typemap properties and plugin setup

q2_feature_table/__init__.py

@@ -6,7 +6,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 
-from ._normalize import rarefy
+from ._normalize import rarefy, normalize
 from ._subsample_ids import subsample_ids
 from ._transform import (presence_absence, relative_frequency, transpose)
 from ._summarize import (summarize, tabulate_seqs, tabulate_sample_frequencies,
@@ -31,4 +31,4 @@
            'filter_seqs', 'subsample_ids', 'rename_ids',
            'filter_features_conditionally', 'split',
            'tabulate_feature_frequencies', 'tabulate_sample_frequencies',
-           'summarize_plus']
+           'summarize_plus', 'normalize']

q2_feature_table/_normalize.py

@@ -75,19 +75,24 @@ def _validate_parameters(method, m_trim, a_trim, gene_length):
     if method in ["tpm", "fpkm"] and not gene_length:
         raise ValueError("gene-length input is missing.")
 
-    # Raise Error if gene-length is given when using methods TMM, UQ, CUF, CPM or CTF
+    # Raise Error if gene-length is given when using methods TMM, UQ, CUF,
+    # CPM or CTF
     if method in ["tmm", "uq", "cuf", "ctf", "cpm"] and gene_length:
         raise ValueError(
             "gene-length input can only be used with FPKM and TPM methods."
         )
 
-    # Raise Error if m_trim or a_trim are given when not using methods TMM or CTF
-    if (method not in ["tmm", "ctf"]) and (m_trim is not None or a_trim is not None):
+    # Raise Error if m_trim or a_trim are given when not using methods
+    # TMM or CTF
+    if ((method not in ["tmm", "ctf"])
+            and (m_trim is not None or a_trim is not None)):
         raise ValueError(
-            "Parameters m-trim and a-trim can only be used with methods TMM and CTF."
+            "Parameters m-trim and a-trim can only be used with "
+            "methods TMM and CTF."
         )
 
-    # Set m_trim and a_trim to their default values for methods TMM and CTF
+    # Set m_trim and a_trim to their default values for methods
+    # TMM and CTF
     if method in ["tmm", "ctf"]:
         m_trim = 0.3 if m_trim is None else m_trim
         a_trim = 0.05 if a_trim is None else a_trim
@@ -106,13 +111,13 @@ def _convert_lengths(table, gene_length):
         skiprows=1,
     ).squeeze("columns")
 
-    # Check if all gene IDs that are present in the table are also present in
-    # the lengths
+    # Check if all gene IDs that are present in the table are also
+    # present in the lengths
     if not set(table.columns).issubset(set(lengths.index)):
         only_in_counts = set(table.columns) - set(lengths.index)
         raise ValueError(
-            f"There are genes present in the FeatureTable that are not present "
-            f"in the gene-length input. Missing lengths for genes: "
-            f"{only_in_counts}"
+            f"There are genes present in the FeatureTable that are "
+            f"not present in the gene-length input. Missing lengths "
+            f"for genes: {only_in_counts}"
         )
     return lengths

q2_feature_table/citations.bib

@@ -43,3 +43,12 @@ @article{NCBI-BLAST
 year = {2008},
 doi = {10.1093/nar/gkn201},
 }
+
+@misc{Zmrzlikar_RNAnorm_RNA-seq_data_2023,
+author = {Zmrzlikar, Jure and Žganec, Matjaž and Ausec, Luka and Štajdohar, Miha},
+month = jul,
+title = {{RNAnorm: RNA-seq data normalization in Python}},
+url = {https://github.com/genialis/RNAnorm},
+version = {2.1.0},
+year = {2023}
+}

q2_feature_table/plugin_setup.py

@@ -5,16 +5,17 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
-
+from qiime2.core.type import Properties
 from qiime2.plugin import (Plugin, Int, Float, Range, Metadata, Str, Bool,
                            Choices, MetadataColumn, Categorical, List,
                            Citations, TypeMatch, TypeMap, Collection,
                            Visualization)
 
 from q2_types.feature_table import (
-    FeatureTable, Frequency, RelativeFrequency, PresenceAbsence, Composition)
+    FeatureTable, Frequency, RelativeFrequency, PresenceAbsence, Composition,
+    Normalized)
 from q2_types.feature_data import (
-    FeatureData, Sequence, Taxonomy, AlignedSequence)
+    FeatureData, Sequence, Taxonomy, AlignedSequence, SequenceCharacteristics)
 from q2_types.metadata import ImmutableMetadata
 
 import q2_feature_table
@@ -723,3 +724,77 @@
                 "Tabulate sample and feature frequencies.",
     examples={'feature_table_summarize_plus': ex.feature_table_summarize_plus}
 )
+
+P_method, T_normalized_table = TypeMap(
+    {
+        Str
+        % Choices("tpm"): (
+            FeatureTable[Normalized % Properties("TPM")],
+        ),
+        Str
+        % Choices("fpkm"): (
+            FeatureTable[Normalized % Properties("FPKM")],
+        ),
+        Str
+        % Choices("tmm"): (
+            FeatureTable[Normalized % Properties("TMM")],
+        ),
+        Str
+        % Choices("uq"): (
+            FeatureTable[Normalized % Properties("UQ")],
+        ),
+        Str
+        % Choices("cuf"): (
+            FeatureTable[Normalized % Properties("CUF")],
+        ),
+        Str
+        % Choices("ctf"): (
+            FeatureTable[Normalized % Properties("CTF")],
+        ),
+        Str
+        % Choices("cpm"): (
+            FeatureTable[Normalized % Properties("CPM")],
+        ),
+    }
+)
+
+plugin.methods.register_function(
+    function=q2_feature_table.normalize,
+    inputs={
+        "table": FeatureTable[Frequency],
+        "gene_length": FeatureData[
+            SequenceCharacteristics % Properties("length")],
+    },
+    parameters={
+        "method": P_method,
+        "m_trim": Float % Range(
+            0, 1, inclusive_start=True, inclusive_end=True
+        ),
+        "a_trim": Float % Range(
+            0, 1, inclusive_start=True, inclusive_end=True
+        ),
+    },
+    outputs=[("normalized_table", T_normalized_table)],
+    input_descriptions={
+        "table": "Feature table with gene counts.",
+        "gene_length": "Gene lengths of all genes in the feature table.",
+    },
+    parameter_descriptions={
+        "method": "Specify the normalization method to be used. Use FPKM or "
+        "TPM for within comparisons and TMM, UQ, CUF or CTF for between "
+        "sample camparisons. Check https://www.genialis.com/wp-content/uploads"
+        "/2023/12/2023-Normalizing-RNA-seq-data-in-Python-with-RNAnorm.pdf "
+        "for more information on the methods.",
+        "m_trim": "Two sided cutoff for M-values. Can only be used for "
+        "methods TMM and CTF. (default = 0.3)",
+        "a_trim": "Two sided cutoff for A-values. Can only be used for "
+        "methods TMM and CTF. (default = 0.05)",
+    },
+    output_descriptions={
+        "normalized_table": "Feature table normalized with specified method."
+    },
+    name="Normalize FeatureTable",
+    description="Normalize FeatureTable by gene length, library size and "
+    "composition with common methods for RNA-seq.",
+    citations=[citations["Zmrzlikar_RNAnorm_RNA-seq_data_2023"]],
+)

q2_feature_table/tests/test_normalize.py

@@ -6,7 +6,6 @@
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
 import os
-import shutil
 from unittest import TestCase, main
 from unittest.mock import MagicMock, patch
 
@@ -18,8 +17,8 @@
 from q2_types.feature_data import SequenceCharacteristicsDirectoryFormat
 
 from q2_feature_table import rarefy
-from q2_feature_table._normalize import _validate_parameters, _convert_lengths, \
-    normalize
+from q2_feature_table._normalize import (_validate_parameters, \
+    _convert_lengths, normalize)
 
 
 class RarefyTests(TestCase):
@@ -89,16 +88,19 @@ def test_validate_parameters_uq_with_m_a_trim(self):
 
     def test_validate_parameters_tpm_missing_gene_length(self):
         # Test Error raised if gene-length is missing with TPM method
-        with self.assertRaisesRegex(ValueError, "gene-length input is missing."):
+        with self.assertRaisesRegex(
+                ValueError, "gene-length input is missing."):
             _validate_parameters("tpm", None, None, None)
 
     def test_validate_parameters_tmm_gene_length(self):
         # Test Error raised if gene-length is given with TMM method
         with self.assertRaisesRegex(
                 ValueError,
-                "gene-length input can only be used with FPKM and TPM methods."
+                "gene-length input can only be used with FPKM and "
+                "TPM methods."
         ):
-            _validate_parameters("tmm", None, None, gene_length=MagicMock())
+            _validate_parameters(
+                "tmm", None, None, gene_length=MagicMock())
 
     def test_validate_parameters_default_m_a_trim(self):
         # Test if m_trim and a_trim get set to default values if None
@@ -115,7 +117,8 @@ def test_validate_parameters_m_a_trim(self):
     def test_convert_lengths_gene_length(self):
         # Test _convert_lengths
         gene_length = SequenceCharacteristicsDirectoryFormat()
-        with open(os.path.join(str(gene_length), "sequence_characteristics.tsv"),
+        with open(os.path.join(
+                str(gene_length), "sequence_characteristics.tsv"),
                   'w') as file:
             file.write("id\tlength\nARO1\t1356.0\nARO2\t1173.0")
 
@@ -125,21 +128,24 @@ def test_convert_lengths_gene_length(self):
     def test_convert_lengths_short_gene_length(self):
         # Test Error raised if gene-length is missing genes
         gene_length = SequenceCharacteristicsDirectoryFormat()
-        with open(os.path.join(str(gene_length), "sequence_characteristics.tsv"), 'w') as file:
+        with open(os.path.join(
+                str(gene_length),
+                "sequence_characteristics.tsv"), 'w') as file:
             file.write("id\tlength\nARO1\t1356.0")
         with self.assertRaisesRegex(
                 ValueError,
-                "There are genes present in the FeatureTable that are not present "
-                "in the gene-length input. Missing lengths for genes: "
-                "{'ARO2'}",
+                "There are genes present in the FeatureTable that are "
+                "not present in the gene-length input. Missing lengths "
+                "for genes: {'ARO2'}",
         ):
             _convert_lengths(self.table, gene_length=gene_length)
 
     @patch("q2_feature_table._normalize.TPM")
     def test_tpm_fpkm_with_valid_inputs(self, mock_tpm):
         # Test valid inputs for TPM method
         gene_length = SequenceCharacteristicsDirectoryFormat()
-        with open(os.path.join(str(gene_length), "sequence_characteristics.tsv"),
+        with open(os.path.join(
+                str(gene_length), "sequence_characteristics.tsv"),
                   'w') as file:
             file.write("id\tlength\nARO1\t1356.0\nARO2\t1173.0")
         normalize(table=self.table, gene_length=gene_length, method="tpm")
@@ -148,7 +154,8 @@ def test_tpm_fpkm_with_valid_inputs(self, mock_tpm):
     def test_tmm_uq_cuf_ctf_with_valid_inputs(self, mock_tmm):
         # Test valid inputs for TMM method
         gene_length = SequenceCharacteristicsDirectoryFormat()
-        with open(os.path.join(str(gene_length), "sequence_characteristics.tsv"),
+        with open(os.path.join(
+                str(gene_length), "sequence_characteristics.tsv"),
                   'w') as file:
             file.write("id\tlength\nARO1\t1356.0\nARO2\t1173.0")
         normalize(table=self.table, method="tmm", a_trim=0.06, m_trim=0.4)