Merge pull request #18 from Coppini/master

feat: add Dockerfile

Dockerfile

@@ -0,0 +1,22 @@
+FROM python:3.6
+
+RUN apt-get update \
+    && apt-get install -y \
+    libopenblas-dev=0.3.13+ds-3 \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Copy libraries
+COPY --from=quay.io/biocontainers/htslib:1.14--h9093b5e_0 /usr/local/lib/libhts.so.3 /usr/local/lib/libtinfow.so.6 /usr/local/lib/
+COPY --from=quay.io/biocontainers/bcftools:1.14--h88f3f91_0 /usr/local/lib/libgsl.so.25 /usr/local/lib/libcblas.so.3 /usr/local/lib/
+
+# Copy binaries
+COPY --from=quay.io/biocontainers/htslib:1.14--h9093b5e_0 /usr/local/bin/bgzip /usr/local/bin/htsfile /usr/local/bin/tabix /usr/local/bin/
+COPY --from=quay.io/biocontainers/spoa:4.0.7--h9a82719_1 /usr/local/bin/spoa /usr/local/bin/
+COPY --from=quay.io/biocontainers/racon:1.4.20--h9a82719_1 /usr/local/bin/racon /usr/local/bin/
+COPY --from=quay.io/biocontainers/minimap2:2.23--h5bf99c6_0 /usr/local/bin/minimap2 /usr/local/bin/
+COPY --from=quay.io/biocontainers/samtools:1.14--hb421002_0 /usr/local/bin/samtools /usr/local/bin/
+COPY --from=quay.io/biocontainers/bcftools:1.14--h88f3f91_0 /usr/local/bin/bcftools /usr/local/bin/
+
+RUN pip install medaka==1.5.0 NGSpeciesID
+
+ENTRYPOINT [ "NGSpeciesID" ]

modules/cluster.py

@@ -221,7 +221,7 @@ def reads_to_clusters(clusters, representatives, sorted_reads, p_emp_probs, mini
 
     ## For multiprocessing only
     prev_b_indices = [ prev_batch_index for (read_cl_id, prev_batch_index, acc, seq, qual, score) in sorted_reads ]
-    lowest_batch_index = max(1, min(prev_b_indices))
+    lowest_batch_index = max(1, min(prev_b_indices or [1]))
     skip_count = prev_b_indices.count(lowest_batch_index)
     print("Saved: {0} iterations.".format(skip_count) )
     ###################################
@@ -369,7 +369,7 @@ def reads_to_clusters(clusters, representatives, sorted_reads, p_emp_probs, mini
     print("Total number of reads iterated through:{0}".format(len(sorted_reads)))
     print("Passed mapping criteria:{0}".format(mapped_passed_criteria))
     print("Passed alignment criteria in this process:{0}".format(aln_passed_criteria))
-    print("Total calls to alignment mudule in this process:{0}".format(aln_called))
+    print("Total calls to alignment module in this process:{0}".format(aln_called))
 
     return { new_batch_index : (clusters, representatives, minimizer_database, new_batch_index)}
 

modules/consensus.py

@@ -271,6 +271,7 @@ def form_draft_consensus(clusters, representatives, sorted_reads_fastq_file, wor
     print(f"{singletons} singletons were discarded")
     print(
         f"{len(discarded_clusters)} clusters were discarded due to not passing the abundance_cutoff: "
-        f"a total of {sum(discarded_clusters)} reads were discarded"
+        f"a total of {sum(discarded_clusters)} reads were discarded. "
+        f"Highest abundance among them: {max(discarded_clusters or [0])} reads."
     )
     return centers