IMP: migrate types/formats/transformers from types-genomics (#309)

ci/recipe/meta.yaml

@@ -25,11 +25,12 @@ requirements:
     - ijson
     - h5py
     - qiime2 {{ qiime2_epoch }}.*
+    - samtools
 
 test:
   commands:
     - py.test --pyargs q2_types
-    
+
   requires:
     - pytest
     - qiime2 >={{ qiime2 }}

q2_types/feature_data_mag/__init__.py

@@ -0,0 +1,25 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import importlib
+
+from ._format import (
+        MAGSequencesDirFmt,
+        OrthologAnnotationDirFmt,
+        OrthologFileFmt
+        )
+
+from ._type import MAG, NOG, OG, KEGG
+from ._transformer import MAGIterator
+
+__all__ = [
+        'MAG', 'MAGSequencesDirFmt', 'MAGIterator', 'NOG', 'OG', 'KEGG',
+        'OrthologAnnotationDirFmt', 'OrthologFileFmt',
+        ]
+
+importlib.import_module('q2_types.feature_data._transformer')

q2_types/feature_data_mag/_format.py

@@ -0,0 +1,78 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import re
+
+from q2_types.feature_data import DNAFASTAFormat
+from q2_types.genome_data._format import OrthologFileFmt
+from qiime2.plugin import model
+
+from ..plugin_setup import plugin
+
+
+class MAGSequencesDirFmt(model.DirectoryFormat):
+    pathspec = (
+        r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-"
+        r"[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}\.(fa|fasta)$"
+    )
+
+    sequences = model.FileCollection(pathspec, format=DNAFASTAFormat)
+
+    @sequences.set_path_maker
+    def sequences_path_maker(self, mag_id):
+        return r'%s.fasta' % mag_id
+
+    def feature_dict(self, relative=False):
+        '''
+        Returns a mapping of mag id to filepath for each mag.
+
+        Parameters
+        ---------
+        relative : bool
+            Whether to return filepaths relative to the directory's location.
+            Returns absolute filepaths by default.
+
+        Returns
+        -------
+        dict
+            Mapping of feature id -> filepath as described above. Sorted
+            alphabetically by key.
+        '''
+        pattern = re.compile(self.pathspec)
+        ids = {}
+        for path in self.path.iterdir():
+            if not pattern.match(path.name):
+                continue
+
+            id = path.stem
+            absolute_path = path.absolute()
+            if relative:
+                ids[id] = str(
+                    absolute_path.relative_to(self.path.absolute())
+                )
+            else:
+                ids[id] = str(absolute_path)
+
+        return dict(sorted(ids.items()))
+
+
+plugin.register_formats(MAGSequencesDirFmt)
+
+
+class OrthologAnnotationDirFmt(model.DirectoryFormat):
+    annotations = model.FileCollection(
+        r'.+\.annotations',
+        format=OrthologFileFmt
+    )
+
+    @annotations.set_path_maker
+    def annotations_path_maker(self, file_name):
+        return file_name.split(sep="_")[0]
+
+
+plugin.register_formats(OrthologAnnotationDirFmt)

q2_types/feature_data_mag/_transformer.py

@@ -0,0 +1,91 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+import collections.abc
+import glob
+import os.path
+from itertools import repeat
+
+import pandas as pd
+import skbio
+from q2_types.feature_data._transformer import _fastaformats_to_series
+
+from . import MAGSequencesDirFmt
+from ..plugin_setup import plugin
+
+CONSTRUCTORS = {
+    'DNA': skbio.DNA,
+    'RNA': skbio.RNA,
+    'protein': skbio.Protein
+}
+
+
+def _get_filename(full_path):
+    return os.path.splitext(os.path.basename(full_path))[0]
+
+
+def _series_to_fasta(series, ff, seq_type='DNA'):
+    fp = os.path.join(str(ff), f'{series.name}.fasta')
+    with open(fp, 'w') as fh:
+        for id_, seq in series.iteritems():
+            if seq:
+                sequence = CONSTRUCTORS[seq_type](seq, metadata={'id': id_})
+                skbio.io.write(sequence, format='fasta', into=fh)
+
+
+def _fastafiles_to_dataframe(ff):
+    data = {}
+    for fp in sorted(glob.glob(os.path.join(str(ff), '*.fa*'))):
+        fname = _get_filename(fp)
+        data[fname] = _fastaformats_to_series(fp, constructor=skbio.DNA)
+    df = pd.DataFrame.from_dict(data, orient='index')
+    df.index.name = 'Feature ID'
+    df = df.astype(str).replace({'nan': None})
+    return df
+
+
+@plugin.register_transformer
+def _2(ff: MAGSequencesDirFmt) -> pd.DataFrame:
+    return _fastafiles_to_dataframe(ff)
+
+
+@plugin.register_transformer
+def _3(df: pd.DataFrame) -> MAGSequencesDirFmt:
+    result = MAGSequencesDirFmt()
+    df.apply(_series_to_fasta, axis=1, ff=result, seq_type='DNA')
+    return result
+
+
+class MAGIterator(collections.abc.Iterable):
+    def __init__(self, generator):
+        self.generator = generator
+
+    def __iter__(self):
+        yield from self.generator
+
+
+@plugin.register_transformer
+def _4(ff: MAGSequencesDirFmt) -> MAGIterator:
+    def _multi_generator(files):
+        for fp in files:
+            fname = _get_filename(fp)
+            fg = skbio.read(fp, format='fasta', constructor=skbio.DNA)
+            yield from zip(repeat(fname), fg)
+
+    fps = sorted(glob.glob(os.path.join(str(ff), '*.fa*')))
+    return MAGIterator(_multi_generator(fps))
+
+
+@plugin.register_transformer
+def _5(data: MAGIterator) -> MAGSequencesDirFmt:
+    result = MAGSequencesDirFmt()
+    for fn, seq in data:
+        fp = os.path.join(str(result), f'{fn}.fasta')
+        with open(fp, 'a') as fin:
+            skbio.io.write(seq, format='fasta', into=fin)
+    return result

q2_types/feature_data_mag/_type.py

@@ -0,0 +1,48 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+from q2_types.feature_data import FeatureData
+
+from q2_types.feature_data_mag._format import (
+        MAGSequencesDirFmt, OrthologAnnotationDirFmt
+        )
+from qiime2.core.type import SemanticType
+
+from ..plugin_setup import plugin
+
+
+MAG = SemanticType('MAG', variant_of=FeatureData.field['type'])
+
+plugin.register_semantic_types(MAG)
+plugin.register_semantic_type_to_format(
+    FeatureData[MAG],
+    artifact_format=MAGSequencesDirFmt
+)
+
+NOG = SemanticType('NOG', variant_of=FeatureData.field['type'])
+
+plugin.register_semantic_types(NOG)
+plugin.register_artifact_class(
+        FeatureData[NOG],
+        directory_format=OrthologAnnotationDirFmt)
+
+
+OG = SemanticType('OG', variant_of=FeatureData.field['type'])
+
+plugin.register_semantic_types(OG)
+plugin.register_artifact_class(
+        FeatureData[OG],
+        directory_format=OrthologAnnotationDirFmt)
+
+
+KEGG = SemanticType('KEGG', variant_of=FeatureData.field['type'])
+
+plugin.register_semantic_types(KEGG)
+plugin.register_artifact_class(
+        FeatureData[KEGG],
+        directory_format=OrthologAnnotationDirFmt)

q2_types/feature_data_mag/tests/__init__.py

@@ -0,0 +1,7 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2023, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------

q2_types/feature_data_mag/tests/data/good_ortholog_annotation/test_output.emapper.annotations

@@ -0,0 +1,2 @@
+1000565.METUNv1_03812	1000565.METUNv1_03812	4.71e-264	714.0	COG0012@1|root,COG0012@2|Bacteria,1MVM4@1224|Proteobacteria,2VJ1W@28216|Betaproteobacteria,2KUD2@206389|Rhodocyclales	206389|Rhodocyclales	J	ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner	ychF	-	-	ko:K06942	-	-	-	-	ko00000,ko03009	-	-	-	MMR_HSR1,YchF-GTPase_C
+362663.ECP_0061	362663.ECP_0061	0.0	1624.0	COG0417@1|root,COG0417@2|Bacteria,1MVY9@1224|Proteobacteria,1RMQ1@1236|Gammaproteobacteria,3XPER@561|Escherichia	1236|Gammaproteobacteria	L	DNA polymerase	polB	GO:0003674,GO:0003824,GO:0003887,GO:0004518,GO:0004527,GO:0004529,GO:0004536,GO:0006139,GO:0006259,GO:0006260,GO:0006261,GO:0006281,GO:0006725,GO:0006807,GO:0006950,GO:0006974,GO:0007154,GO:0008150,GO:0008152,GO:0008296,GO:0008408,GO:0009058,GO:0009059,GO:0009432,GO:0009605,GO:0009987,GO:0009991,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0016796,GO:0016895,GO:0018130,GO:0019438,GO:0031668,GO:0033554,GO:0034061,GO:0034641,GO:0034645,GO:0034654,GO:0043170,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044271,GO:0045004,GO:0045005,GO:0046483,GO:0050896,GO:0051716,GO:0071496,GO:0071704,GO:0071897,GO:0090304,GO:0090305,GO:0140097,GO:1901360,GO:1901362,GO:1901576	2.7.7.7	ko:K02336	-	-	-	-	ko00000,ko01000,ko03400	-	-	-	DNA_pol_B,DNA_pol_B_exo1

q2_types/feature_data_mag/tests/data/mags-fa/23c5b64e-3f3e-4688-9862-e9dae4fa0f5b.fa

@@ -0,0 +1,3 @@
+>k129_5480
+TTATTTTCAAGATAATGAGCCAATTTAAGCGGTGTCTGGCCGCCAAGCTGCACGATCACA
+CCTTTAA

q2_types/feature_data_mag/tests/data/mags-fa/70c5a728-96a6-4eed-b9f9-9a73153c1385.fa

@@ -0,0 +1,3 @@
+>k129_5112
+CCCCGGAAAGGGCTGGCGACCGACGATGACCTCGGGAAGCCCCAACTCGCGGCCGATGGC
+GCGTACCTCGTC

q2_types/feature_data_mag/tests/data/mags-fa/7e2a749a-a19a-4b62-8195-0ee601b5fdfb.fa

@@ -0,0 +1,6 @@
+>k129_6525
+AAACTCTATCAAGCGTATACCAAAGTGAGTGGTGTATTGATCAGTCAGCTCATTATTGAA
+TCGGA
+>k129_6531
+TCGGATTTGCCGAATGCTTTTTGTAAGGGCCTTCAATTGATTTGGCGATAGCGAGCCCGT
+ATTTACGGT

q2_types/feature_data_mag/tests/data/mags-fasta/3b7d53fb-5b60-46c6-8819-aeda065b12e9.fasta

@@ -0,0 +1,3 @@
+>k129_5401
+CCATTGTATGTCTTTAGGTAGCTCCTCATGTTTGAGGTTCATGTCTTGGATTTTGTTTTC
+TCCAAAAATC

q2_types/feature_data_mag/tests/data/mags-fasta/6232c7e1-8ed7-47c8-9bdb-b94706a26931.fasta

@@ -0,0 +1,10 @@
+>k129_4684
+TGATACCGACGCGGCACTTGAGTGCGCGCTATCCTTCAAGGAAGCCACATGCGTTATTGT
+TAAACA
+>k129_5618
+GTGCTAATCGCACCCTCATGAGCGACACCATTATTCTTTATTTTTGAGTCTTCAGCAAAA
+>k129_5631
+TCATGATGATCCAAAAGCAGTTGCGGAAGCATCTGGGATAATTACGCGGAGTGGATGTCG
+CCG
+>k129_2817
+GTCGCCAATTAGCAACTATGATGTCTTCTGGAGTACCTTTGGTCCAATCATTTGAAATCA

q2_types/feature_data_mag/tests/data/ortholog_annotation_extra/test_output.emapper.annotations

@@ -0,0 +1,2 @@
+1000565.METUNv1_03812	1000565.METUNv1_03812	4.71e-264	714.0	COG0012@1|root,COG0012@2|Bacteria,1MVM4@1224|Proteobacteria,2VJ1W@28216|Betaproteobacteria,2KUD2@206389|Rhodocyclales	206389|Rhodocyclales	J	ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner	ychF	-	-	ko:K06942	-	-	-	-	ko00000,ko03009	-	-	-	MMR_HSR1,YchF-GTPase_C
+362663.ECP_0061	362663.ECP_0061	0.0	1624.0	COG0417@1|root,COG0417@2|Bacteria,1MVY9@1224|Proteobacteria,1RMQ1@1236|Gammaproteobacteria,3XPER@561|Escherichia	1236|Gammaproteobacteria	L	DNA polymerase	polB	GO:0003674,GO:0003824,GO:0003887,GO:0004518,GO:0004527,GO:0004529,GO:0004536,GO:0006139,GO:0006259,GO:0006260,GO:0006261,GO:0006281,GO:0006725,GO:0006807,GO:0006950,GO:0006974,GO:0007154,GO:0008150,GO:0008152,GO:0008296,GO:0008408,GO:0009058,GO:0009059,GO:0009432,GO:0009605,GO:0009987,GO:0009991,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0016796,GO:0016895,GO:0018130,GO:0019438,GO:0031668,GO:0033554,GO:0034061,GO:0034641,GO:0034645,GO:0034654,GO:0043170,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044271,GO:0045004,GO:0045005,GO:0046483,GO:0050896,GO:0051716,GO:0071496,GO:0071704,GO:0071897,GO:0090304,GO:0090305,GO:0140097,GO:1901360,GO:1901362,GO:1901576	2.7.7.7	ko:K02336	-	-	-	-	ko00000,ko01000,ko03400	-	-	-	DNA_pol_B,DNA_pol_B_exo1

q2_types/feature_data_mag/tests/data/ortholog_annotation_extra/test_output.emapper.orthologs

@@ -0,0 +1,2 @@
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