ENH: add sample_dict method to MultiFASTADirectoryFormat (#311)

* ENH: add sample_dict method to MultiFASTADirectoryFormat

* Add a MultiMAGSequencesDirFmt -> MultiFASTADirectoryFormat transformer

* ENH: add FeatureData[Contig] type

* Lint

* Add missing files

* Revert "ENH: add FeatureData[Contig] type"

This reverts commit edbd24a.
This commit was moved to a separate branch/PR.

q2_types/per_sample_sequences/_format.py

@@ -597,13 +597,60 @@ def _validate_(self, level):
 
 class MultiFASTADirectoryFormat(MultiDirValidationMixin,
                                 model.DirectoryFormat):
-    sequences = model.FileCollection(r'.+\.(fa|fasta)$', format=DNAFASTAFormat)
+    pathspec = r'.+\.(fa|fasta)$'
+    sequences = model.FileCollection(pathspec, format=DNAFASTAFormat)
 
     @sequences.set_path_maker
     def sequences_path_maker(self, sample_id, mag_id):
         # write out with fasta extension, regardless if input was fa or fasta
         return '%s/%s.fasta' % (sample_id, mag_id)
 
+    def sample_dict(self, relative=False):
+        """
+        Returns a mapping of sample id to another dictionary where keys
+        represent the MAG ID and values correspond to the 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 sample id -> dict {mag_id: mag_filepath} as
+            described above. Both levels of the dictionary are
+            sorted alphabetically by key.
+        """
+        mags_pattern = re.compile(self.pathspec)
+        ids = {}
+        for d in self.path.iterdir():
+            if not d.is_dir():
+                continue
+
+            sample_id = d.name.rsplit('/', 1)[0]
+            if sample_id not in ids:
+                ids[sample_id] = {}
+
+            for path in d.iterdir():
+                if not mags_pattern.match(path.name):
+                    continue
+
+                mag_id = os.path.splitext(os.path.basename(path.name))[0]
+                absolute_path = path.absolute()
+                if relative:
+                    ids[sample_id][mag_id] = str(
+                        absolute_path.relative_to(self.path.absolute())
+                    )
+                else:
+                    ids[sample_id][mag_id] = str(absolute_path)
+
+            ids[sample_id] = dict(sorted(ids[sample_id].items()))
+
+        return dict(sorted(ids.items()))
+
 
 class MultiMAGSequencesDirFmt(MultiFASTADirectoryFormat):
     manifest = model.File('MANIFEST', format=MultiMAGManifestFormat)

q2_types/per_sample_sequences/_transformer.py

@@ -7,6 +7,7 @@
 # ----------------------------------------------------------------------------
 
 import os
+import shutil
 import functools
 import re
 import warnings
@@ -276,3 +277,16 @@ def _29(ff: MultiMAGManifestFormat) -> pd.DataFrame:
         lambda f: os.path.join(ff.path.parent, f))
     df.set_index(['sample-id', 'mag-id'], inplace=True)
     return df
+
+
+@plugin.register_transformer
+def _30(dirfmt: MultiMAGSequencesDirFmt) \
+        -> MultiFASTADirectoryFormat:
+    result = MultiFASTADirectoryFormat()
+    for sample_id, mag in dirfmt.sample_dict().items():
+        os.makedirs(os.path.join(result.path, sample_id))
+        for mag_id, mag_fp in mag.items():
+            shutil.copy(
+                mag_fp, os.path.join(result.path, sample_id, f"{mag_id}.fa")
+            )
+    return result

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/MANIFEST

@@ -0,0 +1,6 @@
+sample-id,mag-id,filename
+sample1,mag1,sample1/mag1.fasta
+sample1,mag2,sample1/mag2.fasta
+sample1,mag3,sample1/mag3.fasta
+sample2,mag1,sample2/mag1.fasta
+sample2,mag2,sample2/mag2.fasta

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/sample1/mag1.fa

@@ -0,0 +1,51 @@
+>k129_5480
+TTATTTTCAAGATAATGAGCCAATTTAAGCGGTGTCTGGCCGCCAAGCTGCACGATCACA
+CCTTTAACTTTCCCATGCTCATTTTCTGCTTCAATCAATGACAATACATCTTCGCCTGTG
+AGCGGCTCGAAATATAATCTGTCAGAGGTATCATAATCCGTTGAAACGGTTTCAGGATTA
+CAATTAACCATGATTGTTTCATAACCCGCCTCTTTTAGTGCATAGGCGGCATGGACACAG
+CAATAATCAAATTCAATACCTTGCCCGATACGGTTTGGCCCGCCACCTAGAATAACGATT
+TTGTCTTTTTTAGTTGCTGTAATTTCAGAAGTAGAATTAAGTGTTTCATAGGTGCCGTAC
+ATATACGATGTTAATGACGGTATTTCTGCCGCACAGCTATCCACCCGCTTATAAACAGGT
+TTTACTTTGTGCATCAAACGTGTTTTACGGATCGTTGCTTCTGCAACCCCTACCAATTCA
+GCCAGACGCGCATCCGAAAATCCTGCGCGCTTCAATGCCATCCATCCCTGAGGATCTTTC
+GGCAGGCCGTTTTTCTTAATGGAGGCCTCAGTATCAATAAGAGATTTTATACGCTCTAAA
+TACCACATATCAAATTTTGTTAATTGATAGATAGTTTCTAAATCCATACCGTGTCGCATC
+GCTTCGGCTGCATAGAGTAAGCGGGCTGGCGTTGGACGTGAAAGTGCTGCCCGAATATCG
+TCCATATCAGGCTCAGACTTACCAGCAATCGGAATGGAGCTAAGCCCCTCTAAGCCCTTT
+TCTAAAGAGCGCAAAGCTTTTTGCAGAGACTCTTCGAAGCTACGCCCTATAGCCATGGCT
+TCACCGACTGACTTCATTGCTGTGGTTAAGGTGTTATCAGAGCCTTTAAATTTCTCGAAA
+GCAAAACGAGGCACTTTTGTCACGACATAATCAATGGATGGCTCAAAGGCTGCGGGTGTT
+TTGCCGCCTGTAATATCATTGCCTAATTCATCAAGTGTATACCCTACCGCCAATTTCGCT
+GCCACTTTAGCAATCGGAAAACCTGTAGCTTTTGAGGCTAAAGCAGAAGAACGAGACACA
+CGAGGGTTCATCTCAATCACCACCATACGGCCTGTCTCTGGATCCATTCCAAATTGGACA
+TTCGATCCACCTGTTTCAACACCAATCACACGAAGTACGGCCAATGAGGCATTGCGCATG
+ATTTGATACTCTTTATCTGTCAGTGTTAAGGCTGGAGCAACGGTAATAGAATCACCTGTA
+TGCACGCCCATAGGGTCAATGTTTTCAATCGAACAAATAATGATAGCGTTGTCCTTTGTA
+TCACGAACAACCTCCATCTCGTATTCTTTCCAACCCAATAAACTCTCATCAATCAACACT
+TCATTGGTTGGTGACGCATCCAAGCCTTCACGAATGATTTGTTCAAACTCATCTTTGTTA
+TAAGCAACCCCGCCACCAGAACCACCCATGGTAAAGGATGGACGAATAATCGCTGGTAAG
+CCTGTATGTTTCAGAGCCTCTCTAGCCTCTTCCATAGAATGCACCACCGCACTTTTAGGA
+CTTTCAAGACCAATCTTCTCCATACAATCTTTAAATAATTGGCGGTCTTCAGCCTTTTCA
+ATGGCTTCTTTATTGGCACCGATCAGTTCAATATTGAGTCTTTTTAATACACCCATTTTA
+TCAAGAGCCAGTGCAGCATTCAGTGCCGTCTGACCACCCATGGTTGGAAGCAACGCATCG
+GGGCGTTCTTTTTCTAAAATCTTTGCGACAATTTCTGGGGTGATTGGCTCAATATAAGTC
+GCATCAGCCATATTCGGATCAGTCATAATTGTGGCTGGATTAGAATTAATCAGGACAACG
+CGGTACCCCTCTTCTTTCAGCGCTTTACAGGCTTGTGCACCTGAATAGTCAAATTCACAG
+GCTTGACCTATCACGATAGGACCAGCGCCAATAATACAAATGGAGGAAATGTCGGTGCGT
+TTAGGCATGTGAATCTCGGTTTCTTTTTTTTATACTTACCGAGAGTTAGTTTATGCACTT
+ATCAGGGTGTGCAGACAAGCTCTTTCTTGACCTTACCCGCAAGTTTAGCTATATTCTATC
+AACAGCCCGCCCTTGATGGCGGGTTATTTTATTGAAAAGGTGCAAGGCTATGCAAAAAAT
+ACCCTTAACAAAACAAGGCCACACAGACCTTGAAGCAGAATTAAAAGATTTAAAACACCG
+CCAACGTCCAGCGGTTATTGCTGCGATATCTGAAGCCAGAGAACATGGCGATTTATCAGA
+AAACGCTGAATATCACGCCGCCCGTGAGCAGCAAAGCTTTATCGAAGGTCGTATCGAGCA
+AGTCGAAGCTATTTTATCGCTCGCTGAGATTATTGACCCGGCCAAAATTTCTGGTGACAC
+GGTAAAATTTGCAGCAACTGTTAAAGTCGTTGATTGTGACACAGATGATGAACATATCTA
+CCAAATCGTCGGTGATGAAGAATCAGACATTGAAACAGGAAAACTGGCTATCTCGTCACC
+TGTTGCCCGCGCTTTAATCGGCAAAAAAGTTGAGGACTCAGTCGAAGTCCGCACACCAAA
+AGGCACAAGAGAATACGAAATTTTAGAAATTCTGTATAAGTAATTTCTATTCTTCGATCG
+GTACGCCAGGCTTCTTGAAATTACGTTTCATAATAAGTGATGACTTAACAGAGCGAACAT
+TTTTTAGCGCTGTCAGTTCTTCTGTAATAAAACGCTGATAAGCATCCCAATCTTTGGCCA
+CAATACGGAGTGTGAAATCCATATCACCCGCAATCATGTAACAATCACGAACGAGATCCA
+TTTTCTCAACGGCTTTGATAAAGGCCTGAAGGTCTTTTTCTGAAGTGTCTTCTAAAGCTA
+CATTGGCAAAAACCGCCACACCATAGCCTAACATTGAAGCACTTAAATCCGCATGATAAC
+TTTGGATATAACCATAATCTTCCAAT

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/sample1/mag2.fa

@@ -0,0 +1,64 @@
+>k129_5112
+CCCCGGAAAGGGCTGGCGACCGACGATGACCTCGGGAAGCCCCAACTCGCGGCCGATGGC
+GCGTACCTCGTCTTTGAAGAGGGTGCGAAGGGGCTCGACGAGGTCGAACTGGAGGTCTTC
+GGGCAGCCCACCGACGTTGTGGTGGCTCTTGATGTTGGCGGTTCCAGCCCCGCCACCGGA
+CTCGACGACATCCGGATACAGGGTGCCCTGCACGAGGAAGCGGATGGGTTCGCCGTCGGC
+CTTGGCCTCATCCACGAGCTCGCGCTGCACCCGCTCGAACGCACGGATGAACTCGCGACC
+GATGATCTTGCGCTTCTCTTCGGGATCGCTGACGCCGGCGAGGGCCTCGAGGAACGTCTC
+GCGGGCGTCGACGGTCACGAGGCGCACACCGGTCGAGGCTACGTAATCCTGCTCGACCTG
+TTCGCGTTCGCCCTTGCGCAGCAGGCCGTGGTCGACGAACACGGCAACGAGCTGGTCGCC
+GACTGCCTTGTGAACGAGGGCCGTCGAGACAGCCGAGTCGACTCCGCCCGACAGCGCCGA
+GAGCACACGACCCGAGCCGACCTGCGCGCGGATCCGATCGACCTGCTCGGCGATGACGTT
+GCCGCTGTTCCAGTCTGCGGGGAGGCCCGCAGCCTTGTGCAGGAAGTTCTCGATGATGCG
+CTGCCCGTGGTCGGAGTGCTTGACCTCGGGATGCCACTGCACACCGTACATGCGGCGAGC
+GTCGTTGCCGAAAGCGGCGACCGGGGTGGCACCGGTGCGGGCGAGCACCTCGAACCCGGC
+GGGGGCTTCGGACACCTGGTCACCATGGCTCATCCAGACGTTCTGCTCCGCGGGCTGGCC
+ATCGAACAGTACGCTCTCGTCACGGATGATGCTGGCGTCAGTCGCCCCGTACTCGCGCAG
+CCCCGTGTTCGCAACGACGCCACCGAGCGCCTGCGCCATGACCTGGAATCCGTAGCAGAT
+GCCAAGGGTCGGAACGCCCAGGTCGAACACCGCCGGGTCGAGCGTCGGCGCGCCAGGCTC
+GTACACCGATGACGGTCCGCCCGACAGGATGATGCCGATCGGATCTTTTGCGGCAATCTC
+TTCAGCTGTCGCGGTGTGCGGAACCAGCTCGCTGTAGACGCCCGCTTCGCGCACGCGACG
+GGCAATGAGCTGGGCGTACTGCGCGCCGAAGTCGACGACGAGGACGGGTCGCTGCGAGGT
+CTCGGTCTGTTCTGTCACCGGATGCTTTCGGTCGGCGCCCCTGGAACCCAGGAGCGAAGG
+TCAGGACACTGTGGGGTTCTGGCGGGTCACGCTGGAGTGTTCGGCGAGATCGTGGTTCTC
+GGACTCGCGCGCAGCAAGGTACGTCTTGACCTCACGGGCGACCCGTGCCTCCATGAAGAA
+CGACAGGAACGGGACGATTCCGCCCAGCGCGAGGGCGATGAACCGACCGAACCGCCACCG
+CATCAGGCTCCAGATGCGGAAGCACGCGAAGAGGTACACGACGTAGAACCAGCCGTGGCC
+GACGAGGATCGACAGCGACACATTGACGCCGTCGCCCGCCGACTCGAGGTCGCAGCCCAG
+ACCCCCGGGCACGAAGAGCGAGTACCACTCGCATCCGGGCCCGACCAGCACCGGTGCGAA
+CCAGAGGAAGCCACCGGACCCGCCGGCGAACAGTTCGACGTGCAGCGGCGAGTACTTGAG
+GATCATCTCGGCCAGCAGCAGGAGCAGCATGACACCGGTGATGATCGAGGCGACCTGGTA
+GAAGGTCAAGGCTCCGCGAATGGCCGGGAAAGACGACGGTTTCGGCTCACGGGGCATGGG
+CCCATTCTAGTCGCCGGTTGCGGTCGCGCTTCCCGACGAGGATGCCGCGGCTGCGGCATC
+CTCGAGCTCTTCGACTTCCTTCTCCCACGCATCCTTGGCGAGGCGGTACCAGAAATAGAA
+GGCGAAGCCGGCGAAGACCACCCACTCGGCGGCGTAGAAGATGTTCAGCCAGTTGACTGT
+GGACCCGGCATCCGGCGCGGGCGAGGCGATGTCCACAAGGCCCGCCGGCGCAGACTGCGA
+GGCGATGTAGCTGCGATAGACGTCCAGGCCCGCGGTGTCGTGCCACTGCGACAGGAGCGC
+CGCCGGCGACATCCGTGTCATCGTGAACGGCGGCTCGCCGCGCGGCGGCGGCACCGGACC
+CTCGTCCGAGATCAACCGACCGACGACCGTCACGGACTCCCCCGCGACCGCAGTCTGCTC
+GAGCGCCTCGGCGGCGGATTCGGCGACGGTGAGCGTCGGCGCCCAGCCGACGGCGACGGC
+CACGGATGTCGGCGTCGCGGTGTCGGCGATACGCAGCTGACCGGTGACCCAGAAGCCTTC
+GACGCCGTCGTTGAAGCGCGACGAAACGACAAGGAAATCCTCGGGAACCCACGTGCCCGT
+CACCTCGACGCGCTGGCCCACGAGCGGCTCGGGAAGGTACTCGCCGGGCCCGGCGATCTC
+GGCGAGCGGCCTGACCTCTTCGGTGGTCCCGGGCGGGAGTGGGTCGGTGTCGATAGCGCG
+CGAGAGCTGCCACTGCCCGAGCCACGCGAACACCCCCGCTACGACGAGCGCGAGCAGCAG
+GACGCCGATCCAGCGGGGTCGGAGCATGACCTCCCGCAGGGTCGGGGGAAAGACTGTCTG
+GTCTGTCATCCGCCCGTATACGGCGCGACGACCACCTCGACGCGCTGGAACTCCTTGAGA
+TCGGAGTACCCGGTCGTGGCCATCGACTTCTTCAGCGCCCCGATCAGGTTCGCGGTTCCG
+TCAGCCACCGGAGCCGGACCGTAGAGCACGGATTCGAGGTTCGTCACCTGATCCACCTTC
+ACGCGGCGACCGCGCGGGAGCTTCGAGTGGTGAGCCTCCGGCCCCCAGTGGTATCCACGA
+CCGGGGGCGTCGGTTGCCCGCGAGAGAGCGACGCCGAGCATGACGGCATCCGCTCCCATC
+GCGAGCGCCTTGACGATGTCGCCTGACGTTCCCACACCGCCATCGGCGATGACGTGGACG
+TAGCGCCCGCCCGACTCGTCGAGGTAGTCGCGGCGCGCGCCGGCGACGTCGGCTACCGCC
+GTGGCCATCGGGGCGTGGATGCCGAGAACCCCGCGCGTCGTCGAGGCTGCGCCCCCGCCG
+AAGCCGACGAGCACGCCCGCGGCGCCCGTGCGCATGAGGTGCAGGGCTGCCGTGTAGGTC
+GCAGCACCGCCGACGATGACAGGCACGTCGAGGTCGTAGATGAACTTCTTGAGGTTGAGG
+GGCTCGTCGACGCTCGAGACGTGCTCGGCCGAAACCGTCGTGCCACGGATGACGAACAGG
+TCCACACCCGCGGCGACCACGGTTTCGTACAGCTGCTGGGTGCGCTGCGGAGTCAAAGCA
+CCGGCCACCGTGACTCCGGCGTCACGGATCTGCTGCAGTCGCTCACGGATGAGCTCGGGC
+TTGATCGGCTCGGAGTAGAGCTCCTGCATCCGGCAGGTTGCCGTCGCCTCGTCGAGAGAC
+GCGATCTCAGCCAGCAGCGGCTCGGGGTCGTCGTACCGGGTCCAGAGCCCCTCGAGATCG
+AGGACACCGAGTCCGCCGAGCTGACCGAGCATGATCGCCGTCTGCGGGCTCACAACCGAA
+TCCATCGGGGCGCCGAGCACCGGGATGTCGAACTGGAACGCGTCGATCGACCATGCGGTC
+GAGACATCCTCGGGATTGCGGGTGCGGCGCGAGGGAACGACGGCGATGTCGTCGAACGAG
+TACGCGCGGCGAGCCCGCTTGGCGCGGCCGATCTCGATC

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/sample1/mag3.fa

@@ -0,0 +1,46 @@
+>k129_6525
+AAACTCTATCAAGCGTATACCAAAGTGAGTGGTGTATTGATCAGTCAGCTCATTATTGAA
+TCGGACTTCTGTCTCCAATCGATATATTGATGGAGAAGAAGGGCTCCATAAAAGAGGATT
+ATTAAGTTCTAAATTAACCTCTGCTGTCTCTTTATTTTCCGCTTCTACATTAAGCGAATG
+ATCCATCTGCAGTAATGGTTTATCGCCTTCATTAGAAAATATTTTAAATACTACAGTAAC
+TGCGCTCCAATGATTATACGTATTAAAGACCTCTGCGCGTAACAATAATTCTACTTTATT
+TAGGTCTTGCTGATCATGGAAATGGCAGCGCACTTGAGTTCCGCAGTAGGGCACATAGAC
+GCAATTAGTAGCTATTAGTCGAACATCGCGGTAGATGCCGCCGCCCTCATACGACCATAG
+TTCAAATTCTCTGGCATCGCAGCGAACCGCGACCACGTTCGGCACATTCGCATCGCAAAG
+CTCAGTGATATCGAGAGTGAAACTGGTGTAGCCTGATAGATGCCGCCCAGCTAAATGGCC
+ATTTACCCATATTGTTGCATCTCGGTAAATGCCATCAAATTCAAGGTGAATACGCTGCTT
+GCTAGCTTCTTTGGGAATTTCAAACGTTTTGCGATACCAGCCTACATCAGTCGGCAGTGA
+GCCATGCACAGCATTCGCGGATGCCCGAAATTCGCCTTCAATTACGAAATCATGAGGTAG
+GTTTATGTCGCGCCATGCTTCATCTGGATAGCCCAAGCGCGCGACCCCATGGTTTCCTGC
+CTTTAACCACTCGGCTCGCTTAAAACGATTAGCATGAATGGCTTGATGGTTAGTGCTGTC
+TAGCTCACCTCGATGAAACTTCCAACCTTGGTTAAATTCATAAGTGGTACGCATAGAATT
+ACTGATGTCTTTTAAAAGATTCTACAAGTGGAGTCTATTAATTATTTGATAAGTTACTCT
+GATTATTTTTAGAGATTTCTAATACAACTCCGCTGCACGTGCCGTAACGTCCGCCTTGGT
+ATGCGCAAAACAGATGGGTGGGGACGCCTTCAGAGTTAATCAGTAACTGCGGTCGTTCGA
+ATCGCCCTTCACGATCCAGTCCAGGCAATGTCTCGTCGAAGTAAGTTCCAGCATCTTTGT
+AAGCAACCTGCGGATTTTGCCAAATAAGGCCATCGCTGGATTCCATATACAGCCCATACT
+CGTGGTTATAAAAACCCATGTCACGCATGATTATTTTATATGGTGCGCAATCCTTCGGTT
+CGTACCATGTGTACGCGTC
+>k129_6531
+TCGGATTTGCCGAATGCTTTTTGTAAGGGCCTTCAATTGATTTGGCGATAGCGAGCCCGT
+ATTTACGGTTGCCGTTAAATCGCCGCCCAGTGTCCCAATCCCAACCTTTATAGTAGAGCC
+AATATTCGCCATTAGGATTTTGTAATAGCGATGGGTTGCTAACGACGGCATCGTCCCAAT
+CGCCATCGCTGCCAACATTAATAACAGGTTCATCTCCAACGCGTCGCCAAGGTCCATTTA
+TATTATCGGCAATGGCTAAACCGATGCGTTTGGTGTAGACTAATTGATTGAAGTATTTTT
+CGTACTCTGCAGTAGATAAATTGGGTAGCTCATTTTGCTCGATATCTAGTTTCGAGCCAT
+CTGCTCCCATGTAGAAAAGAGCATACTTGTCGCCGACCTTTTGCACAGTCGGATTGTGGA
+TTGCCCATGAGTCCCAAGCATTTGCACCGCTGCCTTTTAGAACGACTCCTAAATCTTCGT
+AGGGGCCTTCCGGAAGATCAGCAACCGCATGGGCCACTTCGCAGGCACTTACCCAACCAG
+AAAATGTATACTCGTTTCGCCAACGTGAGTAAAAAACATGAATGCGCCCGTCGGGTCCGT
+AGATAGGCGAACAGCACCAAACATGATAGCCTTCTACTTCAAGAATTCGCCCCAGTGGTT
+TGAGTTTTTGCTCGAAGTTCGAAGTGCTTACTTCAGAGGTGATGGGACGTAGCTTCTGTA
+AATTAATGAGCGACTTATTGCTAACTGTAGAGTCCATGAAAAAAAGGTAAACTTTATACG
+AGTAATGTTATGCTCCTTAAAACTGTCAAGGTTTAGGCATTTTGCTGAGCATTATGGTGT
+TTAATGGGCTTGAATCATAACAGGATTAAGCGACATTTAAATATTAATGATAAGAATTAG
+TGATATAGCTAAAGAGTTAGGGCTTTCGAGGGTTACAGTCTCGGCTATTTTAAATGGACG
+ACACCAGAAAATAGGTATTTCCGAAAAGACCGCGCAAAGGGTTCGTTCGAGTGCAAAGGC
+TATGGGTTATCTACCCAATCAGAATGCATTGAGTATGAAGAGAGGTCGAAGCATGACTAT
+TGGTATGCTGAGTAGTGCGCTATCGGAGGAGTGGGGTGCTAAAATTCTTGTTGGTGCATT
+AAGTGCGATAAAGAACACGCCTTATTCACTGCGCGTTGAGTCAGTACAGGGAGCAGCAGA
+AGAGCGCGGTGCCCTAGAGCGCCTCTTGGGGTCACGAATTGAAGGGTTGTTGTGCTGCAA
+TATAAAT

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/sample2/mag1.fa

@@ -0,0 +1,41 @@
+>k129_4684
+TGATACCGACGCGGCACTTGAGTGCGCGCTATCCTTCAAGGAAGCCACATGCGTTATTGT
+TAAACATGCAAACCCCTGTGGTGTTGCAACTGGGTCATCATTACTTGAGGCATATGAGGG
+AGCTTACGCTACAGACCCAACATCTGCTTTTGGTGGCATTATTGCTTTTAATCGAGAATT
+AGATTCAAAAACAGCAAAGGCAGTTATTGATAGACAGTTTGTTGAGGTAATCATTGCCCC
+ATCTATATCACCCGACAGCATTAAAATTATTGCAAAAAAAGATGGTATACGTTTATTAGA
+AGCTGGTTCACGACAAGAAGACATCAAAACTCTTAACATGAAGCGAGTCAGCGGAGGTTT
+ATTACTGCAAGACAATGATATTGGGATTATTGATCGTGGTGATATAAAAATTGTTTCAAA
+CGAGGTAATTG
+>k129_5618
+GTGCTAATCGCACCCTCATGAGCGACACCATTATTCTTTATTTTTGAGTCTTCAGCAAAA
+ATAAATACAGTCAAGTCACAACTCTTAGCGTATTCAAATGCGCGTCTTAATACTTCTGTA
+TTTTCAATAGCAACATCACCATTACTTACGCCGATGCAGCCTGCAGCTTTTAATAAAAAC
+ATCTCTGTCAGTTCTTTTCCATTTAGTTCTTGTGTTAAAGCGCCAAGTGGAAAAATATTT
+GCGCGGTTAGATTCACTAGCACGCCGATTTATAAATTCCACAATGGCCGGCGTATCAATA
+GTTGGTTGTATATCAGGTGGGACACAAATTGATGTTATACCACTACGGTTTGCAGCTTTA
+AGTTCATTTTTGATAGCTATGTTTTTTTCTGAACCAATTTCGCCAAGCCTACCGCAAATA
+TCAACTAATCCAGGTAAAATTATTTTATCTTTTGCGTTTATATCCAGATCCGATTTAAAA
+>k129_5631
+TCATGATGATCCAAAAGCAGTTGCGGAAGCATCTGGGATAATTACGCGGAGTGGATGTCG
+CCGAATCGCAAGATTTACTTTTGATTATGCTATTAAAACAGGAAGAAAAAAAATTACAAT
+AGTTCATAAAGCAAATATCCTAAAAGCTCTAACAGGTCTGTTTCTAGAAACAGCAATGGA
+AATCGGCAAAGAGTATGGAAATAAACTGGAAATTGAAGAGCGAATTGTCGACAACACAGC
+AATGCAATTAGTAATCGATCCAGCGCAATTTAATATAATACTAACAACAAATATGTTCGG
+TGATATTCTCTCAGATGAGATTGCGGGTCTAATAGGCGGACTCGGGTTGGCGCCAGGGGG
+GAATATTGGTGATGATATAGCAATTTTTGAAGCGGTACACGGAACGGCTCCTGATATTGC
+TGGAAAAGGGATTGCGAATCCAACAGCACTTTACCTAGCTTCAGCAATGATGTTGGAACA
+TATAAATCAAAATAATATGGCCAATAACCTAAGGAAAGCAATTAGAGAAACATTGAAGAA
+TAAAAAAAATCGCACAATCGATCTAGGTGGCGAAGCATCCACAAAAGATTATATGTCATA
+TGTTATCGATAATTTAAACTAGAAAACAAATGAATGCACTTATACTCTTAGCACATGGAA
+GTCGAAGAAGTGAATCTAACCTCGAAGTAGAGAGTTTATCAAATGAAATTTATGCGCTGA
+TTAGCAACAAATT
+>k129_2817
+GTCGCCAATTAGCAACTATGATGTCTTCTGGAGTACCTTTGGTCCAATCATTTGAAATCA
+CAGGTCGTGGCCATGACAACCCAGGAATGCAGAGCCTAATTTTAGCCATCAAGGCTGATG
+TTGAATCTGGAAATAGTTTGGTTGATGCCCTTAGAAAACATCCATTACATTTTAACTCGC
+TTTATTGCAATTTAATTGAAGCTGGTGAACACGCCGGTATTTTAGAGGCAATTTTACACA
+AATTAGCAACATACTTAGAAAAGACAGAAGCTCTGAAATCAAAAATAAAATCGGCTTTAT
+TTTATCCAATGGCAGTTATTGTCGCAGCAATTATTGTGGTAACAATTCTGATGATATTTG
+TAATACCTCAATTTTCTGAATTATTTGGAAGTTTTGGTGCTGACTTACCGGGTTTGACAC
+AATTTTTAATAGATGCATCAGATTTCTTTGTTAGCCACTGGTGGAAATTATTTGGGTTAT

q2_types/per_sample_sequences/tests/data/mags/mags-fa-with-manifest/sample2/mag2.fa

@@ -0,0 +1,42 @@
+>k129_5401
+CCATTGTATGTCTTTAGGTAGCTCCTCATGTTTGAGGTTCATGTCTTGGATTTTGTTTTC
+TCCAAAAATCCTTTGTCCTGCATCATAAGCTTGCATTACTTCCTCATTGGATTTAGTTTT
+AGAAACAGCCACCAGTTGGACTGATGGGGGTATCTCCTTGATTATCCTAGAAATATTTTC
+TGCTATATTCATAATACAAACTTACAATTTTCACAGAGTATTTTTTAAAGAATGAATTGA
+AATTGAAGTTGAATTAAAGCATTTAAAATTTACAACATTCCATGATTTGATGTGCAAGTT
+TCAAAGCACGGGTTCCGCTTTCCAGAGGAACAATAATTGGATCATTATTTTCGATGGCAT
+CAGCAAAAACCTCTAACTCTTCCAGTATGGCGTTGGAATCTTCAATTCGTGGATTTTCAA
+AATAGATTTGTTTTTTTTCTCCCTGTGCATTTTCAAGAATCATGGCAAAGTCTTTCGGTT
+TTTTTGGAGCTTTTTTCATTTTTACTACCTCGACTTTTTTCTCTAGAAAATCTACTGCGA
+TATAAGTGTTTTTCTGGAAAAAGCGCGTTTTACGCATTTTTTTTAGTGAAATCCTGCTTG
+CGGTAAGGTTGGCAACACAGCCGTTTTCAAACTCAATTCTTGCGTTAGTTATATCGGGGG
+TGGAGCTTATTACCGCCACCCCAGAAGCGGATACGGATTTTACTTTGGCATCGACAACAC
+TCAACAATACATCAATATCGTGAATCATCAAATCTAAAACCACTGGAACATCGGTTCCTC
+TTGGATTGAATTCTGCCAAACGATGGGACTCTATAAATTTTGGGTGGGTAATCGATGATT
+TTACCGCCTTAAAAGCCGGATTAAAACGTTCTACGTGTCCCACCTGACCAAGAACCATTT
+TTTTTGTAGCCATTTCGGTAATTTCAAGGGCTTCGGTAACATTATTGGCAATAGGCTTTT
+CTATAAATATATGCTTTCCTTTTTGGATTGCATTTATGGCATTTTTATGGTGGAAAAATG
+TAGGAGTGACAATATCTACCATATCGCAAGCTTGGATCAAATCGGCTTCACTTTTAAAAG
+CGGTATAGCCATTTTCTTTAGCTAAGGCCTTGGTGTTTTTTTTATCCTGATCATAAAACC
+CCACTAATTGGTATCGTTTAGAGGCCTCTAGTAAACGCAGATGAATTTTACCCAAATGTC
+CTGCACCCAAGACGCCGACTTTTATCATAGCACTTAATTTTTAATCAAAAATACCATCTT
+TTTCTGATTTTTTTTTGGAAGTAATTACATTTGTCCTCATGATTGATTCAACCAAGCATC
+AAGGACAAAGAAGACAGTTGGTAAAATTGTTAGAGGAGAAAGGAGTCTACGACAAAAGGG
+TTTTGAATGCTGTTGGAAGTGTTCCCCGTCATCTGTTTATGGATTCGGGTTTGGAGGAGT
+ATTCCTATATTGACAAAGCCTATCCCATTGCGGCTAATCAGACCATATCACAGCCTTACA
+CCGTAGCTTTTCAGACCCAATTGCTGGAACTTCAGAAAGGGGATCGAGTTTTGGAAATCG
+GAACGGGTTCGGGCTATCAAACAGCTATTTTAATCGCCCTTGAAGGTCTAAAAGTGTATA
+CCATTGAACGCCAACTGGAGTTATATAAAACAACTGTTTTGTTATTTAAAAAGTTGGGGT
+TAAATCCCAAAAAAGTGATATTTGGTGATGGTTACCAAGGTTTACCAGATCAAGCACCTT
+TTGATGCCATCATCGTTACTGCAGGTGCGCCTCAAGTACCCAAACCTTTGTTGGAACAAT
+TGACCATTGGAGGGAGACTCGTAATCCCTGTGGGAGAGAAAGACCAAGTCATGACCCGAT
+ATATGCGAACAGGGGAAAAGACCTTTGATCGACAAACCTTTGGGAATTTCAGATTTGTCC
+CTTTGCTAAAGGATGAGAGATAGAGCTTGTTAAGTACTTCGTGAATATCGGATTTTCCTT
+ACTGAATTTATAGCTCTTGACAATATCAATTGTTTGAAGATGGAAGGTGAAGTATACTTC
+AGGCTTCGTAGCTGATAAGAATATTCACTCTTCGATTTTATAAATTTTGTTAAAAAATTG
+CTCTACGTCGGTAGTTTTTTGGATTGATTAGAGCAGGTTTACTGTGTGTTGTAAAATTTT
+TATAATCTTTAATTTGAGGTTGTTCACTATAATTTGGTGAGAAAAACTATTTATTGAAAT
+TTTTTTTAATCCTATCTAAATCCCTTTTATTGTCTAAATCTTTAAGGGCTTCTCTTTTAT
+CGTAAAGTTTTTTCCCCCGAGCTAAAGCGATCAACATTTTGGCAAAACCTTTTTCGTTGA
+TGAAAAGCTTAAGTGGTACAATGGTCAAGCCGGAATTTTTCACCTGTTTGAAAAGTTTGT
+TTAATTCTCTTTTTTTAA