Merge pull request #347 from jodyphelan/dev

Dev

.github/workflows/testing.yml

@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on:
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run: 
+        shell: bash -el {0}
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+          python-version: 3.8
+          mamba-version: "*"
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+
+    - name: install dependancies
+      run: |
+        mamba create -n test tb-profiler -y
+        
+    - name: Install dependencies
+      run: |
+        conda activate test
+        pip install --force-reinstall .
+    - name: Run tests
+      run: |
+        cd tests
+        mamba install pytest -y
+        pytest -x .
+    

tbprofiler/phylo.py

@@ -60,20 +60,44 @@ def generate_low_dp_mask(bam: str,ref: str,outfile: str,min_dp: int = 10) -> Non
         for x in missing_positions:
             O.write(f"{x[0]}\t{x[1]}\t{x[1]+1}\n")
 
+def generate_low_dp_mask_vcf(vcf: str,outfile: str,min_dp: int = 10) -> None:
+    missing_positions = []
+    vcf_obj = pysam.VariantFile(vcf)
+    for rec in vcf_obj:
+        # use AD field if available
+        if 'AD' in rec.samples[0]:
+            dp = sum(rec.samples[0]['AD'])
+        else:
+            dp = rec.samples[0]['DP']
+        if dp<min_dp:
+            missing_positions.append((rec.chrom,rec.pos))
+
+    # write missing positions to bed file
+    with open(outfile,"w") as O:
+        for x in missing_positions:
+            O.write(f"{x[0]}\t{x[1]}\t{x[1]+1}\n")
+
 def prepare_usher(treefile: str,vcf_file: str) -> None:
     run_cmd(f"usher --tree {treefile} --vcf {vcf_file} --collapse-tree --save-mutation-annotated-tree phylo.pb")
 
 def prepare_sample_consensus(sample: str,input_vcf: str,args: argparse.Namespace) -> str:
     s = sample
     tmp_vcf = f"{args.files_prefix}.{s}.vcf.gz"
-    run_cmd(f"bcftools norm -m - {input_vcf} | bcftools view -T ^{args.conf['bedmask']} | bcftools filter --SnpGap 50 | bcftools view -v snps | annotate_maaf.py | bcftools filter -S . -e 'MAAF<0.7' |bcftools filter -S . -e 'FMT/DP<20' | rename_vcf_sample.py --sample-name {s} | bcftools view -v snps -Oz -o {tmp_vcf}")
+    run_cmd(f"bcftools norm -m - {input_vcf} | bcftools view -T ^{args.conf['bedmask']} | bcftools filter --SnpGap 50 | bcftools view -v snps | annotate_maaf.py | bcftools filter -S . -e 'MAAF<0.7' |bcftools filter -S . -e 'FMT/DP<{args.conf['variant_filters']['depth_soft']}' | rename_vcf_sample.py --sample-name {s} | bcftools view -v snps -Oz -o {tmp_vcf}")
     run_cmd(f"bcftools index {tmp_vcf}")
 
     mask_bed = f"{args.files_prefix}.{s}.mask.bed"
     if hasattr(args,'supplementary_bam') and args.supplementary_bam:
         args.bam = args.supplementary_bam
-    generate_low_dp_mask(f"{args.bam}",args.conf['ref'],mask_bed)
-    run_cmd(f"bcftools consensus --sample {s} -m {mask_bed} -M N -f {args.conf['ref']} {tmp_vcf} | sed 's/>/>{s} /' > {args.files_prefix}.{s}.consensus.fa")
+    if args.bam:
+        generate_low_dp_mask(f"{args.bam}",args.conf['ref'],mask_bed)
+        mask_cmd = f"-m {mask_bed} -M N"
+    elif args.vcf:
+        generate_low_dp_mask_vcf(args.vcf,mask_bed)
+        mask_cmd = f"-m {mask_bed} -M N"
+    else:
+        mask_cmd = ""
+    run_cmd(f"bcftools consensus --sample {s} {mask_cmd} -f {args.conf['ref']} {tmp_vcf} | sed 's/>/>{s} /' > {args.files_prefix}.{s}.consensus.fa")
     return f"{args.files_prefix}.{s}.consensus.fa"
 
 def get_consensus_vcf(sample: str,input_vcf: str,args: argparse.Namespace) -> str:

tests/run_test.py

@@ -31,9 +31,10 @@
 ]
 
 db = 'testdb'
+branch = 'who'
 
 def test_db():
-    run_cmd(f"tb-profiler update_tbdb --branch test --prefix {db}")
+    run_cmd(f"tb-profiler update_tbdb --branch {branch} --prefix {db}")
 
 
 def check_assertations(filename):