Add unit test and test data for RunRedup task

workflows/amr/test/RunRedup/clusters.csv

@@ -0,0 +1,11 @@
+M05295:617:000000000-KL64F:1:1101:2016:13202,M05295:617:000000000-KL64F:1:1101:2016:13202
+M05295:617:000000000-KL64F:1:1101:3078:7376,M05295:617:000000000-KL64F:1:1101:3078:7376
+M05295:617:000000000-KL64F:1:1101:3125:11405,M05295:617:000000000-KL64F:1:1101:3125:11405
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:1101:2666:12975
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:1119:25439:5751
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:2101:21157:16235
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:2106:11795:12187
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:2108:9015:16045
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:2112:3938:13885
+M05295:617:000000000-KL64F:1:1101:2666:12975,M05295:617:000000000-KL64F:1:2117:7228:7910
+M05295:617:000000000-KL64F:1:1101:1908:15400,M05295:617:000000000-KL64F:1:1101:1908:15400

workflows/amr/test/RunRedup/duplicate_cluster_sizes.tsv

@@ -0,0 +1,5 @@
+1	M05295:617:000000000-KL64F:1:1101:2016:13202
+1	M05295:617:000000000-KL64F:1:1101:3078:7376
+1	M05295:617:000000000-KL64F:1:1101:3125:11405
+7	M05295:617:000000000-KL64F:1:1101:2666:12975
+1	M05295:617:000000000-KL64F:1:1101:1908:15400

workflows/amr/test/RunRedup/host_filter_1.fastq

@@ -0,0 +1,44 @@
+@M05295:617:000000000-KL64F:1:1101:3078:7376
+TTTTGCCGTAACGGCTTTTTACCACAGCCAGCTTGCGGCGCAACACCTCCGCCAGAAAGTTGCCGTTGCCGCAGGCGGGTTCCAGAAAACGGCTCTCGATGCGCTCCGTCTCGCTCTTTACAAGGTCGCACATCGCCTTTACCTCC
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG8DF@FDEGGGGGGGGGGGGGGGCDGGFFFFEFFFFFF>/
+@M05295:617:000000000-KL64F:1:1101:3125:11405
+TCTTTGGTATACTGCAGTGCTTATATGCGGTTTGCTGATTTTTTCGGCGGCAGCTTGTGCAGGAACGATTCTTTCCTGCAATAACCGGCTGAAAAGAAAAAGGAAAAAGATACGCAAGGCGGCACTCTTGTCAACTATGTGCATTA
++
+CCCCCGGGGGGGGFFFDFGGGAFGCFGGEGGGG>AECFGEFFGGCEFGGEGGGGGGGGGGGGGGFGGGGFFGGGGGGFGGGGGGFG:FGGGFGGGG7DFCGGGGGDFGEGGGGGGCGGGFGEGGGGGFGCGGGGFF5D9CD7<DF+
+@M05295:617:000000000-KL64F:1:1101:2016:13202
+CCACCAAATAACACTCAAGGACTTCAAATGTCGGAGAGTGTGAGATGTTCTTTGAAAATTGAATAACGAAACAACAAAGAGGAAATTAAAGATATCCAATTAAAGAAATTTAATGGGTAAAATACAATTTCAAACAATTCTTCTGT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGFGGGGGGGGGGGGGGFFFFFFFFFFFF
+@M05295:617:000000000-KL64F:1:1101:2666:12975
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFBBF
+@M05295:617:000000000-KL64F:1:2112:3938:13885
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGDEGGGGEGGCFGGGGGGEGGCGGGGGGFGG8FGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+@M05295:617:000000000-KL64F:1:2108:9015:16045
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGDGGGGCGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFG
+@M05295:617:000000000-KL64F:1:2106:11795:12187
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGCGGGGGGGDGEFCFFDFFCGGGGGGGFGGGGGGGGGGFEF8FDCEGGGGGGGGGD>FFGGGGGGGGGGGFGGGGDGGGGGGGGGGGGGGG
+@M05295:617:000000000-KL64F:1:2117:7228:7910
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGFFGGGGGGFFGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCDGGGGGGGGGGGDGGGGFGGAFGG7FGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGF
+@M05295:617:000000000-KL64F:1:1119:25439:5751
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGFGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGF
+@M05295:617:000000000-KL64F:1:2101:21157:16235
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCTACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTTCACAGAATGCGCACGGCCTTCCAGAT
++
+CCCCCGGGGGGDGGGGFGGGGGGGGF@FGGGGG<FGGGGGGGGGFGGGGGGGFGEGDGGGGGGGGGCF@F<FFGGFGGGGG=@FGEGGGGFFA9E88CCEGGFAGFGGGGGFGG8CCCEEGGGGG??D??CGGD69DFGFF6DFGF
+@M05295:617:000000000-KL64F:1:1101:1908:15400
+CGCTCACATGAACGGAATAATACTCTCCCAAATATTCACTTCCCGCCCCATCTTTGTATACTTCCTCTGTTTCAAGATCATATGTTTGATATAAATACGCCTGTCCATCATTCTTCAGATCTACATAAGCAGCCCAGTCATCAATC
++
+<8-AC@FCGFGGGGGCFFEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGFGFGFGGCGFGGGFBFFFFBFBDDF9

workflows/amr/test/RunRedup/host_filter_2.fastq

@@ -0,0 +1,44 @@
+@M05295:617:000000000-KL64F:1:1101:3078:7376
+CTTTGCCCTCAGATTTGCTTTTGTACCAATTATAGCATATTTCCCGGTTAAATCCACAGATTTTTAGCTATTCGTTTCATCTCTTGAGCCGCTTGTCAAAAGGTACACTTTTTGGCAAGCCCTTCAAAGAGGTGGAACGAATGGCA
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGFGFFFFDFFFFF5
+@M05295:617:000000000-KL64F:1:1101:3125:11405
+TCTTTGGTAAGTCCGAACAGATTTTATTCTACTCCTCGGGTGTTCTGAGCGATTGTTTGTGTTGAAAAGTCATTCAGGTCATAGTACCGCATTGCTTCTGTTCCGTCTTTGGCGATATACTCGACTAAAATGTAATGCTCGGTTAT
++
+CCCCCFGFFFGF<FF@CFG8<<F<FGGFGGGGGGGGGGCFEGG7FGF9FC7@FGFAFGGGGGDCFEFGGGGGGGGFGGEGGGFGGGGGGGGGGGFGEGGC@EFGGFFGCGGFFGDEGGGGDFDGGGDCG?FFGBFFFFFBD>@ABD
+@M05295:617:000000000-KL64F:1:1101:2016:13202
+TTCAGTTCGGGCGGTTCCCCTCATATACCTATTTATTCAGTATATGATACATGGACTTGACTCCATGTGGATTGCTCCATTCGGACATCTACGGATCATATCGTGCTTGCCAATCCCCGTAGCTTTTCGCAGCTTACCACGTCCTT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFFGGGGDGDFFGGGGGGGFGFD?FFFFFFFF
+@M05295:617:000000000-KL64F:1:1101:2666:12975
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGGG9FAFGFGFGFGGGGGGGGGGGGGGGGGGGGGGDEGGGFGGDCGF:FGGGGGGGGFC=CFGGGGGFGGGGGGGGGGGGGFGGGGEEGDCC>EFGDEEGGGGGGGGFFDGGGGCDGG7DFGFFF5**@FFFA
+@M05295:617:000000000-KL64F:1:2112:3938:13885
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTCTGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGCCFF<FGFGGGFCFGGGGGGGGGGGEFGEFGGGGEG7FFDGFEGGG:CFEFFFGGGEGG+CFFGCGGGGGGGGD+?FFCF,AAF,,@B@F7C@D@CCEGGGFFGFGGDGGGGFFGGCFCFG6C>+;*7*AF5
+@M05295:617:000000000-KL64F:1:2108:9015:16045
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGGFEFG8F8AFGG:FFGFGGGGGGGGGGGGG,9BF:E:FD,@@::F8CCEFEG9FGC,7@CFDC9,CF<AFGFG:+84AAE,@9,E9CBCEE6+7BCEE6=6=F,EFGF>CDB:,CFF9CFFF677C57;>7*
+@M05295:617:000000000-KL64F:1:2106:11795:12187
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGGFGGG8EEFEFGGGGGG,FFGGGGGGGGGGFGG@CEFCDFGG77F@CFFGFGCFD@EFFDFEAEFGFGFGGCCC+@FFCFEFFFFFEGG>C6+@EEEC>DCFFGDGGDEGGGFGGGGFFD6CD66?7BFF5;
+@M05295:617:000000000-KL64F:1:2117:7228:7910
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGFE,C9,FFFGFCFGGGGGGFGGGFFCF<FFG8ECFGCFGGGGG7FFGGEF8FG<ECFGGGGGFGGF@9FEEGG+=F@8FF9F9AEEGGEGGGG<BFEEEFGFFGGGGGGGGGAFFFCFGGCCFCE5CGFF?8
+@M05295:617:000000000-KL64F:1:1119:25439:5751
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAGAAAC
++
+CCCCCGGGGGGGGGGF9@FGGGFGGFEGGGGCFEGGGGFGGGGGGGGGGGDDGGGGEDGF=FE@FGGGGFEFGGGGGGGGGGCFGGECC@FGEGFDCDFDGGGGCE@FFCFGGGFCFGGGGGFGGFGGGFGCFGGGF>>CGGGGGD
+@M05295:617:000000000-KL64F:1:2101:21157:16235
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTCGTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTTTGAGCGCGAAGTCGGAAATCTGAAAAAATTTGCAGCCACCACGACAAAAAC
++
+CCCCCGGGGGGGGG<<6@<C66CC8EDC@FC<FFF@FFF9FGGGGGFEGGDEEFC=CCF8FGGGGA?EE?8@F=FF9DE,FFBFDFEEECE8BF,E=,DFEDCEC>F8@CEGCDF:,,@+6=@F8FCGG6;+0=00*3**0**33:
+@M05295:617:000000000-KL64F:1:1101:1908:15400
+TGGTCCTCGCCGTTATGAATCTTACAAAGAAAGTATAGTTGACCATTCAGATATTTTATTGGATGAGAGGTATGCGGAAGCATGGGAATATAAGGACAATCCATTTATTTATGTATCTATCATAGGACCTATTTATGCAACGGGAA
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFGGGGGGGCFGGGDGFGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGFGFGGGDGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGG8DFGFFFFFFF5@A:

workflows/amr/test/RunRedup/subsampled_1.fa

@@ -0,0 +1,16 @@
+>M05295:617:000000000-KL64F:1:1101:2016:13202
+CCACCAAATAACACTCAAGGACTTCAAATGTCGGAGAGTGTGAGATGTTCTTTGAAAATT
+GAATAACGAAACAACAAAGAGGAAATTAAAGATATCCAATTAAAGAAATTTAATGGGTAA
+AATACAATTTCAAACAATTCTTCTGT
+>M05295:617:000000000-KL64F:1:1101:2666:12975
+CCTCTTTTTTTTGCAGAAGAGTACACAACTGCTTTATTTTATGCTAAAAGACCCCTGCCT
+ACGCAAAGGCAGAGGTCCGATTTTTTCATAGTCTGGGGAGATAAAACAACTTTCCGATTT
+CACAGAATGCGCACGGCCTTCCAGAT
+>M05295:617:000000000-KL64F:1:1101:3078:7376
+TTTTGCCGTAACGGCTTTTTACCACAGCCAGCTTGCGGCGCAACACCTCCGCCAGAAAGT
+TGCCGTTGCCGCAGGCGGGTTCCAGAAAACGGCTCTCGATGCGCTCCGTCTCGCTCTTTA
+CAAGGTCGCACATCGCCTTTACCTCC
+>M05295:617:000000000-KL64F:1:1101:3125:11405
+TCTTTGGTATACTGCAGTGCTTATATGCGGTTTGCTGATTTTTTCGGCGGCAGCTTGTGC
+AGGAACGATTCTTTCCTGCAATAACCGGCTGAAAAGAAAAAGGAAAAAGATACGCAAGGC
+GGCACTCTTGTCAACTATGTGCATTA

workflows/amr/test/RunRedup/subsampled_2.fa

@@ -0,0 +1,16 @@
+>M05295:617:000000000-KL64F:1:1101:2016:13202
+TTCAGTTCGGGCGGTTCCCCTCATATACCTATTTATTCAGTATATGATACATGGACTTGA
+CTCCATGTGGATTGCTCCATTCGGACATCTACGGATCATATCGTGCTTGCCAATCCCCGT
+AGCTTTTCGCAGCTTACCACGTCCTT
+>M05295:617:000000000-KL64F:1:1101:2666:12975
+CCTTTTTTTTTTTTAACTGGAATCGACATTGATTTTTATATTCCGTCGGCAAGGCAGGTC
+GTTCAGGTGGCGTATTCCATTCAGGGGGATGCCTATGAGCGCGAAGTCGGAAATCTGAAA
+AAATTTGCAGCCACCACGACAGAAAC
+>M05295:617:000000000-KL64F:1:1101:3078:7376
+CTTTGCCCTCAGATTTGCTTTTGTACCAATTATAGCATATTTCCCGGTTAAATCCACAGA
+TTTTTAGCTATTCGTTTCATCTCTTGAGCCGCTTGTCAAAAGGTACACTTTTTGGCAAGC
+CCTTCAAAGAGGTGGAACGAATGGCA
+>M05295:617:000000000-KL64F:1:1101:3125:11405
+TCTTTGGTAAGTCCGAACAGATTTTATTCTACTCCTCGGGTGTTCTGAGCGATTGTTTGT
+GTTGAAAAGTCATTCAGGTCATAGTACCGCATTGCTTCTGTTCCGTCTTTGGCGATATAC
+TCGACTAAAATGTAATGCTCGGTTAT

workflows/amr/test/test_wdl.py

@@ -1,3 +1,4 @@
+import csv
 import os
 from test_util import WDLTestCase
 
@@ -75,3 +76,101 @@ def testRunResultsPerSample(self):
             "smeB",
         ]:
             self.assertTrue(expected_gene_name in gene_names)
+
+    def testRunRedup(self):
+        inputs = {
+            "host_filtered_reads": [relpath("RunRedup", "host_filter_1.fastq"), relpath("RunRedup", "host_filter_2.fastq")],
+            "subsampled_reads": [relpath("RunRedup", "subsampled_1.fa"), relpath("RunRedup", "subsampled_2.fa")],
+            "clusters": relpath("RunRedup", "clusters.csv"),
+            "cluster_sizes": relpath("RunRedup", "duplicate_cluster_sizes.tsv"),
+        }
+
+        # Get all input read ids
+        with open(relpath("RunRedup", "clusters.csv"), 'r') as clusters_csv:
+            tsvreader = csv.reader(clusters_csv)
+            cluster_read_ids = [row for row in tsvreader]
+
+        # Get subsampled read ids
+        subsampled_read_ids = set()
+        with open(relpath("RunRedup", "subsampled_1.fa"), 'r') as subsampled_1_fa:
+            for line in subsampled_1_fa.readlines():
+                if line.startswith(">"):
+                    subsampled_read_ids.add(line.lstrip(">").rstrip("\n"))
+
+        target_read_ids = set()
+        excluded_read_ids = set()
+        for rep_read_id, read_id in cluster_read_ids:
+            if rep_read_id in subsampled_read_ids:
+                target_read_ids.add(read_id)
+            else:
+                excluded_read_ids.add(read_id)
+
+        # Run task and collect output ids
+        res = self.run_miniwdl(task="RunRedup", task_input=inputs)
+
+        output_1 = dict()
+        with open(res["outputs"]["RunRedup.redups_fa"][0]) as redups_1_fa:
+            reads = []
+            this_read = []
+            for line in redups_1_fa.readlines():
+                if line.startswith(">"):
+                    reads.append(this_read)
+                    this_read = [line.lstrip(">").rstrip("\n")]
+                else:
+                    this_read.append(line.rstrip("\n"))
+            reads.append(this_read)
+            output_1 = {read[0]: "".join(read[1:]) for read in reads if len(read) > 0}
+
+        output_2 = dict()
+        with open(res["outputs"]["RunRedup.redups_fa"][1]) as redups_2_fa:
+            reads = []
+            this_read = []
+            for line in redups_2_fa.readlines():
+                if line.startswith(">"):
+                    reads.append(this_read)
+                    this_read = [line.lstrip(">").rstrip("\n")]
+                else:
+                    this_read.append(line.rstrip("\n"))
+            reads.append(this_read)
+            output_2 = {read[0]: "".join(read[1:]) for read in reads if len(read) > 0}
+
+
+        # Check ids
+        output_ids_1 = output_1.keys()
+        assert len(set(output_ids_1)) == len(output_ids_1)
+        output_ids_1 = set(output_ids_1)
+        output_ids_2 = output_2.keys()
+        assert len(set(output_ids_2)) == len(output_ids_2)
+        output_ids_2 = set(output_ids_2)
+        assert output_ids_1 == output_ids_2
+
+        output_ids = output_ids_1 & output_ids_2
+
+        for read_id in target_read_ids:
+            assert read_id in output_ids
+        for read_id in excluded_read_ids:
+            assert read_id not in output_ids
+
+        # Check sequences
+        host_filter_1 = dict()
+        with open(relpath("RunRedup", "host_filter_1.fastq"), "r") as host_filter_1_fq:
+            lines = host_filter_1_fq.readlines()
+            for index in range(0, len(lines), 4):
+                read_id = lines[index].lstrip("@").rstrip("\n")
+                read_sequence = lines[index + 1].rstrip("\n")
+                host_filter_1[read_id] = read_sequence
+
+        host_filter_2 = dict()
+        with open(relpath("RunRedup", "host_filter_2.fastq"), "r") as host_filter_2_fq:
+            lines = host_filter_2_fq.readlines()
+            for index in range(0, len(lines), 4):
+                read_id = lines[index].lstrip("@").rstrip("\n")
+                read_sequence = lines[index + 1].rstrip("\n")
+                host_filter_2[read_id] = read_sequence
+
+        for read_id, read_sequence in output_1.items():
+            assert read_id in host_filter_1
+            assert read_sequence == host_filter_1[read_id]
+        for read_id, read_sequence in output_2.items():
+            assert read_id in host_filter_2
+            assert read_sequence == host_filter_2[read_id]