ENH: add SampleData[JoinedSequencesWithQuality] as input for classify…

…-kraken2 (#202) Co-authored-by: Michal Ziemski <[email protected]>
bokulich-lab · Oct 21, 2024 · 10bb850 · 10bb850
1 parent 428fcae
commit 10bb850
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/q2_moshpit/kraken2/classification.py b/q2_moshpit/kraken2/classification.py
@@ -14,6 +14,7 @@
 from q2_types.per_sample_sequences import (
     SequencesWithQuality,
     PairedEndSequencesWithQuality,
+    JoinedSequencesWithQuality,
     SingleLanePerSamplePairedEndFastqDirFmt,
     SingleLanePerSampleSingleEndFastqDirFmt,
     ContigSequencesDirFmt, Contigs,
@@ -73,7 +74,8 @@ def classify_kraken2(
     collate_kraken2_outputs = ctx.get_action("moshpit",
                                              "collate_kraken2_outputs")
 
-    if seqs.type <= SampleData[SequencesWithQuality]:
+    if seqs.type <= SampleData[SequencesWithQuality |
+                               JoinedSequencesWithQuality]:
         partition_method = ctx.get_action("demux", "partition_samples_single")
     elif seqs.type <= SampleData[PairedEndSequencesWithQuality]:
         partition_method = ctx.get_action("demux", "partition_samples_paired")

diff --git a/q2_moshpit/plugin_setup.py b/q2_moshpit/plugin_setup.py
@@ -28,7 +28,8 @@
     FeatureTable, Frequency, PresenceAbsence, RelativeFrequency
 )
 from q2_types.per_sample_sequences import (
-    SequencesWithQuality, PairedEndSequencesWithQuality, MAGs, Contigs
+    SequencesWithQuality, PairedEndSequencesWithQuality,
+    JoinedSequencesWithQuality, MAGs, Contigs
 )
 from q2_types.sample_data import SampleData
 from q2_types.feature_map import FeatureMap, MAGtoContigs
@@ -166,7 +167,7 @@
 
 T_kraken_in, T_kraken_out_rep, T_kraken_out_hits = TypeMap({
     SampleData[SequencesWithQuality |
-               PairedEndSequencesWithQuality]: (
+               PairedEndSequencesWithQuality | JoinedSequencesWithQuality]: (
         SampleData[Kraken2Reports % Properties('reads')],
         SampleData[Kraken2Outputs % Properties('reads')]
     ),