add search-and-summarize usage example

q2_dwq2/_examples.py

@@ -6,9 +6,12 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
+import importlib.resources
+
 import skbio
 
 import qiime2
+from q2_types.feature_data import DNAFASTAFormat
 
 
 def seq1_factory():
@@ -46,3 +49,41 @@ def align_and_summarize_example_1(use):
         use.UsageOutputNames(aligned_sequences='msa',
                              msa_summary='msa_summary'),
     )
+
+
+def _get_filepath_from_tests(path):
+    # this utility function may be transferred to the QIIME 2 framework
+    # track progress here: https://github.com/qiime2/qiime2/issues/792
+    return importlib.resources.files('q2_dwq2.tests') / path
+
+
+def query1_factory():
+    fp = _get_filepath_from_tests('data/ss-query.fasta')
+    return qiime2.Artifact.import_data(
+        "FeatureData[Sequence]", fp, view_type=DNAFASTAFormat
+    )
+
+
+def reference1_factory():
+    fp = _get_filepath_from_tests('data/ss-ref.fasta')
+    return qiime2.Artifact.import_data(
+        "FeatureData[Sequence]", fp, view_type=DNAFASTAFormat
+    )
+
+
+def search_and_summarize_example_1(use):
+    query_seqs = use.init_artifact('query_seqs', query1_factory)
+    reference_seqs = use.init_artifact('reference_seqs', reference1_factory)
+    use.comment("This is an example of running this Pipeline serially.")
+    use.comment("The modification to run this in parallel depends on the "
+                "interface you're using (for example, using q2cli you would "
+                "append the --parallel flag).")
+
+    hits, hits_table, = use.action(
+        use.UsageAction(plugin_id='dwq2',
+                        action_id='search_and_summarize'),
+        use.UsageInputs(query_seqs=query_seqs,
+                        reference_seqs=reference_seqs,
+                        split_size=1),
+        use.UsageOutputNames(hits='hits', hits_table='hits-table')
+    )

q2_dwq2/plugin_setup.py

@@ -17,7 +17,9 @@
 from q2_dwq2._visualizers import (
     summarize_alignment, tabulate_las_results)
 from q2_dwq2._pipelines import align_and_summarize, search_and_summarize
-from q2_dwq2._examples import nw_align_example_1, align_and_summarize_example_1
+from q2_dwq2._examples import (nw_align_example_1,
+                               align_and_summarize_example_1,
+                               search_and_summarize_example_1)
 from q2_dwq2 import (
     SingleDNASequence, SingleRecordDNAFASTAFormat,
     SingleRecordDNAFASTADirectoryFormat, LocalAlignmentSearchResults,
@@ -281,7 +283,7 @@
     description=("Perform local alignment search of a query sequence against "
                  "reference sequences and report the results in a table."),
     citations=[],
-    examples={}
+    examples={'Serial local alignment search': search_and_summarize_example_1}
 )
 
 importlib.import_module('q2_dwq2._transformers')

q2_dwq2/tests/data/ss-query.fasta

@@ -0,0 +1,10 @@
+>RS_GCF_018917925.1~NZ_JAHLPO010000048.1 d__Bacteria;p__Bacillota_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Pseudobutyricicoccus;s__Pseudobutyricicoccus sp003477405 [location=3441..4867] [ssu_len=1427] [contig_len=4886]
+TGCTTAGTGGCGGACGGGTGAGTAACGCGTGAGGAACCTGCCTTTCAGTGGGGGATAACACATCGAAAGATGTGCTAATACCGCATAACATAGCGATGGGGCATCCCATTGCTATCAAAGATTTATTGCTGAAAGATGGCCTCGCGTCCAATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGACGATTGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCC
+>RS_GCF_007667405.1~NZ_VDRA01000112.1 d__Bacteria;p__Bacillota;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus;s__Staphylococcus pettenkoferi [location=1..1068] [ssu_len=1068] [contig_len=1108]
+TGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAAACTTGAGTGCAGGAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAA
+>RS_GCF_019900785.2~NZ_CP081891.1 d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae [location=458832..460368] [ssu_len=1537] [contig_len=5310315]
+ATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGTAGCACAGAGAGCTTGCTCTCGGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGTGGGGGACCTTCGGGCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAG
+>RS_GCF_000446645.2~NZ_AIBE01000115.1 d__Bacteria;p__Pseudomonadota;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli [location=46..1583] [ssu_len=1538] [contig_len=1601]
+TTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTA
+>RS_GCF_001589115.1~NZ_LBCU01000025.1 d__Bacteria;p__Bacillota;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus cristatus_K [location=3367..4910] [ssu_len=1544] [contig_len=5233]
+AATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTAGAACGCTGAAGGGAGAGCTTGCTCTTCTGGATGAGTTGCGAACGGGTGAGTAACGCGTAGGTAACCTGCCTGGTAGCGGGGGATAACTATTGGAAACGATAGCTAATACCGCATAACATTGACTATTGCATGATAGTCAATTGAAAGGTGCAAATGCACCACTACCAGATGGACCTGCGTTGTATTAGCT