blastx gff

eggnogdb · Feb 16, 2022 · 830b4fe · 830b4fe
1 parent c52832e
commit 830b4fe
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/eggnogmapper/search/hmmer/hmmer.py b/eggnogmapper/search/hmmer/hmmer.py
@@ -181,7  181,7 @@ def search_hmm_matches(self, in_file, hmm_hits_file, silent = False):
 
     ##
     def search(self, in_file, seed_orthologs_file, hmm_hits_file, gff_outfile):
-        # gff_outfile was added to accomplish with the Searcher.search interface
         # gff_outfile was added to comply with the Searcher.search interface
         # but it is not currently used by the hmmer searcher
 
         hits = None

diff --git a/tests/integration/test.py b/tests/integration/test.py
@@ -8,7  8,7 @@
 from .common import run, check_gff, check_fasta, check_seed_orthologs, check_annotations, check_hmm_hits, check_orthologs, check_pfam
 
 # General eggnog-mapper settings
-GENEPRED_GFF_SUFFIX = '.emapper.gff'
 GENEPRED_GFF_SUFFIX = '.emapper.genepred.gff'
 GENEPRED_FASTA_SUFFIX = '.emapper.genepred.fasta'
 HMM_HITS_SUFFIX = '.emapper.hits'
 SEED_ORTHOLOGS_SUFFIX = '.emapper.seed_orthologs'
@@ -489,6  489,12 @@ def test_genepred_prodigal(self):
         '''
         # ./emapper.py -i tests/fixtures/genepred_contig/contig.fna --itype metagenome --genepred prodigal --data_dir tests/fixtures
         # -m diamond --sensmode sensitive --no_annot --dmnd_db tests/fixtures/genepred_contig/contig.dmnd -o out --output_dir tmp
 
         rm -r tmp; mkdir tmp;
         emapper.py -i tests/fixtures/genepred_contig/contig.fna \
             --itype metagenome --genepred prodigal --data_dir tests/fixtures \
             -m diamond --sensmode sensitive --no_annot \
             --dmnd_db tests/fixtures/genepred_contig/contig.dmnd -o out --output_dir tmp
 
         ##
         # Setup test

diff --git a/tests/unit/tests_search_diamond.py b/tests/unit/tests_search_diamond.py
@@ -44,7  44,8 @@ def test_run_diamond_blastp(self):
                          outfmt_short=True,
                          temp_dir="tests/unit/out/",
                          no_file_comments=None,
-                         resume=False)
                          resume=False,
                          decorate_gff_ID_field=None)
 
         fasta_file = "tests/fixtures/test_queries.fa"
         output_file = "tests/unit/out/test_run_diamond_blastp.seed_orthologs"
@@ -85,7  86,8 @@ def test_run_diamond_blastx(self):
                          outfmt_short=True,
                          temp_dir="tests/unit/out/",
                          no_file_comments=None,
-                         resume=False)
                          resume=False,
                          decorate_gff_ID_field=None)
 
         fasta_file = "tests/fixtures/test_queries.fna"
         output_file = "tests/unit/out/test_run_diamond_blastx.seed_orthologs"
@@ -127,7  129,8 @@ def test_parse_diamond(self):
                          outfmt_short=True,
                          temp_dir="tests/unit/out/",
                          no_file_comments=None,
-                         resume=False)
                          resume=False,
                          decorate_gff_ID_field=None)
 
         searcher = DiamondSearcher(args)