Command fixes

docker/Dockerfile → Dockerfile

@@ -9,6 +9,8 @@ RUN pip3 install cnvkit==0.9.10 --no-cache
 # Let matplotlib build its font cache
 RUN cnvkit.py version
 
+COPY scripts/* /opt/conda/bin
+
 ## USER CONFIGURATION, containers should not run as root
 RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
 USER    ubuntu

cnvlib/cnary.py

@@ -307,11 +307,11 @@ def shift_xx(self, is_haploid_x_reference=False, is_xx=None, diploid_parx_genome
             is_xx = self.guess_xx(is_haploid_x_reference=is_haploid_x_reference, diploid_parx_genome=diploid_parx_genome)
         if is_xx and is_haploid_x_reference:
             # Female: divide X coverages by 2 (in log2: subtract 1)
-            outprobes[outprobes.chromosome == self._chr_x_label, "log2"] -= 1.0
+            outprobes[outprobes.chromosome == self.chr_x_label, "log2"] -= 1.0
             # Male: no change
         elif not is_xx and not is_haploid_x_reference:
             # Male: multiply X coverages by 2 (in log2: add 1)
-            outprobes[outprobes.chromosome == self._chr_x_label, "log2"] += 1.0
+            outprobes[outprobes.chromosome == self.chr_x_label, "log2"] += 1.0
             # Female: no change
         return outprobes
 

cnvlib/commands.py

@@ -221,7 +221,6 @@ def _cmd_batch(args):
                     procs_per_bam,
                     args.cluster,
                     args.fasta,
-                    args.diploid_parx_genome,
                 )
     else:
         logging.info(
@@ -1195,8 +1194,8 @@ def _cmd_call(args):
         args.ploidy,
         args.purity,
         args.male_reference,
-        args.diploid_parx_genome,
         is_sample_female,
+        args.diploid_parx_genome,
         args.filters,
         args.thresholds,
     )
@@ -1449,6 +1448,7 @@ def _cmd_diagram(args):
     action="store_false",
     help="""Disable gene_name labels on plot (useful when a lot of CNV were called).""",
 )
+add_diploid_parx_genome(P_diagram)
 P_diagram.set_defaults(func=_cmd_diagram)
 
 
@@ -1747,6 +1747,7 @@ def _cmd_heatmap(args):
 P_heatmap_aes.add_argument(
     "-t", "--title", help="Plot title. [Default: Range if provided, otherwise none]"
 )
+add_diploid_parx_genome(P_heatmap)
 P_heatmap.set_defaults(func=_cmd_heatmap)
 
 
@@ -2646,6 +2647,7 @@ def _cmd_export_bed(args):
 P_export_bed.add_argument(
     "-o", "--output", metavar="FILENAME", help="Output file name."
 )
+add_diploid_parx_genome(P_export_bed)
 P_export_bed.set_defaults(func=_cmd_export_bed)
 
 

test/Makefile

@@ -25,19 +25,30 @@ picard_targets= build/reference-picard.cnn $(picard_cnrs) $(picard_segs) \
 # ------------------------------------------------------------------------------
 #  Action!
 
-all: $(picard_targets) p2-5_5-metrics.tsv p2-9_2-metrics.tsv p2-20-metrics.tsv
+all: mini $(picard_targets) p2-5_5-metrics.tsv p2-9_2-metrics.tsv p2-20-metrics.tsv
 
 
 .PHONY: clean
 clean:
 	# Picard
 	rm -rf build/p*targetcoverage.cnn $(picard_targets) p*-scatter.pdf p*-diagram.pdf
+	rm -rf build/na12878-chrM-Y-trunc* build/chrM-Y-trunc*
 
 .PHONY: test
 test:
 	pytest
 
 
+# ------------------------------------------------------------------------------
+# Minimal 'batch' command
+
+.PHONY: mini
+mini: build/na12878-chrM-Y-trunc.bintest.cns
+
+build/na12878-chrM-Y-trunc.bintest.cns: formats/na12878-chrM-Y-trunc.bam formats/chrM-Y-trunc.hg19.fa
+	$(cnvkit) batch -n -f formats/chrM-Y-trunc.hg19.fa -m wgs formats/na12878-chrM-Y-trunc.bam -d build
+
+
 # ------------------------------------------------------------------------------
 # Standard workflow