth_stats["atleast_20"] + new_row["samtools_positions_with_depth_atleast_100"] = depth_stats["atleast_100"] + self.add_row_to_table("QC", new_row) diff --git a/python/clockwork/samtools_qc.py b/python/clockwork/samtools_qc.py index 626e90f..71f2ccc 100644 --- a/python/clockwork/samtools_qc.py +++ b/python/clockwork/samtools_qc.py @@ -40,7 +40,7 @@ def depth_stats(cls, filename): with open(filename) as f: for line in f: - _, _, depth = strip().split() + _, _, depth = line.rstrip().split("\t") depth = int(depth) if depth == 0: depths["eq_0"] += 1 diff --git a/python/clockwork/tests/samtools_qc_test.py b/python/clockwork/tests/samtools_qc_test.py index 50827e5..68a0cc9 100644 --- a/python/clockwork/tests/samtools_qc_test.py +++ b/python/clockwork/tests/samtools_qc_test.py @@ -55,6 +55,25 @@ def test_make_stats_and_plots(self): self.assertEqual(expected_files, got_files) shutil.rmtree(tmp_dir) + def test_make_depth_stats(self): + """test _make_depth_stats""" + #ref_fasta = os.path.join(data_dir, "ref.fa") + sam_file = os.path.join(data_dir, "sam") + tmp_dir = "tmp.samtools_qc.make_depth_stats" + os.mkdir(tmp_dir) + outprefix = os.path.join(tmp_dir, "test") + samtools_qc.SamtoolsQc._make_depth_stats(sam_file, outprefix) + + expected_files = [ + "test.depths", + ] + expected_files.sort() + + got_files = sorted(list(os.listdir(tmp_dir))) + self.assertEqual(expected_files, got_files) + shutil.rmtree(tmp_dir) + + def test_stats_from_report(self): """test stats_from_report""" stats_file = os.path.join(data_dir, "stats_from_report.txt") diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile index b81afd8..e7c0c23 100644 --- a/vagrant/Vagrantfile +++ b/vagrant/Vagrantfile @@ -7,8 +7,8 @@ Vagrant.configure(2) do |config| config.disksize.size = '40GB' # Edit these if you want to mount whatever dirs... - config.vm.synced_folder "/Users/mhunt/git/", "/home/vagrant/git" - config.vm.synced_folder "/Users/mhunt/vm_share/", "/home/vagrant/vm_share" +# config.vm.synced_folder "/Users/mhunt/git/", "/home/vagrant/git" +# config.vm.synced_folder "/Users/mhunt/vm_share/", "/home/vagrant/vm_share" # Provider-specific configuration so you can fine-tune various # backing providers for Vagrant. These expose provider-specific options. From 450193fb15cc3eca80a270ffe8399e96350d3bc1 Mon Sep 17 00:00:00 2001 From: Jeff Knaggs Date: Thu, 12 Nov 2020 10:31:16 +0000 Subject: [PATCH 6/9] fix sql syntax error from copy+pasting --- db_schema_patches/3_to_4.sql | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/db_schema_patches/3_to_4.sql b/db_schema_patches/3_to_4.sql index da9c4f1..db2a69b 100644 --- a/db_schema_patches/3_to_4.sql +++ b/db_schema_patches/3_to_4.sql @@ -1,10 +1,10 @@ # Updates schema from version 3 to version 4 ALTER TABLE QC ADD samtools_positions_with_depth_of_0 INT UNSIGNED, samtools_positions_with_depth_atleast_2 INT UNSIGNED, - samtools_positions_with_depth_atleast_5 INT UNSIGNED; + samtools_positions_with_depth_atleast_5 INT UNSIGNED, samtools_positions_with_depth_atleast_10 INT UNSIGNED, - samtools_positions_with_depth_atleast_20 INT UNSIGNED; - samtools_positions_with_depth_atleast_100 INT UNSIGNED, + samtools_positions_with_depth_atleast_20 INT UNSIGNED, + samtools_positions_with_depth_atleast_100 INT UNSIGNED; UPDATE Version SET version=4 WHERE version=3; From a11583d0049f9866e812af31806e8e11efc7c4dc Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 13 Nov 2020 11:37:23 +0000 Subject: [PATCH 7/9] Fix samtools_qc tests --- .../{sam => depth_stats.sorted.sam} | 86 ++++++++++--------- python/clockwork/tests/samtools_qc_test.py | 11 ++- 2 files changed, 51 insertions(+), 46 deletions(-) rename python/clockwork/tests/data/samtools_qc/{sam => depth_stats.sorted.sam} (99%) diff --git a/python/clockwork/tests/data/samtools_qc/sam b/python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam similarity index 99% rename from python/clockwork/tests/data/samtools_qc/sam rename to python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam index ed3742a..f8e23f6 100644 --- a/python/clockwork/tests/data/samtools_qc/sam +++ b/python/clockwork/tests/data/samtools_qc/depth_stats.sorted.sam @@ -1,54 +1,56 @@ +@HD VN:1.6 SO:coordinate @SQ SN:1 LN:2000 @PG ID:bwa PN:bwa VN:0.7.12-r1039 CL:bwa mem samtools_qc.ref.fa samtools_qc.reads.1.fq samtools_qc.reads.2.fq -1-52 83 1 899 60 75M = 774 -200 CTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCATGTACAAGTAAC @D5DHDJHCEHH9IJ@IJJI3GGJJJIJIJDJJIH1?H8IGJJJ):G:JHFFJJ@JFJJJ8JFHH.HFI=J>JIBJJIIIJE?:I0)CEIIHJIH1)>BIFGJJJIEIGJFIE?J;IJGE4JJJGIHIJGII(IJIJJDDIG:=HH@CD NM:i:1 MD:Z:58A16 AS:i:70 XS:i:0 -1-46 147 1 1549 60 75M = 1421 -203 CACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTTCG CDBDEFH;BHHBGJJJJDJDJJIGB?JH0GIJJIIGG*GJ@JFI?I0HFJIHIIJJ?GJ@I0FHFH;FFFFFCCB NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-44 99 1 735 60 75M = 864 204 TATGTGGACGTTGTATAGGGATATTACGTTACGCGTTAACCGATACATACTGGTTTCTCTCCAGTGGAGCTCTTG CBCFFF@D?H)>HJ;IIJIJJGIIHAHFI;JDJ?CDJEJGF>GIJEICHI*FJJ?IGIIHCJJ7';BEFD?EFGDGDEIE.HHE NM:i:1 MD:Z:34C40 AS:i:70 XS:i:0 -1-42 147 1 1473 60 75M = 1355 -193 ATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGTCACATCTAGGAGTCC C(JFCF@(EF.CJD5JHH8HJDGJD3F@8GHHIDHECIJDIJBCJIJ1IJJJJHIEJJIIJG+F8HFF:D:D#C@ NM:i:1 MD:Z:72G2 AS:i:72 XS:i:0 -1-40 83 1 1547 60 75M = 1434 -188 CGCACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTT >EDGJJF=GD77J7EDGJDIJJHJHJDGGIIGII@JFF8IG)IIII*J>HAJIII@IIJJ+CFHFHHFF:FFB?B NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-40 163 1 1434 60 75M = 1547 188 CTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTA @@CFFFAFH?DHG?8JIAJIEE+HFD NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-38 99 1 680 60 75M = 801 196 CCCACATTTGACGGTACGCTACCGCAAAGGTATGTGTTAATGGAACAGACTTGCCTATGTGGACGTTGTATAGGG @CCFFFFF?HHHHAIIEJGAJJJHFIH>EJGIIGGGD/JI?JIJIID:JJIBGIIJ@IBD?IGI-;, NM:i:1 MD:Z:74A0 AS:i:74 XS:i:0 +1-16 163 1 190 60 75M = 311 196 CTCTCGTCATAAAACCTTTCTACTATGTGTTCCGCAACAATCAACAACTACAATGGCGCGTCGTGAATAACGCGA <;@FFAF+DH:HHFHH?IJJ?CJJIB;J8IDJEGHDC@H4BCDFJGBDD NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-34 83 1 396 60 75M = 267 -204 TTCTCAGGACGCCCAACTATTCTTTCCAATCCTACATCTGTTTCTTGCGTCGTAGCGGGACCCTCCACTGTTACT DECJJBHHIJDE?H;FDGEJJGBJIDJ9JIJII>ADGJGGJIGJGIJ9HHIIJJJ3IIIIHEJ>DIB? NM:i:0 MD:Z:75 AS:i:75 XS:i:0 1-32 99 1 248 60 75M = 372 199 CGTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCGCCT C?CFFFF=FHH>HFIIIEJHJJJEHBHCIIIFIDAHJIH9?.AJDIDJJADHJ;ICC@EJHJ;D>BHJIB4'B@F NM:i:1 MD:Z:71C3 AS:i:71 XS:i:0 +1-22 147 1 249 60 75M = 127 -197 GTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTA CBI,DGJD)J:GHJE@HGJFIJ*IJEGFE@HEJCCJAF9EJ9HHIIJJJ3IIIIHEJ>DIB? NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-16 83 1 311 60 75M = 190 -196 AGCCAGTCCCCTACGTCGCATATCCTGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTT EDFEDDDHHAGIF9JHFBCI-J=H0IGGIIF4(G@IIE=JIIJJIIHJCFIIJIBJJJ-JJJHFHHHFFFFFC@@ NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-4 99 1 336 60 75M = 458 197 TGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCA B@CFFFDAHGHFHIIHDE.DJC=8JJ@JHGI?HJJJJIBIGEIFJGIJIJEJIGJJGJCHJJFJAFHCFH66FDFCCC NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-30 163 1 1241 60 75M = 1359 193 GAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCCCAGAA 7C1FDFFFGFHHHHJIJEGIHFAJIGHIGJHHIHC):JGHADGJGGJIGJGIIGIJIGHFJHIGJHEHIJ)EJIF-IE.E?BFIF:FAE3ECD(CCJ5FDHFDI?D@F NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-10 99 1 662 60 75M = 785 198 GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA CCCDFFFDFHHDDJH+IJJEJIG9HJJCIJIHIEIGIEIJCC?GJHGHBDI5J(=BJJEFHJJC=FGHICG6DHD NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-38 99 1 680 60 75M = 801 196 CCCACATTTGACGGTACGCTACCGCAAAGGTATGTGTTAATGGAACAGACTTGCCTATGTGGACGTTGTATAGGG @CCFFFFF?HHHHAIIEJGAJJJHFIH>EJGIIGGGHJ;IIJIJJGIIHDAIF@FFIFJEEJFIIJ?BHGIDG;;EGHIEJ*E=G9HG@?JIDHIHBJII3ID?IIHDHH#FFDFFC@@ NM:i:1 MD:Z:66C8 AS:i:70 XS:i:0 +1-38 147 1 801 60 75M = 680 -196 GAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGCATAATCGAAGAGGGTCCTCCCATC 9HD?EDEEE;:IDJHGFJIIDH*FEI;HF?IJC)I*JGGIIDEJHJJJHDIJ8HGJFJJIJIFDCDHAFDFFC@; NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-44 147 1 864 60 75M = 735 -204 GGTCCTCCCATCTCCTGTGATGCATGGTGTGCTTTCTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGA BEF+AHFI;JDJ?CDJEJGF>GIJEICHI*FJJ?IGIIHCJDHH@FIDJGI;HDGG;J+FIFC? NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-52 83 1 899 60 75M = 774 -200 CTGGGATGAATGCGCCGCAAGTAGCAGGTCCCGGCGTGGATACCTGATAGATGGTGACTAGCATGTACAAGTAAC @D5DHDJHCEHH9IJ@IJJI3GGJJJIJIJDJJIH1?H8IGJJJ):G:JHFFJJ@JFJJJ8JFHH.HFD/JI?JIJIID:JJIBGIIJ@IBD?IGI-;, NM:i:1 MD:Z:74A0 AS:i:74 XS:i:0 -1-22 147 1 249 60 75M = 127 -197 GTCGTGAATAACGCGACGGCTGAGACGAACGGCGCGTGAATGAAGCGCTTAAACAGCTCAGGAGCCAGTCCCCTA CBI,DGJD)J:GHJE@HGJFIJ*IJEGFE@HEJCCJAF9E(CCJ5FDHFDI?D@F NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-18 83 1 1458 60 75M = 1333 -200 GAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGT D>GB;)HE9EA.?FIJJGF.DDEEJI)JGE(B6JIIJCG3GJECIGIJF?JJHJGAGJJEGFHHHGDFFFFD@CB NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-18 163 1 1333 60 75M = 1458 200 GTCGTTGTTCCCGATGAAGACGTCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATTCCGT C@CFFFFFHH?HFIJGHGIII+ICJIF8GHIDJGJGJHEIGGII'H(GJGIGGGID8JDGEJIDDGIB89(DDE@ NM:i:1 MD:Z:70A4 AS:i:70 XS:i:0 -1-16 83 1 311 60 75M = 190 -196 AGCCAGTCCCCTACGTCGCATATCCTGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTT EDFEDDDHHAGIF9JHFBCI-J=H0IGGIIF4(G@IIE=JIIJJIIHJCFIIJIBJJJ-JJJHFHHHFFFFFC@@ NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-16 163 1 190 60 75M = 311 196 CTCTCGTCATAAAACCTTTCTACTATGTGTTCCGCAACAATCAACAACTACAATGGCGCGTCGTGAATAACGCGA <;@FFAF+DH:HHFHH?IJJ?CJJIHFFFFFB@: NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-26 147 1 1156 60 75M = 1031 -200 AGTGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGATACTTATGGCGCAACGGCCACGCCCACTTT +CEDEFDJFJIAD=DJJBJDFFIDDDJJHJEHI(?I0GBGIIJI@?JJJHH:JIIIJJI)EGGAHHGFFFF+BCB NM:i:0 MD:Z:75 AS:i:75 XS:i:0 1-12 163 1 1158 60 75M = 1286 203 TGACTAACGCCGGGAATTCCTCGATATATAGTTTGATAGCTGATACTTATGGCGCAACGGCCACGCCCACTTTGG ??C=DFFBDHHHFHJ?IFEJIGGJJJJJJIJBIIEJCJ?GI(?JGJJ2AAHIG9HF4ED.J>BHIEF4DHD)FEH NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-10 99 1 662 60 75M = 785 198 GACATCTTTGTGAACCGACCCACATTTGACGGTACGCTACCGCAACGGTATGTGTTAATGGAACAGACTTGCTTA CCCDFFFDFHHDDJH+IJJEJIG9HJJCIJIHIEIGIEIJCC?GJHGHBDI5J(=BJJEFHJJC=FGHICG6DHD NM:i:0 MD:Z:75 AS:i:75 XS:i:0 -1-10 147 1 785 60 75M = 662 -198 TGGTTTCTCTCCAGTGGAGGTCTTGGTTGCCTCTAGTTTCTACGATATACTCATGGTAGTGTAACGAATAATCGA BEIJ>DAIF@FFIFJEEJFIIJ?BHGIDG;;EGHIEJ*E=G9HG@?JIDHIHBJII3ID?IIHDHH#FFDFFC@@ NM:i:1 MD:Z:66C8 AS:i:70 XS:i:0 -1-8 99 1 463 60 75M = 586 198 TTGTTACTTATTAGGTTCTCGTTATGTCTCATAATCTCAGTGCTGGTGTGATAAGCAAACCACCCTACTGGCACG CBCFFFFF?HHHHJ(?JJFJHGH8IHDFFJJDHH:JGIHHG5BJ'B)J5DIGHJGFHDJFHFCHEJCFFCJE> NM:i:1 MD:Z:34A40 AS:i:70 XS:i:0 -1-4 99 1 336 60 75M = 458 197 TGGCCACTGGAGGTGAAGCGAATGGTATCGATACGTAGGAGGTGTGCCTTCGTAGGCTGTTTCTCAGGACGCCCA B@CFFFDAHGHFHICECECECB?IGD;5GHGD)IJDIJJH70IIJJEJD>GIIJIIJIIFIJGJJ+GGJJJIEJF3HDHFFFFDC?C NM:i:2 MD:Z:20A8G45 AS:i:65 XS:i:0 +1-48 99 1 1237 60 75M = 1370 208 TGGAGAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCAC B@CDFFFF3HHB)JBIJE7EGEJCJIJJGFJJJIDGHI.IDJIDJJJIJJJE1IGJBGIGIHEEDGIIDICEH(H NM:i:1 MD:Z:73C1 AS:i:73 XS:i:0 +1-30 163 1 1241 60 75M = 1359 193 GAGTTAAGGAATTATCGTCATAGACACTTCGGGTTGAGAGATGGCGACGGTCAGTGCATGAGGCCGTCCCCAGAA 7C1FDFFFGFHHHHJIJEGIHFAJIGHIGJHHIHC):JGHHFFFFFB@: NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-18 163 1 1333 60 75M = 1458 200 GTCGTTGTTCCCGATGAAGACGTCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATTCCGT C@CFFFFFHH?HFIJGHGIII+ICJIF8GHIDJGJGJHEIGGII'H(GJGIGGGID8JDGEJIDDGIB89(DDE@ NM:i:1 MD:Z:70A4 AS:i:70 XS:i:0 +1-42 99 1 1355 60 75M = 1473 193 TCTACTGATATGCTAGCAGAGCCAGTCTTAAAGCATAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAG B?C=FD?AHHHJ7';BEFD?EFGDGDEIE.HHE NM:i:1 MD:Z:34C40 AS:i:70 XS:i:0 1-2 163 1 1358 60 75M = 1483 200 ACTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGCACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAG +@@FBDDFDHHHG<,IDH;#IGG@IJHFFIIFJJJ*:'HEJJJF.JJBCJ@ICHJJGFBJ7I7JGJJHID(HDG< NM:i:1 MD:Z:37A37 AS:i:70 XS:i:0 +1-30 83 1 1359 60 75M = 1241 -193 CTGATATGCTAGCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGG HC5JE@CDDJ>IHDE.DJC=8JJ@JHGI?HJJJJIBIGEIFJGIJIJEJIGJJGJCHJJFJAFHCFH66FDFCCC NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-48 147 1 1370 60 75M = 1237 -208 GCAGAGCCAGTCTTAAAGCCTAGCGAACTTAATACCGTAGCTCAGAATTATGGAGAGCAGCAGGCTTCCATAGCA D(DFAFIJEI@EIJ@5FI@JC>I=J>JIBJJIIIJE?:I0)CEIIHJIH1)>BIFGJJJIEIGJFIE?J;IJGE4JJJGIHIJGII(IJIJJDDIG:=HH@CD NM:i:1 MD:Z:58A16 AS:i:70 XS:i:0 +1-40 163 1 1434 60 75M = 1547 188 CTTCCATAGCACAGGTTGACGGAGGAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTA @@CFFFAFH?DHG?8JIAJIEE+HFD NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-18 83 1 1458 60 75M = 1333 -200 GAGTTTTGCTTGGATATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGT D>GB;)HE9EA.?FIJJGF.DDEEJI)JGE(B6JIIJCG3GJECIGIJF?JJHJGAGJJEGFHHHGDFFFFD@CB NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-42 147 1 1473 60 75M = 1355 -193 ATCGGAAGGGTTCTGTAGTGAATGCACTACACGGTACTGGTACGTGGCAACTTAGGTCGTCACATCTAGGAGTCC C(JFCF@(EF.CJD5JHH8HJDGJD3F@8GHHIDHECIJDIJBCJIJ1IJJJJHIEJJIIJG+F8HFF:D:D#C@ NM:i:1 MD:Z:72G2 AS:i:72 XS:i:0 +1-2 83 1 1483 60 75M = 1358 -200 TTCTGTAGTGAATGCACTACCCGGTACTGATACGTGGCAACTTAGGTCGTCACATCTAGGAGGCCGCACCCTAGG @>CECECECB?IGD;5GHGD)IJDIJJH70IIJJEJD>GIIJIIJIIFIJGJJ+GGJJJIEJF3HDHFFFFDC?C NM:i:2 MD:Z:20A8G45 AS:i:65 XS:i:0 +1-40 83 1 1547 60 75M = 1434 -188 CGCACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTT >EDGJJF=GD77J7EDGJDIJJHJHJDGGIIGII@JFF8IG)IIII*J>HAJIII@IIJJ+CFHFHHFF:FFB?B NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-46 147 1 1549 60 75M = 1421 -203 CACCCTAGGTCAAGTTTTACGATTGCCCTAACGCCGCGGAGCGCGACCCGAAAAGCTATGGTCTGTAACTTTTCG CDBDEFH;BHHBGJJJJDJDJJIGB?JH0GIJJIIGG*GJ@JFI?I0HFJIHIIJJ?GJ@I0FHFH;FFFFFCCB NM:i:0 MD:Z:75 AS:i:75 XS:i:0 +1-50 163 1 1737 60 75M = 1861 199 TCTCTTACCGTGGCTGGGTCCGGCGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAA C1@FF?FFHHH)HI+JCHJH@JJ:IJJIEI9DIGCBHJJGJHGI=GGDJGG,DG=JD,GGIGIDJJFDIDIFICC NM:i:2 MD:Z:11T45A17 AS:i:65 XS:i:0 +1-6 163 1 1760 60 75M = 1880 195 CGGCTGTGGGATTGCGAGAGTGTCCGGCACCACCCATGTACACTTTCGGGAACACTCATTCGAAGAGGTTCTGCA ?1CFFFF@8FDFHGIIJICFIFJIJJ:JBIJGIJ)*II?I(EJJIGFGFHDJFHFCHEJCFFCJE> NM:i:1 MD:Z:34A40 AS:i:70 XS:i:0 +1-50 83 1 1861 60 75M = 1737 -199 GGGCGGCAATGCTGAGGCCCTCTGTTCAATGAAACCCGTACTATATCTTATGATGACAATGAAATAGTCCTGTTT DEC)H8FJDJGA)EH5&JJ7ABJ8IJH&JFIGJFGJJIFAJDIJHJCJIJE@I Date: Fri, 13 Nov 2020 13:47:22 +0000 Subject: [PATCH 8/9] Fix db_test to have new QC depth stats --- .../3/qc/1.0.0/samtools_qc/samtools_qc.depths | 10 ++++++++++ python/clockwork/tests/db_test.py | 6 ++++++ 2 files changed, 16 insertions(+) create mode 100644 python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths diff --git a/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths b/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths new file mode 100644 index 0000000..befaed6 --- /dev/null +++ b/python/clockwork/tests/data/db/update_qc_stats_pipeline_root/00/00/00/01/2/Pipelines/3/qc/1.0.0/samtools_qc/samtools_qc.depths @@ -0,0 +1,10 @@ +1 1 0 +1 2 1 +1 3 2 +1 4 3 +1 5 5 +1 6 7 +1 7 8 +1 8 0 +1 9 11 +1 10 110 diff --git a/python/clockwork/tests/db_test.py b/python/clockwork/tests/db_test.py index ab5faa7..0cc1e9c 100644 --- a/python/clockwork/tests/db_test.py +++ b/python/clockwork/tests/db_test.py @@ -2031,6 +2031,12 @@ def test_update_qc_stats(self): "samtools_inward_oriented_pairs": 27, "samtools_outward_oriented_pairs": 0, "samtools_pairs_with_other_orientation": 0, + "samtools_positions_with_depth_of_0": 2, + "samtools_positions_with_depth_atleast_2": 7, + "samtools_positions_with_depth_atleast_5": 5, + "samtools_positions_with_depth_atleast_10": 2, + "samtools_positions_with_depth_atleast_20": 1, + "samtools_positions_with_depth_atleast_100": 1, "samtools_raw_total_sequences": 54, "samtools_reads_duplicated": 2, "samtools_reads_mapped": 54, From 8df95ae0158b3dbaea638077b3552d51ee6888b6 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 13 Nov 2020 15:21:26 +0000 Subject: [PATCH 9/9] Get nextflow_qc tests to pass --- .../00/00/01/1/Reads/reads.contam.43.1.fq.gz | Bin 273 -> 273 bytes .../00/00/01/1/Reads/reads.contam.43.2.fq.gz | Bin 271 -> 271 bytes .../00/01/1/Reads/reads.original.43.1.fq.gz | Bin 1734 -> 1734 bytes .../00/01/1/Reads/reads.original.43.2.fq.gz | Bin 1742 -> 1742 bytes .../01/1/Reads/reads.remove_contam.43.1.fq.gz | Bin 1522 -> 1522 bytes .../01/1/Reads/reads.remove_contam.43.2.fq.gz | Bin 1521 -> 1521 bytes .../00/00/02/2/Reads/reads.contam.45.1.fq.gz | Bin 270 -> 270 bytes .../00/00/02/2/Reads/reads.contam.45.2.fq.gz | Bin 271 -> 271 bytes .../00/02/2/Reads/reads.original.45.1.fq.gz | Bin 1747 -> 1747 bytes .../00/02/2/Reads/reads.original.45.2.fq.gz | Bin 1738 -> 1738 bytes .../02/2/Reads/reads.remove_contam.45.1.fq.gz | Bin 1531 -> 1531 bytes .../02/2/Reads/reads.remove_contam.45.2.fq.gz | Bin 1530 -> 1530 bytes .../00/00/03/3/Reads/reads.contam.47.1.fq.gz | Bin 306 -> 306 bytes .../00/00/03/3/Reads/reads.contam.47.2.fq.gz | Bin 304 -> 304 bytes .../00/03/3/Reads/reads.original.47.1.fq.gz | Bin 1758 -> 1758 bytes .../00/03/3/Reads/reads.original.47.2.fq.gz | Bin 1757 -> 1757 bytes .../03/3/Reads/reads.remove_contam.47.1.fq.gz | Bin 27 -> 27 bytes .../03/3/Reads/reads.remove_contam.47.2.fq.gz | Bin 28 -> 28 bytes .../00/00/04/4/Reads/reads.contam.49.1.fq.gz | Bin 279 -> 279 bytes .../00/00/04/4/Reads/reads.contam.49.2.fq.gz | Bin 279 -> 279 bytes .../00/04/4/Reads/reads.original.49.1.fq.gz | Bin 1814 -> 1814 bytes .../00/04/4/Reads/reads.original.49.2.fq.gz | Bin 1803 -> 1803 bytes .../04/4/Reads/reads.remove_contam.49.1.fq.gz | Bin 1591 -> 1591 bytes .../04/4/Reads/reads.remove_contam.49.2.fq.gz | Bin 1585 -> 1585 bytes .../data/nextflow_qc/Reads/reads.1.1.fq.gz | Bin 1734 -> 1734 bytes .../data/nextflow_qc/Reads/reads.1.2.fq.gz | Bin 1742 -> 1742 bytes .../tests/data/nextflow_qc/mysql.dump | 70 ++++++++++-------- python/clockwork/tests/nextflow_qc_test.py | 26 ++++--- 28 files changed, 54 insertions(+), 42 deletions(-) diff 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-1,8 +1,8 @@ --- MySQL dump 10.13 Distrib 5.7.19, for Linux (x86_64) +-- MySQL dump 10.13 Distrib 5.7.32, for Linux (x86_64) -- -- Host: localhost Database: test_db -- ------------------------------------------------------ --- Server version 5.7.19-0ubuntu0.17.04.1 +-- Server version 5.7.32-0ubuntu0.18.04.1 /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -66,7 +66,7 @@ CREATE TABLE `Pipeline` ( LOCK TABLES `Pipeline` WRITE; /*!40000 ALTER TABLE `Pipeline` DISABLE KEYS */; -INSERT INTO `Pipeline` VALUES (1,1,NULL,'0.0.1','remove_contam',1,1),(2,2,NULL,'0.0.1','remove_contam',1,1),(3,3,NULL,'0.0.1','remove_contam',1,1),(4,4,NULL,'0.0.1','remove_contam',1,1); +INSERT INTO `Pipeline` VALUES (1,1,NULL,'0.9.0','remove_contam',1,1),(2,2,NULL,'0.9.0','remove_contam',1,1),(3,3,NULL,'0.9.0','remove_contam',1,1),(4,4,NULL,'0.9.0','remove_contam',1,1); /*!40000 ALTER TABLE `Pipeline` ENABLE KEYS */; UNLOCK TABLES; @@ -84,8 +84,8 @@ CREATE TABLE `QC` ( `fastqc1_adapter_content` text, `fastqc1_basic_statistics` text, `fastqc1_kmer_content` text, - `fastqc1_max_sequence_length` int(11) DEFAULT NULL, - `fastqc1_min_sequence_length` int(11) DEFAULT NULL, + `fastqc1_max_sequence_length` int(10) unsigned DEFAULT NULL, + `fastqc1_min_sequence_length` int(10) unsigned DEFAULT NULL, `fastqc1_overrepresented_sequences` text, `fastqc1_per_base_n_content` text, `fastqc1_per_base_sequence_content` text, @@ -94,14 +94,14 @@ CREATE TABLE `QC` ( `fastqc1_per_sequence_quality_scores` text, `fastqc1_sequence_duplication_levels` text, `fastqc1_sequence_length_distribution` text, - `fastqc1_sequences_flagged_as_poor_quality` int(11) DEFAULT NULL, - `fastqc1_total_sequences` int(11) DEFAULT NULL, + `fastqc1_sequences_flagged_as_poor_quality` int(10) unsigned DEFAULT NULL, + `fastqc1_total_sequences` int(10) unsigned DEFAULT NULL, `fastqc2_gc` float DEFAULT NULL, `fastqc2_adapter_content` text, `fastqc2_basic_statistics` text, `fastqc2_kmer_content` text, - `fastqc2_max_sequence_length` int(11) DEFAULT NULL, - `fastqc2_min_sequence_length` int(11) DEFAULT NULL, + `fastqc2_max_sequence_length` int(10) unsigned DEFAULT NULL, + `fastqc2_min_sequence_length` int(10) unsigned DEFAULT NULL, `fastqc2_overrepresented_sequences` text, `fastqc2_per_base_n_content` text, `fastqc2_per_base_sequence_content` text, @@ -110,23 +110,29 @@ CREATE TABLE `QC` ( `fastqc2_per_sequence_quality_scores` text, `fastqc2_sequence_duplication_levels` text, `fastqc2_sequence_length_distribution` text, - `fastqc2_sequences_flagged_as_poor_quality` int(11) DEFAULT NULL, - `fastqc2_total_sequences` int(11) DEFAULT NULL, - `samtools_raw_total_sequences` int(11) DEFAULT NULL, - `samtools_reads_mapped` int(11) DEFAULT NULL, - `samtools_reads_duplicated` int(11) DEFAULT NULL, - `samtools_bases_mapped_cigar` int(11) DEFAULT NULL, - `samtools_bases_trimmed` int(11) DEFAULT NULL, + `fastqc2_sequences_flagged_as_poor_quality` int(10) unsigned DEFAULT NULL, + `fastqc2_total_sequences` int(10) unsigned DEFAULT NULL, + `samtools_raw_total_sequences` int(10) unsigned DEFAULT NULL, + `samtools_reads_mapped` int(10) unsigned DEFAULT NULL, + `samtools_reads_duplicated` int(10) unsigned DEFAULT NULL, + `samtools_bases_mapped_cigar` bigint(20) unsigned DEFAULT NULL, + `samtools_bases_trimmed` bigint(20) unsigned DEFAULT NULL, `samtools_error_rate` float DEFAULT NULL, `samtools_average_quality` float DEFAULT NULL, `samtools_insert_size_average` float DEFAULT NULL, `samtools_insert_size_standard_deviation` float DEFAULT NULL, - `samtools_inward_oriented_pairs` int(11) DEFAULT NULL, - `samtools_outward_oriented_pairs` int(11) DEFAULT NULL, - `samtools_pairs_with_other_orientation` int(11) DEFAULT NULL, - `het_snp_positions` int(11) DEFAULT NULL, - `het_snp_total_snps` int(11) DEFAULT NULL, - `het_snp_het_calls` int(11) DEFAULT NULL + `samtools_inward_oriented_pairs` int(10) unsigned DEFAULT NULL, + `samtools_outward_oriented_pairs` int(10) unsigned DEFAULT NULL, + `samtools_pairs_with_other_orientation` int(10) unsigned DEFAULT NULL, + `het_snp_positions` int(10) unsigned DEFAULT NULL, + `het_snp_total_snps` int(10) unsigned DEFAULT NULL, + `het_snp_het_calls` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_of_0` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_atleast_2` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_atleast_5` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_atleast_10` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_atleast_20` int(10) unsigned DEFAULT NULL, + `samtools_positions_with_depth_atleast_100` int(10) unsigned DEFAULT NULL ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; @@ -148,11 +154,11 @@ DROP TABLE IF EXISTS `Read_counts`; /*!40101 SET character_set_client = utf8 */; CREATE TABLE `Read_counts` ( `seqrep_id` int(11) DEFAULT NULL, - `original_total` int(11) DEFAULT NULL, - `contamination` int(11) DEFAULT NULL, - `not_contamination` int(11) DEFAULT NULL, - `unmapped` int(11) DEFAULT NULL, - `total_after_remove_contam` int(11) DEFAULT NULL + `original_total` int(10) unsigned DEFAULT NULL, + `contamination` int(10) unsigned DEFAULT NULL, + `not_contamination` int(10) unsigned DEFAULT NULL, + `unmapped` int(10) unsigned DEFAULT NULL, + `total_after_remove_contam` int(10) unsigned DEFAULT NULL ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; @@ -162,7 +168,7 @@ CREATE TABLE `Read_counts` ( LOCK TABLES `Read_counts` WRITE; /*!40000 ALTER TABLE `Read_counts` DISABLE KEYS */; -INSERT INTO `Read_counts` VALUES (1,156,12,132,12,144),(2,156,12,132,12,144),(3,156,12,132,12,144),(4,156,12,132,12,144); +INSERT INTO `Read_counts` VALUES (2,156,12,132,12,144),(4,156,12,132,12,144),(1,156,12,132,12,144),(3,156,12,132,12,144); /*!40000 ALTER TABLE `Read_counts` ENABLE KEYS */; UNLOCK TABLES; @@ -230,7 +236,7 @@ DROP TABLE IF EXISTS `Seqrep`; CREATE TABLE `Seqrep` ( `seqrep_id` int(11) NOT NULL AUTO_INCREMENT, `isolate_id` int(11) DEFAULT NULL, - `sequence_replicate_number` int(11) DEFAULT NULL, + `sequence_replicate_number` bigint(20) unsigned DEFAULT NULL, `original_reads_file_1_md5` text, `original_reads_file_2_md5` text, `remove_contam_reads_file_1_md5` text, @@ -252,7 +258,7 @@ CREATE TABLE `Seqrep` ( LOCK TABLES `Seqrep` WRITE; /*!40000 ALTER TABLE `Seqrep` DISABLE KEYS */; -INSERT INTO `Seqrep` VALUES (1,1,43,'a3b22e537be7e1fc03c29df820f65b06','1676bdb60c23159fbaccc6975aed86c4','d9ea5077779c50c82bb9852fe5582cc0','5a1ef78ffdf7a4071a2b91d7c7dde8d5',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(2,2,45,'b08620e2b9231ee66ae56f926d97f097','808911bb28af5c5674bda3b7c71e3a75','0da67fe9d1f3b4313304c87c4dbc635f','4f20723c34220b96995550b0e627cc1f',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(3,3,47,'9981927389818aa1b57d6285ff490d23','5ffb53b040c7491807f963c3a94ad8fb','8e59250c494f103450c55f373a28ed96','e0c29c85b29af66dd810c5b0e741d0b7',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(4,4,49,'9306e04decb6b721daf0ea765d860c3a','fb0f64bf6f7ff2b05d1fb521634b41b4','164f99ffb7f4416b2c60d7491019d65e','fd7a1fdfe55bcc47ffc5cfa0a655b52f',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0); +INSERT INTO `Seqrep` VALUES (1,1,43,'25c461ececa0271428a283c534497417','ece4028afddf2365477e130d84748c56','2096a6996aef36c5c75c0a9dba3ed3a4','e77815e19d1f81db41888900039cb1b1',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(2,2,45,'e52a403846ab49eeb5cb9573822e1d92','3eef5d5e74295f7951526e23c7de656a','a4b21345c9ee84baeb4ce3b94aa478ca','3dc2b9875ddbf95de24990aa916492e4',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(3,3,47,'bba6cc17819a133c18e8f0c0e099a55e','e72c48a02f49ee98a45682b6e4dfac56','f35b1d902a4fcfd475b4e3e325942683','a00056bcca5a6c99a4448a2354f6245c',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0),(4,4,49,'866e1700d3c7e0d8c37edf8bb8399ffe','58ea111df4310f356460023a5483229f','e615dc85493f66a33594f8ff22292aa7','a69ad444c1b84271101f460c63e43e2b',0,1,'2017-12-25',0,'Illumina HiSeq 2000',NULL,0); /*!40000 ALTER TABLE `Seqrep` ENABLE KEYS */; UNLOCK TABLES; @@ -274,7 +280,7 @@ CREATE TABLE `Version` ( LOCK TABLES `Version` WRITE; /*!40000 ALTER TABLE `Version` DISABLE KEYS */; -INSERT INTO `Version` VALUES (1); +INSERT INTO `Version` VALUES (4); /*!40000 ALTER TABLE `Version` ENABLE KEYS */; UNLOCK TABLES; /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; @@ -287,4 +293,4 @@ UNLOCK TABLES; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; --- Dump completed on 2017-10-13 16:08:54 +-- Dump completed on 2020-11-13 14:09:42 diff --git a/python/clockwork/tests/nextflow_qc_test.py b/python/clockwork/tests/nextflow_qc_test.py index c074e2d..caa6cab 100644 --- a/python/clockwork/tests/nextflow_qc_test.py +++ b/python/clockwork/tests/nextflow_qc_test.py @@ -87,7 +87,7 @@ def test_nextflow_qc_using_database(self): "isolate_id": 1, "seqrep_id": 1, "seqrep_pool": None, - "version": "0.0.1", + "version": "0.9.0", "pipeline_name": "remove_contam", "status": 1, "reference_id": 1, @@ -105,7 +105,7 @@ def test_nextflow_qc_using_database(self): "isolate_id": 2, "seqrep_id": 2, "seqrep_pool": None, - "version": "0.0.1", + "version": "0.9.0", "pipeline_name": "remove_contam", "status": 1, "reference_id": 1, @@ -123,7 +123,7 @@ def test_nextflow_qc_using_database(self): "isolate_id": 3, "seqrep_id": 3, "seqrep_pool": None, - "version": "0.0.1", + "version": "0.9.0", "pipeline_name": "remove_contam", "status": 1, "reference_id": 1, @@ -141,7 +141,7 @@ def test_nextflow_qc_using_database(self): "isolate_id": 4, "seqrep_id": 4, "seqrep_pool": None, - "version": "0.0.1", + "version": "0.9.0", "pipeline_name": "remove_contam", "status": 1, "reference_id": 1, @@ -197,6 +197,12 @@ def test_nextflow_qc_using_database(self): "samtools_inward_oriented_pairs": 66, "samtools_outward_oriented_pairs": 0, "samtools_pairs_with_other_orientation": 0, + "samtools_positions_with_depth_atleast_10": 562, + "samtools_positions_with_depth_atleast_100": 0, + "samtools_positions_with_depth_atleast_2": 968, + "samtools_positions_with_depth_atleast_20": 0, + "samtools_positions_with_depth_atleast_5": 876, + "samtools_positions_with_depth_of_0": 17, "samtools_raw_total_sequences": 144, "samtools_reads_duplicated": 4, "samtools_reads_mapped": 132, @@ -248,18 +254,18 @@ def test_nextflow_qc_using_database(self): "samtools_inward_oriented_pairs": 66, "samtools_outward_oriented_pairs": 0, "samtools_pairs_with_other_orientation": 0, + "samtools_positions_with_depth_atleast_10": 547, + "samtools_positions_with_depth_atleast_100": 0, + "samtools_positions_with_depth_atleast_2": 955, + "samtools_positions_with_depth_atleast_20": 0, + "samtools_positions_with_depth_atleast_5": 902, + "samtools_positions_with_depth_of_0": 17, "samtools_raw_total_sequences": 144, "samtools_reads_duplicated": 0, "samtools_reads_mapped": 132, "het_snp_het_calls": 0, "het_snp_positions": 983, "het_snp_total_snps": 0, - "samtools_positions_with_depth_of_0": 0, #TODO - "samtools_positions_with_depth_atleast_2": 0, #TODO - "samtools_positions_with_depth_atleast_5": 0, #TODO - "samtools_positions_with_depth_atleast_10": 0, #TODO - "samtools_positions_with_depth_atleast_20": 0, #TODO - "samtools_positions_with_depth_atleast_100": 0, #TODO }, ] self.assertEqual(expected_qc_rows, got_qc_rows)