Merge pull request #254 from mgalardini/issue_253

Add option to allow intersection with other feature types other than CDSs
mgalardini · Nov 9, 2023 · 0714ece · 0714ece
2 parents 0233353 + 0b1392a
commit 0714ece
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Showing 3 changed files with 13 additions and 2 deletions.
diff --git a/pyseer/kmer_mapping/annotate_hits.py b/pyseer/kmer_mapping/annotate_hits.py
@@ -28,6 +28,11 @@ def get_options():
     parser.add_argument("output",
                         help="Output file")
 
+    parser.add_argument("--feature-type",
+                        action="append",
+                        help="Which feature types to consider "
+                        "[default=CDSs only]",
+                        default=["CDS"])
     parser.add_argument("--bwa",
                         help="Location of bwa executable "
                         "[default=bwa]",
@@ -138,7 +143,7 @@ def main():
             # python prior to 3.5
             subprocess.check_call("gff2bed < \"" + ref_gff + "\" > \"" + tmp_bed.name + "\"", shell=True)
         ref_annotation = pybedtools.BedTool(tmp_bed.name)
-        filtered_ref = ref_annotation.filter(lambda x: True if x[7] == "CDS" else False).saveas('tmp_bed')
+        filtered_ref = ref_annotation.filter(lambda x: True if x[7] in options.feature_type else False).saveas('tmp_bed')
         ref_annotation = pybedtools.BedTool('tmp_bed')
 
         for bwa_algorithm in bwa_algorithms:

diff --git a/tests/run_test.sh b/tests/run_test.sh
@@ -75,6 +75,11 @@ cd "test (1)"
 python ../../annotate_hits_pyseer-runner.py ../significant_kmers.txt references.txt /dev/null > /dev/null 2> /dev/null || die 'Annotate hits with weird folder names'
 cd ..
 #
+# issue 253
+python ../annotate_hits_pyseer-runner.py significant_kmers.txt references.txt with_rRNA.txt --feature-type rRNA > /dev/null 2> /dev/null || die 'Annotate hits with rRNA (1)'
+grep TAGCACTCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAGCCAGAGAGCCGCTT with_rRNA.txt | grep FM211187.6350 > /dev/null 2> /dev/null || die 'Annotate hits with rRNA (2)'
+rm with_rRNA.txt
+#
 python ../phandango_mapper-runner.py significant_kmers.txt Spn23F.fa phandango.test.out > /dev/null 2> /dev/null || die 'Phandango mapper'
 python ../enet_predict-runner.py --vcf variants.vcf.gz enet_vcf_model.pkl subset.samples_list > /dev/null 2> /dev/null || die "Enet predict"
 
@@ -115,4 +120,4 @@ do
   python compare_tests $t.log $t.err baseline/$t.log baseline/$t.err || die "Baseline comparison failed for $t";
 done
 
-echo -e $green"All good!"$reset
+echo -e $green"All good!"$reset
diff --git a/tests/significant_kmers.txt b/tests/significant_kmers.txt
@@ -1,4 +1,5 @@
 variant	af	filter-pvalue	lrt-pvalue	beta	beta-std-err	variant_h2	notes
+TAGCACTCATCGTTTACAGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAAGCCAGAGAGCCGCTT	6.47E-02	2.08E-12	2.10E-09	7.97E-01	1.31E-01	2.41E-01	
 TTTTTTTCTACAATAAAATAGGCTCCATAATATCTATAGTGGATTTACCCACTACAAATATTATAGAACCCGTTTTATTATGGAAAGACTTATTGGACTT	6.47E-02	2.08E-12	2.10E-09	7.97E-01	1.31E-01	2.41E-01	
 TTTTTTTATAGATTTCAGGATCAGCCAAATAGTAATCCG	8.42E-01	1.03E-36	2.99E-10	-4.38E-01	6.83E-02	2.53E-01	
 TTTTTTTATAGATTTCAGGATCAGCCAAATAGTAATCCGCCAGCTGGCGTT	8.39E-01	3.38E-35	4.04E-09	-3.95E-01	6.62E-02	2.37E-01