Fix the HMMER coordinate output; increment version

dib-lab · Dec 16, 2015 · bfacd28 · bfacd28
1 parent 51c0f9f
commit bfacd28
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Showing 10 changed files with 63 additions and 21 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,10 @@
+2015-12-15  Camille Scott  <[email protected]>
+
+	* Remap hmmscan coordinates with respect to the
+	  original transcripts.
+	* Update test data.
+	* Increment version 0.2.3.
+
 2015-12-10  Camille Scott  <[email protected]>
 
 	* Fix error with output directory creation.

diff --git a/dammit/VERSION b/dammit/VERSION
@@ -1 +1 @@
-0.2.2
+0.2.3
diff --git a/dammit/annotate.py b/dammit/annotate.py
@@ -17,6 +17,7 @@
                    get_transdecoder_predict_task, \
                    get_transdecoder_orf_task, \
                    get_hmmscan_task, \
+                   get_remap_hmmer_task, \
                    get_cmscan_task, \
                    get_lastal_task, \
                    get_crb_blast_task, \
@@ -75,19 +76,20 @@ def _init_filenames(self):
         self.transdecoder_dir = '{0}.transdecoder_dir'.format(self.transcriptome_fn)
         self.transdecoder_orf_fn = os.path.join(self.transdecoder_dir,
                                                 'longest_orfs.pep')
+        self.transdecoder_orf_gff3_fn = os.path.join(self.transdecoder_dir,
+                                                     'longest_orfs.gff3')
         self.transdecoder_pfam_fn = '{0}.pfam.tbl'.format(self.transdecoder_orf_fn)
         self.transdecoder_pep_fn = '{0}.transdecoder.pep'.format(self.transcriptome_fn)
         self.transdecoder_gff3_fn = '{0}.transdecoder.gff3'.format(self.transcriptome_fn)
 
-        self.pfam_fn = '{0}.pfam.tbl'.format(self.transcriptome_fn)
+        self.pfam_fn = '{0}.pfam.csv'.format(self.transcriptome_fn)
         self.rfam_fn = '{0}.rfam.tbl'.format(self.transcriptome_fn)
 
         self.orthodb_fn = '{0}.x.orthodb.maf'.format(self.transcriptome_fn)
 
         self.user_pep_fn_dict = {}
 
 
-
     def handle(self):
 
         common.print_header('Running annotate!', level=2)
@@ -177,6 +179,10 @@ def transdecoder_tasks(self):
                                self.args.n_threads, 
                                common.CONFIG['settings']['hmmer']['hmmscan'])
 
+        yield get_remap_hmmer_task(self.transdecoder_pfam_fn,
+                                   self.transdecoder_orf_gff3_fn,
+                                   self.pfam_fn)
+
         predict_cfg = common.CONFIG['settings']['transdecoder']['predict']
         yield get_transdecoder_predict_task(self.transcriptome_fn, 
                                             self.transdecoder_pfam_fn,

diff --git a/dammit/gff.py b/dammit/gff.py
@@ -126,9 +126,8 @@ def hmmscan_to_gff3_df(hmmscan_df, tag, database=''):
     gff3_df['source'] = ['HMMER'] * len(hmmscan_df)
     gff3_df['type'] = ['protein_hmm_match'] * len(hmmscan_df)
 
-    # This is kludgy and quite wrong
     gff3_df['start'] = hmmscan_df['env_coord_from']
-    gff3_df['end'] = hmmscan_df['env_coord_to'] * 3
+    gff3_df['end'] = hmmscan_df['env_coord_to']
 
     # Confirm whether this is the appropriate value to use
     gff3_df['score'] = hmmscan_df['domain_i_evalue']

diff --git a/dammit/report.py b/dammit/report.py
@@ -31,9 +31,9 @@ def get_report_tasks(transcriptome, annotator, databases, n_threads=1):
     )
     outputs.append(orthodb_gff3)
 
-    pfam_gff3 = annotator.transdecoder_pfam_fn + '.gff3'
+    pfam_gff3 = annotator.pfam_fn + '.gff3'
     tasks.append(
-        get_hmmscan_gff3_task(annotator.transdecoder_pfam_fn,
+        get_hmmscan_gff3_task(annotator.pfam_fn,
                               pfam_gff3, 
                               'Pfam')
     )

diff --git a/dammit/tasks.py b/dammit/tasks.py
@@ -451,6 +451,35 @@ def get_transdecoder_orf_task(input_filename, transdecoder_cfg):
             'clean': [(clean_folder, [input_filename + '.transdecoder_dir'])]}
 
 
+@create_task_object
+def get_remap_hmmer_task(hmmer_filename, remap_gff_filename, output_filename):
+
+    name = 'remap_hmmer:{0}'.format(os.path.basename(hmmer_filename))
+
+    def cmd():
+        gff_df = pd.concat([group for group in
+                            parsers.parse_gff3(remap_gff_filename)])
+        hmmer_df = pd.concat([group for group in
+                              parsers.hmmscan_to_df_iter(hmmer_filename)])
+
+        merged_df = pd.merge(hmmer_df, gff_df, left_on='full_query_name', right_on='ID')
+
+        hmmer_df['env_coord_from'] = (merged_df.start + \
+                                      (3 * merged_df.env_coord_from)).astype(int)
+        hmmer_df['env_coord_to'] = (merged_df.start + \
+                                    (3 * merged_df.env_coord_to)).astype(int)
+        assert(all(hmmer_df.env_coord_to <= merged_df.end))
+
+        hmmer_df.to_csv(output_filename, header=True, index=False)
+
+    return {'name': name,
+            'title': title_with_actions,
+            'actions': [cmd],
+            'file_dep': [hmmer_filename, remap_gff_filename],
+            'targets': [output_filename],
+            'clean': [clean_targets]}
+
+
 # TransDecoder.Predict -t lamp10.fasta --retain_pfam_hits lamp10.fasta.pfam-A.out
 @create_task_object
 def get_transdecoder_predict_task(input_filename, db_filename, transdecoder_cfg):
@@ -528,7 +557,8 @@ def get_hmmscan_gff3_task(input_filename, output_filename, database):
 
     def cmd():
         with open(output_filename, 'a') as fp:
-            for group in parsers.hmmscan_to_df_iter(input_filename):
+            for group in pd.read_csv(input_filename, chunksize=10000):
+                print(group.head())
                 gff_group = gff.hmmscan_to_gff3_df(group, 'dammit.hmmscan',
                                                    database)
                 gff.write_gff3_df(gff_group, fp)

diff --git a/dammit/tests/test-data/pom.single.fa.dammit.fasta.evalue10 b/dammit/tests/test-data/pom.single.fa.dammit.fasta.evalue10
@@ -1,2 +1,2 @@
->Transcript_0 len=5662 CDS=1-5662 RNA_matches=SPRY4-IT1_2:3799-3913,ceN69:4609-4666,SNORD75:4992-4926,mir-598:5160-5256,CRISPR-DR63:5504-5473 exon=1-5663 gene=1-5663 mRNA=1-5663 hmm_matches=DEAD:1194-4093,Helicase_C:1396-4549,Helicase_C:1735-5308,zf-CCHC:1804-5464,zf-CCHC:20-76,Poxvirus_B22R_N:248-871,Poxvirus_B22R_N:349-1228,Poxvirus_B22R_N:803-2515 three_prime_UTR=5662-5663 homologies=TLH2_SCHPO:1-5663
+>Transcript_0 len=5662 CDS=1-5662 RNA_matches=SPRY4-IT1_2:3799-3913,ceN69:4609-4666,SNORD75:4992-4926,mir-598:5160-5256,CRISPR-DR63:5504-5473 exon=1-5663 gene=1-5663 mRNA=1-5663 hmm_matches=Poxvirus_B22R_N:1048-1229,Poxvirus_B22R_N:2410-2516,DEAD:3583-4094,Helicase_C:4189-4550,Helicase_C:5206-5309,zf-CCHC:5413-5465,zf-CCHC:61-77,Poxvirus_B22R_N:745-872 three_prime_UTR=5662-5663 homologies=TLH2_SCHPO:1-5663
 ATGGTCGTCGCTTCAGAAATTGCTAAAGTCGCTTCAAAAACTGCTAGAGATATCGCCGGATGCTTTACTTGTCAATGTGGAACTCAATTTGATAATGTAGAAAGGATCGTTCAACATTTCAAGGAATGTCGATACAGAGACGAAACTTGTAAAGACGATGATATCGTCGTCTATGAACCCAGCTCTTTCGTTCAGGACGAGAAAAAGGATAAGCCAATCATCGTTGAGGCTGCCAGTGAGGCTACCAGTGAGGAGGCTTGCAATTCTTCCAAGGAGCGTCAACTACCCGCTCTCTCTGCTCTCTCTGCTCTCTCTACTCTCACTACGAGTGCAAATGACGACTTGTGGACTGCACGGCTAATTTGGCAAAGTACAAATGACACCAAATTGGACAACAGCCCATCATCAAATTATACTGACTTGAATCACAAGTTGGCTAATTATGGACTCTCCATTTTGTCTATTCATGCTTTGATGTGCGTAGAATGTGAATGCTTGTTAAACGTGATTCACACTGCGCAACATATGCAAATTGTGCATAAACTAGAGTTAAACGAAGATCTTTTGTGGTTTCAAGAACTAAGGACTTTAAAGTTAAAAAGTCCAACAAATGTTTTACAAACTCATTCTTCTCAAACCCATGTATACCCATACATCAGAGGACTACCAGTACTTTTAAATGGATATGAGTGTGTGCCGTGCACAAAAAACGGAACAGGATTCGTACATGCAATCATGGATACCTTTCGCCATCATGTTCGACGTACTCATGGAAAAGTTATAAAATTGGAAAATTGTATACGTCGAACAGCTTTGCAAACGGTTAAGAACAAGTATGCTCAACGATGTCAGTTCTTCAAAGTCGATTATGTACCTTTGAATGGAGGAGAAGAAGAAGAAGAGGAGGAGGGGGAGGAGAAAGAAGATGCACAAAACATCAAGGAAAGAATGGTGGACTTTTGCTTTTCAAAATTTATGGAGAAGAATCAACAGCGGCGGGAGCAGCAAGACAAAGGTGAAAATAAAAAACGACAAGATGATGTTGACCAAGCAACAGACAACAACACTAACACTATTCTTGAAGATGATGAAAAAGATAACGATGAAGAGGAAGAGGAAGAGATTGTCAATGCACGAGAGAAAAATCTTTTAAATCAACAATTCAATTGGACGGCAATTGTGAAAAAACTTGGAGAAAATTGGGATCAGCTGGTTCGATTCGAATATACGAATGGAATTGTAACTTTGGATACCATTGTAAACCAGTTGATTCGTTATTACTATCGAGGATTCCGTCATCTAAGTGGAATGACCATGGGCATGAGACGAATGTTTACTCAAGGAGGAAGCTATAGTGCACAAGAGCGAGGACTTTGTCGCTTAGAGCAAAAGGATACAGTTGTGAGATATGCTCAAAGTGCAGCACTATACCTAATATTTCTGTTACGTCGTCCATCAGCGGACTCGGGGATAAGAAGACACTTGGAAGCAATGTGTGGAGCAACAGTGGAGAGAAAAGAAGGTGGCAGTAACAGCAGCAGTAACATCAGCAACGTCGCCAACTTTGATAGTGCTGAAGACGACAATGACAATGACAATGACAATGACAGAGACAGTAACAATAACAATAACAATAACAACACCAATACTGACGATGATGATAAGCTGGCATACTTGGAACTGCACGAGGCATTAAAATTGGCTTTTCTGCAACAATACGATTTTTCTAAAAATGTTCAAGACTTGGAAATCATGGAGTTTCTTGCATGCATGTCTTTGCATAAAGATGGTACTTCAAAATATGCCTATGAAATCTCTGCCTGCTTTGCACCCCTAATATACACGTGTCGTCTTGTAGCAGCATGTGAGTTACAACGATTGATCGATGAAAAACAAATCGACTTGTTGTCCATTCCATCGTTTCAAACCGCTGGTTCTATTGCTTATGCTCATGTGTTTTGCTTTATCACGCTTGGTCAAAGAAATTTATATGATGTTCTTTACGAAACCCAAAAAGTCGTTAGGGATATCATTCGAACGGAAGGGTATGCAAATACACTGCAAGGACTAAGCCCAAGTACCGTATTGTTTCAGCCACGAAGTAATTCTATGTACCCGTGCATTGGAGATGCATTCAATAACATGGTGCGATTGGACTTGAGTGAGCTGACAGCTCTGTATGAGGGGATGTTTGCCAAAGTTCAGGACTTGTTAAAAGAGCTATGTTTTGATATGAATGTGGAAAAACTATTACCCATTTCGTTACTAAGGTCAATTGGAGATGACATAAACAATAGTAAATTGGGATATTCATTCTTTAAAGAGTCGATAGAGATACGTTCATCTCATAGTGTGCTGTTACGAACAATACTTAAGAACAGTGAACTTTGTCATCGGTTTTTCCCATCGATGTCTAAGAAGGATCTGACAAAGTTGTTTGGTGGAGTAAGTGATCAGCAAAGAAATGAGTGCGACAACTATAGCAACCACTACAACGACAACTCTAATGATAATGACAATGATGTGTTTCTCAAATTACATTGGTCTAAATCTGCTATTAAAAAGTATGAGACAAAGGCATCTATCTTCAATGAGTTATTGTTTTGTCTAGTGTACATATCTGCTGGACAACCAGCCAGAGCACAAGAGATGGTGTATTGGACTTTGCGGAATGGCAAGTATAAGACTCGCGAATTGTATTTGATGTTTGGAAGGCTGATGATTTACAGCAGATACGATAAGACTCGTAATATGAAGTTTGCTGAAAAGCCAATCCCCAGGTTTCTTTCTGAGCCGCTTTCCATTTTAGCACTTCGGTACTATGTTTTGGTTCGACCATTGGAAGCATTGATGAAGTATGTGACAACCGCTGATAGGTCGAAAGTAGCTGTATACTTGGATTTCATGTTTGTGATTGCTGGCGAACGATTGCAAAGAGATTTACCGTATCGAATTTTTCCAAAGGCCACCTACCAATGCATTCAAAAACCGTTGGGATTTCGAAACTACAGGCACATTGCTCACTATTTTAAAGAAAAAAACATCGAGGAAGAAATGACGAGGGAATCATATTTCGATTTACAGGCTGGACATACACGAAACACAGCGCTCTACATCTATGGGCGCACTATGGACAACTTGCATTATCTGCCGTCGGATTATTTCGCCAACTTTTTTCGTGCAAGCTATAAGTGGCAGGAACTATTACAGATTCGAGATAACCCGACCCATGGACTGTTGGTGGAAACAAAGCACCCATTCATCAAGCGAGTTGATCAATTGGAGGAAGCGCTGAATGAGAAGCTGGCAAGGTTGGTAGGTGAACAAATGGTGGAGGGGGACAAGGAAAAGGACAAGACAAATGAGGAGAAGAACAAGGACGAGGTAAAGGCTGAAATGACACAGCCCGTTGTAAATCAAGACTCTCATGACTTACAAGACCAATTGGCCACTACGCCCACCGCGCCCACCGCATTTCACTACCGCCCAGGACTTCTTCAACCATCTCAAACTTCTGTTCAACATTGTTGTTGGGCATTGTCTCAATATTATGGTCTCGAAGCGAAATTCCGTTCGCTGAAACAATTTCAATCGGTTTATTTTTCTCTTTTAAATCGTATGAATTTGATTACCGTACTCCCAACTGGAGGTGGAAAGTCTTTGTCGTTTTTGATACCGGCGCTCATCGAAAAAAAAAGACAAACCCCAGGAAAGGTGATGAATATGGTCACGCTGGTTCTAGTGCCCATGATGTCGTTACGGCAAGATATGATGCTCAGAGTGAATGAAAAGGGACTGCTTGTTTGTTCGGGGAATTGGACCGCATTCAAAGATGTACGATTGACTTTAGAGACGCAACTTCCCGATTTGTTTATCTTGACATACGAGTCAGCATTAACCAACAGTGGTCTTCGGTTTTTTGAAAGTTTGGCAACACTTGGTCGTTTGGCACGAGTGGTAATTGATGAAGCACATTTGTTACTCACCAGTGGAGCATGGAGAACGGCTTTGTCGAGAGCATCGCGGTTGTCTGGCTTGTATGCACCATTGCACTTGTTGAGTGCCACCTTTCCCAGGCAACTAGAGATGGTTGCCAGACAAACGTTTTGTACAAACTTTTACGTTTTACGAGAAACGTCTACTGCACGGGAAAACATCTTTTACTTTTTGCATCCCTATGATAATACCGAGTTTTTGTTGGACTTGCGAACGTTGATGAAACGAACAAAGGTCTTTGAAGGTGATGGACGTGCTATCATCTTTTGTCGAACCAAAAAGGATGTCGAATACATTCATCGTCGTCTTCACCAGTCGGACTTGTTCGCTCACACCCATGTAACCATTTACACAGGAGATGTAAGCGACGAAGAACGACAAATGAACTTTGACGCGTTTCGAAATGCAAATGGGAAGACACGAATCATGATCGCTACCAAGGCATTCGGACTCGGTATCAACTATATGGGAGTGCGTTTAGTAGTACACTATGGATTACCAGCTTCATCTATGGATTATGTACAGGAGACAGGTCGAGCTGGAAGAGATGGCAAGTATGCGATTGCAGCATTGTTTTACGAGAAATATGATTCTACATGGTCGAGCTACGTAGAGGATTCGATGAAAAACTTTCTTAATGATAATACGATGTGTGTTCGATCGTTTCTCGCAAGTGAAATGGATGGCGAATGTGTATGTTGTGCATCGTTTGCTAACTGTGTTTACTGCTCAAGATGCTCAGATTCGTTACTTGGTGAAGAATCAACTGTGTCTACGATGTATGGAGTGAAACCGACATTGCCAGAAACACCGAAACCAGCCATTGCAACACATTCGCGTTATAATGCATCGTTTTCGTCTTCCCCCCCACCACAGCCAGGGAATAGCAGTGGTATGAGTGCTATGAACACTAACACTACTAGTACTACGCCAGTGTCTTTGTCGGAATTATCGGAAATCACTTTGTTCCCTTCGTCTGTATCGCCAACATGGAAGAAAAGCTTTGGCAATGCTAATACGAATCTAAAGTATGGTTTGGAAGACATGTCGCTCAGCCATCGTCGTGGTCATAAACGCACATACGATGAACATTTGAACAATGTACAACAGGGCGTCAACCATGACATGAATCGTGTTCATGGTAGTGTTGGAGGTATGAGTGGTATTGTTGGTATTGGTATTGGTATTGGTGATGGTGATGGTGATGGTGATGTTGATTCTCGTACCATTCATTTCGCCGAGTATAAAAGTCGTGTGCAAGCCGTCAAAAAACAATGGGTAGACTCAACTGACATTTCAGCACAACTCGAGCGATTCTTTCGAGTGTATAAAGATGAATGTCTAAGTTGCACTCTTGGTAACCCAGACACAGAAATTCGTGCTCATACCGGGAAAGCATGCCCCGTACGCTTATCTACTTGTTATAAATGTGGCAAGGCCGACCACAACTTGCGAGAATGTAAACTACGTATTCGATTTCAAGGACTTTGTTTATTTTGTGGTTTGACAAAGTTTGAACATGCCGACAGTGATATGGCTTACACTTCTGACTGTAGGTCATGGGCTAGAAAGGCAAACTTGATATCGTTAGTTTACTATGCTTGGAACAATGTACAATACCGAAGGACTATTGCAGATAAATTCTTACAAGGTGATGTACGTGATC
diff --git a/dammit/tests/test-data/pom.single.fa.dammit.gff3 b/dammit/tests/test-data/pom.single.fa.dammit.gff3
@@ -1,7 +1,7 @@
 ##gff-version 3.2.1
-Transcript_0	HMMER	protein_hmm_match	1194	4092	2.1e-10	.	.	ID=homology:3;Name=DEAD:dammit.hmmscan;Target=DEAD 10 174 +;Note=DEAD/DEAH box helicase;accuracy=0.75;Dbxref="Pfam:PF00270.25"
-Transcript_0	HMMER	protein_hmm_match	1396	4548	3.2e-18	.	.	ID=homology:1;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 8 105 +;Note=Helicase conserved C-terminal domain;accuracy=0.87;Dbxref="Pfam:PF00271.27"
-Transcript_0	HMMER	protein_hmm_match	1735	5307	11000.0	.	.	ID=homology:2;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 16 34 +;Note=Helicase conserved C-terminal domain;accuracy=0.78;Dbxref="Pfam:PF00271.27"
+Transcript_0	HMMER	protein_hmm_match	3583	4093	2.1000000000000002e-10	.	.	ID=homology:3;Name=DEAD:dammit.hmmscan;Target=DEAD 10 174 +;Note=DEAD/DEAH box helicase;accuracy=0.75;Dbxref="Pfam:PF00270.25"
+Transcript_0	HMMER	protein_hmm_match	4189	4549	3.2e-18	.	.	ID=homology:1;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 8 105 +;Note=Helicase conserved C-terminal domain;accuracy=0.87;Dbxref="Pfam:PF00271.27"
+Transcript_0	HMMER	protein_hmm_match	5206	5308	11000.0	.	.	ID=homology:2;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 16 34 +;Note=Helicase conserved C-terminal domain;accuracy=0.78;Dbxref="Pfam:PF00271.27"
 Transcript_0	LAST	translated_nucleotide_match	1	5662	0.0	+	.	ID=homology:0;Name=TLH2_SCHPO:dammit.last;Target=TLH2_SCHPO 0 1887 +;database=OrthoDB
 Transcript_0	transdecoder	CDS	1	5661	.	+	.	ID=cds.Transcript_0|m.1;Parent=Transcript_0|m.1
 Transcript_0	transdecoder	exon	1	5662	.	+	.	ID=Transcript_0|m.1.exon1;Parent=Transcript_0|m.1

diff --git a/dammit/tests/test-data/pom.single.fa.dammit.gff3.evalue10 b/dammit/tests/test-data/pom.single.fa.dammit.gff3.evalue10
@@ -1,12 +1,12 @@
 ##gff-version 3.2.1
-Transcript_0	HMMER	protein_hmm_match	1194	4092	2.1e-10	.	.	ID=homology:3;Name=DEAD:dammit.hmmscan;Target=DEAD 10 174 +;Note=DEAD/DEAH box helicase;accuracy=0.75;Dbxref="Pfam:PF00270.25"
-Transcript_0	HMMER	protein_hmm_match	1396	4548	3.2e-18	.	.	ID=homology:1;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 8 105 +;Note=Helicase conserved C-terminal domain;accuracy=0.87;Dbxref="Pfam:PF00271.27"
-Transcript_0	HMMER	protein_hmm_match	1735	5307	11000.0	.	.	ID=homology:2;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 16 34 +;Note=Helicase conserved C-terminal domain;accuracy=0.78;Dbxref="Pfam:PF00271.27"
-Transcript_0	HMMER	protein_hmm_match	1804	5463	0.067	.	.	ID=homology:5;Name=zf-CCHC:dammit.hmmscan;Target=zf-CCHC 2 17 +;Note=Zinc knuckle;accuracy=0.93;Dbxref="Pfam:PF00098.19"
-Transcript_0	HMMER	protein_hmm_match	20	75	7000.0	.	.	ID=homology:4;Name=zf-CCHC:dammit.hmmscan;Target=zf-CCHC 2 7 +;Note=Zinc knuckle;accuracy=0.85;Dbxref="Pfam:PF00098.19"
-Transcript_0	HMMER	protein_hmm_match	248	870	6800.0	.	.	ID=homology:6;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 47 68 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.73;Dbxref="Pfam:PF13169.2"
-Transcript_0	HMMER	protein_hmm_match	349	1227	0.13	.	.	ID=homology:7;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 33 63 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.8;Dbxref="Pfam:PF13169.2"
-Transcript_0	HMMER	protein_hmm_match	803	2514	3900.0	.	.	ID=homology:8;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 53 77 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.78;Dbxref="Pfam:PF13169.2"
+Transcript_0	HMMER	protein_hmm_match	1048	1228	0.13	.	.	ID=homology:7;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 33 63 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.8;Dbxref="Pfam:PF13169.2"
+Transcript_0	HMMER	protein_hmm_match	2410	2515	3900.0	.	.	ID=homology:8;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 53 77 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.78;Dbxref="Pfam:PF13169.2"
+Transcript_0	HMMER	protein_hmm_match	3583	4093	2.1000000000000002e-10	.	.	ID=homology:3;Name=DEAD:dammit.hmmscan;Target=DEAD 10 174 +;Note=DEAD/DEAH box helicase;accuracy=0.75;Dbxref="Pfam:PF00270.25"
+Transcript_0	HMMER	protein_hmm_match	4189	4549	3.2e-18	.	.	ID=homology:1;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 8 105 +;Note=Helicase conserved C-terminal domain;accuracy=0.87;Dbxref="Pfam:PF00271.27"
+Transcript_0	HMMER	protein_hmm_match	5206	5308	11000.0	.	.	ID=homology:2;Name=Helicase_C:dammit.hmmscan;Target=Helicase_C 16 34 +;Note=Helicase conserved C-terminal domain;accuracy=0.78;Dbxref="Pfam:PF00271.27"
+Transcript_0	HMMER	protein_hmm_match	5413	5464	0.067	.	.	ID=homology:5;Name=zf-CCHC:dammit.hmmscan;Target=zf-CCHC 2 17 +;Note=Zinc knuckle;accuracy=0.93;Dbxref="Pfam:PF00098.19"
+Transcript_0	HMMER	protein_hmm_match	61	76	7000.0	.	.	ID=homology:4;Name=zf-CCHC:dammit.hmmscan;Target=zf-CCHC 2 7 +;Note=Zinc knuckle;accuracy=0.85;Dbxref="Pfam:PF00098.19"
+Transcript_0	HMMER	protein_hmm_match	745	871	6800.0	.	.	ID=homology:6;Name=Poxvirus_B22R_N:dammit.hmmscan;Target=Poxvirus_B22R_N 47 68 +;Note=Poxvirus B22R protein N-terminal;accuracy=0.73;Dbxref="Pfam:PF13169.2"
 Transcript_0	Infernal	RNA_sequence_secondary_structure	3799	3912	7.9	+	.	ID=homology:11;Name=SPRY4-IT1_2:dammit.cmscan;Target=SPRY4-IT1_2 1 121 +;Note=-;Dbxref="Rfam:RF02039";trunc=no;bitscore=13.6
 Transcript_0	Infernal	RNA_sequence_secondary_structure	4609	4665	8.3	+	.	ID=homology:12;Name=ceN69:dammit.cmscan;Target=ceN69 1 107 +;Note=-;Dbxref="Rfam:RF01651";trunc=no;bitscore=17.4
 Transcript_0	Infernal	RNA_sequence_secondary_structure	4992	4925	9.6	-	.	ID=homology:13;Name=SNORD75:dammit.cmscan;Target=SNORD75 1 62 +;Note=-;Dbxref="Rfam:RF00612";trunc=no;bitscore=14.1

diff --git a/dammit/tests/test_main.py b/dammit/tests/test_main.py
@@ -97,7 +97,7 @@ def test_dammit_database_install_full(self):
             status, out, err = run(args)
 
     def test_annotate_basic(self):
-        '''Run a basic annotation and veryify the results.
+        '''Run a basic annotation and verify the results.
         '''
 
         with TemporaryDirectory() as td,\