Merge pull request #69 from colinvwood/classify-contigs

Classify contigs

q2_moshpit/kraken2/classification.py

@@ -20,6 +20,7 @@
 from q2_moshpit._utils import run_command, _process_common_input_params
 from q2_moshpit.kraken2.utils import _process_kraken2_arg
 from q2_types_genomics.feature_data import MAGSequencesDirFmt
+from q2_types_genomics.per_sample_data import ContigSequencesDirFmt
 from q2_types_genomics.kraken2 import (
     Kraken2ReportDirectoryFormat,
     Kraken2OutputDirectoryFormat,
@@ -50,7 +51,7 @@ def _construct_output_paths(
 def _classify_kraken2(
         seqs, common_args
 ) -> (Kraken2ReportDirectoryFormat, Kraken2OutputDirectoryFormat):
-    if isinstance(seqs, MAGSequencesDirFmt):
+    if isinstance(seqs, (MAGSequencesDirFmt, ContigSequencesDirFmt)):
         manifest = None
     else:
         manifest: Optional[pd.DataFrame] = seqs.manifest.view(pd.DataFrame)
@@ -68,16 +69,24 @@ def get_paths_for_reads(index, row):
     def get_paths_for_mags(mag_id, fp):
         return mag_id, [fp]
 
+    def get_paths_for_contigs(contig_id, fp):
+        # HACK: remove after adding manifest or other solution, see
+        # https://github.com/bokulich-lab/q2-types-genomics/issues/56
+        return contig_id.rstrip('_contigs'), [fp]
+
     try:
         if manifest is not None:  # we got reads - use the manifest
             iterate_over = manifest.iterrows()
             path_function = get_paths_for_reads
-        else:  # we got MAGs - use the filenames directly
+        else:
             iterate_over = (
                 (os.path.basename(fp).split(".")[0], fp)
                 for fp in sorted(glob.glob(os.path.join(seqs.path, "*.fasta")))
             )
-            path_function = get_paths_for_mags
+            if type(seqs) is MAGSequencesDirFmt:
+                path_function = get_paths_for_mags
+            elif type(seqs) is ContigSequencesDirFmt:
+                path_function = get_paths_for_contigs
 
         for args in iterate_over:
             _sample, fn = path_function(*args)
@@ -103,6 +112,7 @@ def classify_kraken2(
         seqs: Union[
             SingleLanePerSamplePairedEndFastqDirFmt,
             SingleLanePerSampleSingleEndFastqDirFmt,
+            ContigSequencesDirFmt,
             MAGSequencesDirFmt,
         ],
         kraken2_db: Kraken2DBDirectoryFormat,

q2_moshpit/kraken2/select.py

@@ -137,7 +137,7 @@ def _kraken_to_ncbi_tree(df):
     for _, row in df.iterrows():
         r = row['rank']
         label = row['name']
-        otu = str(row['ncbi_tax_id'])
+        otu = str(row['taxon_id'])
 
         if r in ('U', 'R'):
             continue  # unclassified or root
@@ -174,7 +174,6 @@ def _kraken_to_ncbi_tree(df):
     if parent_node.children:
         parent_node.children[0].is_actual_tip = True
 
-    print(tree)
     return tree
 
 

q2_moshpit/kraken2/tests/data/contigs/README.md

@@ -0,0 +1,8 @@
+## samples/
+simulated contigs taken from reference genomes from refseq for each of the 
+species Bacillus anthracis, Mus musculus, Staphylococcus aureus, and
+Staphylococcus epidermidis
+
+## small-kraken2-db/
+kraken2 database created using ~20k nt of each of the above mentioned genomes,
+the ncbi taxonomy, and all default paramters (kraken2 version 2.1.3)

q2_moshpit/kraken2/tests/data/contigs/samples/ba_contigs.fasta

@@ -0,0 +1,40 @@
+>contig0
+TCGGGAAAGTAGTAGAAGAAGTTCAATGTGAAAAAGTAGATGGAGAAGAGTTAAAAATATCTTTTAGTGCAAAATATATGATGGATGCACTAAAGGCATTAGATAGTACTGAAATTAAGATTAGCTTTACTGGAGCAATGAGACCATTCTTAATTCGTACGGTAAATGATGAATCCATTATTCAATTAATTTTACCGGTTCGTACTTACTAAGTAAGAAATAAGGGTTGCTAGTTTTCAGATGCTAGTAGCCCTTATTTGATTTTTGGGTATTACTTTCCTAATGCTAGTTTATTTAGTACAATGAAAGAATGA
+>contig1
+TCGTTATATGCGTCAAATTATTGAACATGGTTATATCTATATTGCACAGCCACCGTTGTTTAAAGTACAACAAGGTAAAAAAATTCAATATGCTTATAATGAGAAAGAGCTTGAAAAGATTTTAGCTGAATTACCAGCTCAACCTAAACCTGGAATCCAACGTTACAAAGGTTTAGGAGAAATGAATCCAACTCAGCTTTGGGAAACAACAATGGACCCAGAAGTACGTTCATTACT
+>contig2
+AAAGTGGCGTTATTTCAGACCCATTCTTTTTAACTCCAGAACATCAAGTGTATGATGCAGAGCATCTTATGGGAAAATACCGTATCTCAGGTGTACCGGTTGTAAATAATTTAGATGAGCGAAAATTAGTTGGTATTATTACAAACCGTGATATGCGTTTTATCCAAGACTACTCAATCAAAATTTCCGACGTAATGACAAAAGAACAGCTAATTACAGCTCCAGTTGGTACAACGCTAAGTGAAGCTGAAAAGATCCTACAAAAGTATAAAATTGAAAAACTCCCTCTTGTTGATAACAACGGTGTATTACAAGGGCTTATTACAATAAAAGATATTGAAAAAGTAATTGAATTCCCAAATTCTGCGAAGGATAAGCAAGGGCGCTTATTAGTTGGAGCAGCAGTTGGTGTAACGGCTGATGCTATGACTCGTATCGACGCATTAGTAAAAGCTAGCGTAGATGCAATCGTACTTGATACAGCTCACGGACATTCTCAAGGTGTTATTGATAAAGTAAAAGAAGTTCGTGCAAAGTATCCATCATTAAATATTATCGCTGGAAATGTTGCTACTGCTGAAGCAACAAAAGCATTAATTGAAGCAGGTGCAAACGTAGTTAAAGTTGGTATTGGACCAGGTTCTATCTGTACAACACGTGTTGTAGCCGGCGTTGGTGTACCACAATTAACAGCGGTTTATGATTGTGCAACAGAAGCTCGTAAACACGGTATTCCAGTTATTGCTGATGGTGG
+>contig3
+TTACACTAGGGCAATTTTTAAAGTTAGCCGATGTAATTGATACAGGTGGCGCTGTAAAATGGTTTTTACAAGAATATGAAGTGTACGTGAATCAAGAACTTGAAAATAGAAGAGGGCGCAAGCTATATGCGAACGATATTATTGAAATTCCAGGAAGCGGAAGTTTCCAAGTTCAGTCATAAAGGGGGAGCCCTTTGTTTATTTCAGAAATACAATTAAAAAACTATCGCAATTATGAAAAATTAGAGCTTTCCTTTGAAGATAAAGTAAATGTAATTATCGGCGAGAACGCGCAAGGGAAAACGAATTTGATGGAAGCTATTTATGTTTTGGCGATGGCGAAATCTCATAGAACCTCTAATGATCGTGAGCTTATCCGTTGGGATGAAGATTTCGGTCAAATTAAAGGAAAGTTACAAAAGAGAAATAGTT
+>contig4
+TTTTCCGTTTACGAGTCGTAACACCATGAGCTAAAACAGTAGTGGATTCAGGATAGTTCGGATCAATAGTTAATAAGCACGCTTTAAAAAGTTGGCTTATTCCATAAAACAATAACATTGGTTGAATTGAAAAGGGAGCTACCTTATATAATTCGTAATAATTTTTCCCATGTTCTAAGTAATAAATAAAGGGATAACAATTTTCGAAACTTTTTTTCAGCATCTTGTATGGAGGATTTTTCATAACAACGGGCAAGATAACGTTGTACATTTTGAGATGAAAAGAAGAAACTTAATTGCTGCCAAGTACAATGTGTTTGATGCATATATTACGCTCCTTTTATTGTCTAAAAATTCTAACATATAAATACGTCCTTGACAGTATTTTAACCAATTGATAAGCTACTAATAATAATTTCTGGTATCATGGGG
+>contig5
+TGTGGCATTAGAAAATGGTGGTTCTTATACGGTAAAAGAGTTGTACGAGGCAATGGCAATCTTCTCTGCAAACGGTGCAACGATTGCATTAGCAGAAGCAATTGCAGGTAAAGAAGTAGATTTCGTAAAAATGATGAATGATAAATCGAAAGAGCTAGGGTTGAAAAATTATAAATTTGTCAATTCTACAGGTTTAACGAATAAGGATTTAAAGGGAATGCATCCAGAAGGAACAACAGCAGATGAAGAAAATAAAATGTCTGCAAAGGATGTTGCAACTTTAGCACAACATTTAATTAAAGATTATCCGAAAGTGTTAGATACAGCAAAAATCCCGAAAAAAGAATTCCGTCCAGAAAAAGAGAAGTTTGCAATGTCGAACTGGAACTGGATGTTAAAAGGTTTAGTTAAAGAATATGATGGCGTAGATGGCCTAAAAACAGGTTCAACTCCAGAAGCAGGAGATTGCTTCACTGGTACGGTTGAAAGAAACGGTATGCGTTTTATTTCTGTAGTAATTAAAACAAGTTCTCATACAGCACGTTTTGATGAAACAAAGAAGCTATATGATTATGGATTTGCTAACTTTGAAATGAAACAAATGTATAAAAAAGGTTCTTCAGTAAAAGGACAAGAAACAGTACGAGTAGAAAATGCGAAAGATAAGGATGTAGCAGTTCAAACGAAACAAGCCATTTCACTTCCAGTACCAAAAGGAAGTAAAGAAGTTTATAAAACAGAATTAAAAGAATCAAGTAAAGGACAAGAAGCAC
+>contig6
+GGAACACGTGAAATTCCGTCGGAATCTGGGAGGACCATCTCCCAAGGCTAAATACTCCCTAGTGATCGATAGTGAACCAGTACCGTGAGGGAAAGGTGAAAAGCACCCCGGAAGGGGAGTGAAAGAGATCCTGAAACCGTGTGCCTACAAATAGTCAGAGCCCGTTAACGGGTGATGGCGTGCCTTTTGTAGAATGAACCGGCGAGTTACGATCCCGTGCGAGGTTAAGCTGAAGAGGCGGAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGTTTAGTACGTGGTCGTAGACCCGAAACCAGGTGATCTACCCATGTCCAGGGTGAAGTTCAGGTAACACTGAATGGAGGCCCGAACCCACGCACGTTGAAAAGTGCGGGGATGAGGTGTGGGTAGCGGAGAAATTCCAATCGAACCTGGAGATAGCTGGTTCTCCCCGAAATAGCTTTAGGGCTAGCCTTAAGTGTAAGAGTCTTGGAGGTAGAGCACTGATTGGACTAGGGGTCCTCATCGGATTACCGAATTCAGTCAAACTCCGAATGCCAATGACTTATCCTTAGG
+>contig7
+TCTTGACATCCTCTGACAACCCTAGAGATAGGGCTTCTCCTTCGGGAGCAGAGTGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGATCTTAGTTGCCATCATTTAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACGGTACAAAGAGCTGCAAGACCGCGAGGTGGAGCTAATCTCATAAAACCGTTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGAGAGTTTGTAACACCCGAAGTCGGTGGGGTAACCTTTTTGGAGCCAGCCGCCTAAGGTGGGACAGATGATTGGGGTGAAGTCGTAACAAGGTAGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTCTATGGAGAATTGATGAACGCTGTTCATCAATATAAGTTTCCGTGTTTCGTTTTCGTTTAGTTTTGAGAGTTCAATAAAAAGTATTGACTCTTAAATGAGGATATGATAT
+>contig8
+AGCAATTACCTATAAGATATGCTGCATTTAGCTCTTGTTTCCGTTCTGAAGCAGGTTCAGCTGGCCGTGATACACGTGGTTTAATTCGTCAGCATCAGTTCAATAAAGTAGAGCTTGTAAAGTTCGTAAAACCAGAAGATTCTTACGAAGAGTTAGAAAAACTAACAAATGATGCAGAACGCGTGTTACAATTATTAGAGTTGCCATATCGCGTTATGAGCATGTGCACAGGCGATTTAGGATTTACAGCAGCGAAGAAATACGATATCGAAGTATGGATTCCAAGCTATGGCACATATCGTGAAATCTCTTCTTGTAGTAATTTCGAGGCTTTCCAAGCGAGACGTGCAAATATCCGTTTCCGTCGTGAGCCAAACGGCAAACCAGAACATGTTCATACATTAAATGGATCTGGTCTTGCAATTGGACGTACGGTAGCAGCTATTTTAGAGAACTACCAACAAGAAGATGGTACAATTATAATTCCAGAAGTTCTTCGCCCTTATATGGGAGGAAAAACAGTTATTAAGTAAATTTATAAACATTCATCGGTATGAGTGATTGGTAATTATGAGCGTTGTCAGTACTATAATGTAGGAGGGGAAAAGTAAAATTTTCCTTTCCTCATAATTTATTTTAGTAGGGTTGACTAACTGTTTTTCTTTTGATATTATATTTGATGTCAATATGGAGGTATACCCAAGTCTGGCTGAAGGGATCGGTCTTGAAAA
+>contig9
+CTAAGGTGTGCGAGAGAACTCTGGTTAAGGAACTCGGCAAAATGACCCCGTAACTTCGGGAGAAGGGGTGCTTTCTTAACGGAAAGCCGCAGTGAATAGGCCCAAGCGACTGTTTAGCAAAAACACAGCTCTCTGCGAAGCCGTAAGGCGAAGTATAGGGGGTGACACCTGCCCGGTGCTGGAAGGTTAAGGAGAGGGGTTAGCGTAAGCGAAGCTCTGAACTGAAGCCCCAGTAAACGGCGGCCGTAACTATAACGGTCCTAAGGTAGCGAAATTCCTTGTCGGGTAAGTTCCGACCCGCACG
+>contig10
+TTGGTGAAGTAATCGGTAAGTATCACCCTCATGGTGATTCAGCTGTTTATGAAACGATGGTACGTATGGCGCAAGATTTCAGTCAACGTTATATGCTTGTTGATGGGCATGGTAACTTTGGATCTGTCGATGGAGATTCAGCGGCAGCAATGCGTTATACAGAAGCAAGAATGTCTAAAATCTCTATGGAATTAATACGTGATATTTCAAAAAATACAATTGATTATCAAGATAACTATGATGGTTCTGAAAGAGAGCCGATTGTGTTACCAGCGCGTTTTCCTAACTTACTAGTAAATGGTACGACAGGTATTGCAGTTGGTATGGCAACAAATATTCCGCCGCATCAACTTGGTGAAGTAATTGATGGCGTATTGGCATTAAGTCATAATCCCGATATTACTATTGCAGAATTAATGGAGTGCATTCCAGGACCAGATTTTCCGACGGCAGGTTTAATTTTAGGAAGAAGTGGTATTCGTAGAGCTTATGAAACAGGACGCGGGTCTATTATACTTCGTGCTAAAGTTGAAATTGAAGAGAAGTCAAATGGCAAACAATCTATTATCGTAACGGAATTACCTTATCAAGTGAATAAGGCGCGATTGATTGAAAAAATTGCAGAATTAGTTCGCGATAAGAAAATTGAAGGTATTACAGATTTACGTGATGAATCAGATCGAAATGGTATGCGTATTGTTATGGAAGTACGTCGTGATGCCAATGCTAATGTATTATTAAATAACTTATATAAACATACAGCACTTCAAACAAGTTTTGGTATTAACATGCTGTCTCTTGTAAATGGAGAACCACAAGTACTGAATTTAAAACAAAATTTATATCATTACTTGGAACATCAAAAGGTAGTAATTCGTAGACGTACTGCTTATGAACTTGAAAAGGCAGAAGCACGTGCTCATATCTTAGAAGGATTACGAAT
+>contig11
+GGTTGTAAACTTTGCAGCAGGTGGTGTAGCAACACCAGCAGATGCAGCGTTAATGATGCAATTAGGTGCGGATGGTGTATTTGTTGGATCTGGTATCTTTAAATCAGAGAACCCAGCGAAATTTGCACGTGCAATCGTTGAAGCAACAACTCATTATGAAGATTACGAACTAATTGCAAGCCTTTCAAAAGGATTAGGTAATGCGATGAAGGGTATCGAAATTTCAACGTTATTACCAGAACAACGCATGCAAGAGCGTGGATGGTAATTGAAGGAGAACTTTAAAATGGTGAAAATTGGTGTACTAGGTCTTCAAGGTGCAGTTCGTGAACATGTAAAATCAGTTGAAGCAAGTGGTGCAGAAGCTGTTGTTGTAAAGCGTATAGAACAACTTGAAGAGATTGATGGTCTTATTTTACCAGGCGGTGAAAGTACAACTATGCGCCGTCTTATTGATAAGTATGATTTCATGGAACCACTTCGTACATTCGC
+>contig12
+ATCTTTGTGTCAATGGAACAAAAGCAAATGCAAGAAAATTCATATGATGAAAGTCAAATACAGGTACTTGAAGGACTAGAAGCAGTTCGAAAACGCCCTGGTATGTATATTGGATCTACAAGTGGAAAAGGACTTCACCATCTTGTATGGGAAATCGTTGATAATAGTATCGATGAAGCACTTGCAGGGTACTGTGACGAAATTAACGTTAGTATCGAAGAAGATAATAGTATTCGTGTAACAGATAATGGACGTGGTATTCCAGTTGGTATACAAGAAAAAATGGGACGTCCTGCTGTAGAAGTTATTATGACCGTTCTTCATGCTGGTGGTAAGTTTGGCGGCGGCGGTTATAAAGTTTCTGGTGGTTTGCATGGTGTTGGGGCATCTGTAGTAAATGCTCTATCAACAGAACTAGAGGTATTTGT
+>contig13
+CTATTTTTTATCTTTATTAATTAAATAAAATCTTATACTTACCGGAGGTTCTTCTTTATGCGTTTTTCAATTCAAAAAGACTATCTTGTAAGAAGTGTACAAGATGTAATGAAGGCTGTTTCTTTTCGTACAACAATTCCGATCCTTACAGGAATTAAAGTTGTCGCTACGGAAGAAGGAGTTACATTAACAGGAAGCGATGCTGATATTTCGATTGAATCTTTTATCCCAGTTGAAGAGGATGGAAAAGAAATTGTAGAAGTAAAACAATCAGGAAGTATTGTTTTACAGGCTAAATATTTTAGTGAAATTGTAAAAAAATTGCCGAAAGAAACTGTAGAAATTTCTGTCGAAAATCATTTAATGACAAAAATAACTTCTGGGAAATCAGAATTTAATTTAAATGGTTTAGATTCTGCAGAATATCCATTGTTACCACAAATTGAAGAACATCATGTTTTTAAGATTCCAACAGATTTACTTAAACATATGATCAGACAAACTGTATTTGCAGTCTCCACTTCTGAAACAAGACCAATCTTGACAGGTGTAAACTGGAAGGTATATAACAGCGAACTAACTTGTATTGCTACAGATAGTCACAGGTTAGCTCTTCGAAAAGCAAAAATTGAAGGTATTGTAGATGAATTCCAGGCAAATGTTGTTATTCC
+>contig14
+TAATTACGCCAAAAGATACAAACGACCCTGGATTTTTAACTGGTAAGTCGTTGCAAGTGGATCTTGTAACAACATCTGAAGTAGAAGAAGCAAACTGGTTTACTCGTGCTATGCGCGGAATTGGTTCTTTCTTTAGTGGTATATGGAATAGTGCTGTTGATACAGTAAAAGGTTGGTTTTAAAAGCTCCTCATTGTAGGGGCTTTTTCTTATTCCTATTTTTCATACCGACTTTATGAAAAAGTAGTAGACAAGCATCTGATAGTTAGTGGTAGAATGTAAGAGTATTCTTAATTTTCGCCTTTAACGGGGAAAAGCAATTCACCTAGGGGGGGTTTTGTAACATGACAAATGTAACAGGGACAGAACGTGTAAAACGTGGAATGGCAGAAATGCAAAAAGGCGGCGTTATTATGGACGTAATTAACGCTGAACAAGCAAAAATTGCAGAAGAGGCAGGCGCAGTTGCCATTATGGCATTAGAGCGCGTACCAGCAGATATTCGTGCAGCAGGTGGCGTTTCTCGTATGGCAGATCCAACAATCGTTGAAGAAGTTATGGGTGCTGTGTCAATTCCGGTTATGGCAAAATGCCGTATCGGTCACCTTGTAGAAGCACGTGTATTAGAATCATTAGGGGT
+>contig15
+TTCTGCTAGTAAAAAAGACGAAATGTAGTAAGGAACTTTTTGAGCAGAAATAGTAAGGAATTGATAAATAAAGGGGTAATCTTCAGATCCATAGCTTCCAAGTAAATCATACCACCAATCTGTTTCGTATCTAGAAATCATACTTAAATTGTAGAGCAATAAATAATGAACAAGAAGTTCAGGTAATGCGGGTTTAGGATTTCTAGGGTCAGTTGTAAGTGGTAAGTAATAAGTATCAGCAAGATATTCGTAGTATAAAGGCGTACTATATA
+>contig16
+AAACCAGATCCAGAAATTTTTCAGGAAACAACAGTATACGAATTTGATACACTAGCAACTCGTATGCGTGAATTAGCATTTTTAAATCGTAATATTAAACTGACGATTGAAGATAAACGTGAACATAAGCAAAAAAAAGAATTCCATTATGAAGGTGGAATTAAATCATATGTTGAGCATTTAAACCGCTCAAAACAACCAATCCATGAAGAGCCTGTATATGTAGAAGGATCAAAAGATGGTATTCAAGTTGAAGTTTCCTTACAGTATAACGAAGGATATACAAATAATATTTACTCATTTACGAACAACATTCACACGTATGAAGGTGGAACACATGAAGTAGGGTTTAAAACAGCTTTAACTCGTGTGATTAACGATTATGGGCGTAAAAATAGTATTCTAAAAGATGCAGACAGTAATTTAACTGGTGAGGACGTTCGTGAAGGTTTAAC
+>contig17
+CTTGCTCTTATGAAGTTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCATAAGACTGGGATAACTCCGGGAAACCGGGGCTAATACCGGATAACATTTTGAACCGCATGGTTCGAAATTGAAAGGCGGCTTCGGCTGTCACTTATGGATGGACCCGCGTCGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCAT
+>contig18
+GCTAGCTTCGGTGGAGGCGCTGGTGGGATACCGCCCTGACTGTATTGAAATTCTAACCTACGGGTCTTATCGACCCGGGAGACAGTGTCAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAGTGTAACGGAGGCGCCCAAAGGTTCCCTCAGAATGGTTGGAAATCATTCGTAGAGTGCAAAGGCATAAGGGAGCTTGACTGCGAGACCTACAAGTCGAGCAGGGACGAAAGTCGGGCTTAGTGATCCGGTGGTTCCGCATGGAAGGGCCATCGCTCAACGGATAAAAGCTACCCCGGGGATAACAGGCTTATCTCCCCCAAGAGTCCACATCGACGGGGAGGTTTGGCACCTCGATGTCGGCTCATCGCATCCTGGGGCTGTAGTCGGTCCCAAGGGTTGGGCTGTTCGCCCATTAAAGCGGTACGCGAGCTGGGTTCAGAACGTCGTGAGACAGTTCGGTCCCTATCCGTCGTGGGCGTAGGAAATTTGAGAGGAGCTGTCCTTAGTACGAGAGGACCGGGATGGACGCACCGCTGGTGTACCAGTTGTTCTGCCAAGGGCATAGCTGGGTAGCTATGTGCGGAAGGGATAAGTGCTGAAAGCATCTAAGCATGAAGCCCCCCTCAAGATGAGATTTCCCATAGCGTAAGCTAGTAAGATCCCTGAAAGATGATCAGGTTGATAGGTTCGAGGTGGAAGCATGGTGACATGTGGAGCTGACGAATACTAATAGATCGAGGACTTAACCATATAATATGTAGCAATGTTATCTAGTTTTGAAGGAATATGCCTTCATAGTTTGGTGATGATGGCAGAGAGGTCACACCCGTTCCCATACCGAACACGGAAGTTAAGCTCTCTAGCGCCGATGGTAGTTGGGACCTTGTCCCTGTGAGAGTAGGACGTCGCCAAGCAACTAAAAACACAAGTC
+>contig19
+CGGTAAAGCAAGGGCCGTTTTTAGCTGCTTCTTTCCATCCAGAATTAACGGATGATCATCGTGTAACAGCATACTTTGTAGAAATGGTAAAAGAAGCGAAAATGAAAAAAGTTGTATAAGTAACTTGCAACTTGTATAAGATTATAGTAAATTGATGGTAACAATTTTATAAAATAAGCGTGTTGATAGGAAGTAGTAACAAATGTCGTTTCTTATAGAGAGTCGATGGTTGGTGGAAATCGATAGAAACAGTTTGTGAATCCATCCTGGAATGGAATGTGGAATATCTTTATGATTAGTAAACATTCCCGGTGAAGAGCCGTTATTTCTACTTGAGAGGAAGGCGGTAATGCTTTCAACTAGG