update package data

bokulich-lab · Oct 18, 2023 · ca91868 · ca91868
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Showing 28 changed files with 8 additions and 8 deletions.
diff --git a/q2_moshpit/kraken2/tests/data/new/README.md → .../tests/data/simulated-sequences/README.md b/q2_moshpit/kraken2/tests/data/new/README.md → .../tests/data/simulated-sequences/README.md
diff --git a/...ata/new/contigs/ba-mm-mixed_contigs.fasta → ...quences/contigs/ba-mm-mixed_contigs.fasta b/...ata/new/contigs/ba-mm-mixed_contigs.fasta → ...quences/contigs/ba-mm-mixed_contigs.fasta
diff --git a/...2/tests/data/new/contigs/ba_contigs.fasta → ...ulated-sequences/contigs/ba_contigs.fasta b/...2/tests/data/new/contigs/ba_contigs.fasta → ...ulated-sequences/contigs/ba_contigs.fasta
diff --git a/...2/tests/data/new/contigs/mm_contigs.fasta → ...ulated-sequences/contigs/mm_contigs.fasta b/...2/tests/data/new/contigs/mm_contigs.fasta → ...ulated-sequences/contigs/mm_contigs.fasta
diff --git a/...2/tests/data/new/contigs/sa_contigs.fasta → ...ulated-sequences/contigs/sa_contigs.fasta b/...2/tests/data/new/contigs/sa_contigs.fasta → ...ulated-sequences/contigs/sa_contigs.fasta
diff --git a/...2/tests/data/new/contigs/se_contigs.fasta → ...ulated-sequences/contigs/se_contigs.fasta b/...2/tests/data/new/contigs/se_contigs.fasta → ...ulated-sequences/contigs/se_contigs.fasta
diff --git a/...raken2/tests/data/new/kraken2-db/hash.k2d → ...a/simulated-sequences/kraken2-db/hash.k2d b/...raken2/tests/data/new/kraken2-db/hash.k2d → ...a/simulated-sequences/kraken2-db/hash.k2d
diff --git a/...raken2/tests/data/new/kraken2-db/opts.k2d → ...a/simulated-sequences/kraken2-db/opts.k2d b/...raken2/tests/data/new/kraken2-db/opts.k2d → ...a/simulated-sequences/kraken2-db/opts.k2d
diff --git a/...raken2/tests/data/new/kraken2-db/taxo.k2d → ...a/simulated-sequences/kraken2-db/taxo.k2d b/...raken2/tests/data/new/kraken2-db/taxo.k2d → ...a/simulated-sequences/kraken2-db/taxo.k2d
diff --git a/...693d0e1-be8e-40ab-9427-94a0ffc62963.fasta → ...693d0e1-be8e-40ab-9427-94a0ffc62963.fasta b/...693d0e1-be8e-40ab-9427-94a0ffc62963.fasta → ...693d0e1-be8e-40ab-9427-94a0ffc62963.fasta
diff --git a/...797bbd1-4f3c-4482-9828-fa4be13c9977.fasta → ...797bbd1-4f3c-4482-9828-fa4be13c9977.fasta b/...797bbd1-4f3c-4482-9828-fa4be13c9977.fasta → ...797bbd1-4f3c-4482-9828-fa4be13c9977.fasta
diff --git a/...adb2c2f-bb49-4b1a-a9ac-daf985b35070.fasta → ...adb2c2f-bb49-4b1a-a9ac-daf985b35070.fasta b/...adb2c2f-bb49-4b1a-a9ac-daf985b35070.fasta → ...adb2c2f-bb49-4b1a-a9ac-daf985b35070.fasta
diff --git a/...231448e-b591-4afc-9d8a-5255b1a24f08.fasta → ...231448e-b591-4afc-9d8a-5255b1a24f08.fasta b/...231448e-b591-4afc-9d8a-5255b1a24f08.fasta → ...231448e-b591-4afc-9d8a-5255b1a24f08.fasta
diff --git a/...pit/kraken2/tests/data/new/reads/MANIFEST → ...s/data/simulated-sequences/reads/MANIFEST b/...pit/kraken2/tests/data/new/reads/MANIFEST → ...s/data/simulated-sequences/reads/MANIFEST
diff --git a/...aken2/tests/data/new/reads/ba-R1.fastq.gz → .../simulated-sequences/reads/ba-R1.fastq.gz b/...aken2/tests/data/new/reads/ba-R1.fastq.gz → .../simulated-sequences/reads/ba-R1.fastq.gz
diff --git a/...aken2/tests/data/new/reads/ba-R2.fastq.gz → .../simulated-sequences/reads/ba-R2.fastq.gz b/...aken2/tests/data/new/reads/ba-R2.fastq.gz → .../simulated-sequences/reads/ba-R2.fastq.gz
diff --git a/...ts/data/new/reads/ba-mm-mixed-R1.fastq.gz → ...d-sequences/reads/ba-mm-mixed-R1.fastq.gz b/...ts/data/new/reads/ba-mm-mixed-R1.fastq.gz → ...d-sequences/reads/ba-mm-mixed-R1.fastq.gz
diff --git a/...ts/data/new/reads/ba-mm-mixed-R2.fastq.gz → ...d-sequences/reads/ba-mm-mixed-R2.fastq.gz b/...ts/data/new/reads/ba-mm-mixed-R2.fastq.gz → ...d-sequences/reads/ba-mm-mixed-R2.fastq.gz
diff --git a/...aken2/tests/data/new/reads/mm-R1.fastq.gz → .../simulated-sequences/reads/mm-R1.fastq.gz b/...aken2/tests/data/new/reads/mm-R1.fastq.gz → .../simulated-sequences/reads/mm-R1.fastq.gz
diff --git a/...aken2/tests/data/new/reads/mm-R2.fastq.gz → .../simulated-sequences/reads/mm-R2.fastq.gz b/...aken2/tests/data/new/reads/mm-R2.fastq.gz → .../simulated-sequences/reads/mm-R2.fastq.gz
diff --git a/...tests/data/new/reads/nonsense-R1.fastq.gz → ...ated-sequences/reads/nonsense-R1.fastq.gz b/...tests/data/new/reads/nonsense-R1.fastq.gz → ...ated-sequences/reads/nonsense-R1.fastq.gz
diff --git a/...tests/data/new/reads/nonsense-R2.fastq.gz → ...ated-sequences/reads/nonsense-R2.fastq.gz b/...tests/data/new/reads/nonsense-R2.fastq.gz → ...ated-sequences/reads/nonsense-R2.fastq.gz
diff --git a/...aken2/tests/data/new/reads/sa-R1.fastq.gz → .../simulated-sequences/reads/sa-R1.fastq.gz b/...aken2/tests/data/new/reads/sa-R1.fastq.gz → .../simulated-sequences/reads/sa-R1.fastq.gz
diff --git a/...aken2/tests/data/new/reads/sa-R2.fastq.gz → .../simulated-sequences/reads/sa-R2.fastq.gz b/...aken2/tests/data/new/reads/sa-R2.fastq.gz → .../simulated-sequences/reads/sa-R2.fastq.gz
diff --git a/...aken2/tests/data/new/reads/se-R1.fastq.gz → .../simulated-sequences/reads/se-R1.fastq.gz b/...aken2/tests/data/new/reads/se-R1.fastq.gz → .../simulated-sequences/reads/se-R1.fastq.gz
diff --git a/...aken2/tests/data/new/reads/se-R2.fastq.gz → .../simulated-sequences/reads/se-R2.fastq.gz b/...aken2/tests/data/new/reads/se-R2.fastq.gz → .../simulated-sequences/reads/se-R2.fastq.gz
diff --git a/q2_moshpit/kraken2/tests/test_classification.py b/q2_moshpit/kraken2/tests/test_classification.py
@@ -247,7 +247,7 @@ def test_contigs(
         report_format_mock,
         output_format_mock
     ):
-        samples_dir = self.get_data_path(os.path.join('new', 'contigs'))
+        samples_dir = self.get_data_path(os.path.join('simulated-sequences', 'contigs'))
         contigs = ContigSequencesDirFmt(samples_dir, "r")
 
         common_args = ["--db", "/some/where/db", "--quick"]
@@ -398,8 +398,8 @@ def setUpClass(cls):
             os.path.dirname(os.path.abspath(__file__)), 'data'
         )
 
-        db_path = os.path.join(datadir, 'new', 'kraken2-db')
-        reads_path = os.path.join(datadir, 'new', 'reads')
+        db_path = os.path.join(datadir, 'simulated-sequences', 'kraken2-db')
+        reads_path = os.path.join(datadir, 'simulated-sequences', 'reads')
 
         db = Kraken2DBDirectoryFormat(db_path, 'r')
         samples = SingleLanePerSamplePairedEndFastqDirFmt(reads_path, 'r')
@@ -507,8 +507,8 @@ def setUpClass(cls):
             os.path.dirname(os.path.abspath(__file__)), 'data'
         )
 
-        db_path = os.path.join(datadir, 'new', 'kraken2-db')
-        contigs_path = os.path.join(datadir, 'new', 'contigs')
+        db_path = os.path.join(datadir, 'simulated-sequences', 'kraken2-db')
+        contigs_path = os.path.join(datadir, 'simulated-sequences', 'contigs')
 
         db = Kraken2DBDirectoryFormat(db_path, 'r')
         samples = ContigSequencesDirFmt(contigs_path, 'r')
@@ -581,8 +581,8 @@ def setUpClass(cls):
             os.path.dirname(os.path.abspath(__file__)), 'data'
         )
 
-        db_path = os.path.join(datadir, 'new', 'kraken2-db')
-        mags_path = os.path.join(datadir, 'new', 'mags')
+        db_path = os.path.join(datadir, 'simulated-sequences', 'kraken2-db')
+        mags_path = os.path.join(datadir, 'simulated-sequences', 'mags')
 
         db = Kraken2DBDirectoryFormat(db_path, 'r')
         samples = MAGSequencesDirFmt(mags_path, 'r')

diff --git a/setup.py b/setup.py
@@ -68,7 +68,7 @@
             'data/kraken2-reports-select/*/*',
             'data/kraken2-to-ncbi-tree/*',
             'data/kraken2-to-ncbi-tree/*/*/*',
-            'data/contigs/*/*',
+            'data/simulated-sequences/**/*',
         ],
         'q2_moshpit.dereplication.tests': [
             'data/*', 'data/mags/*', 'data/mags/*/*',