test: add unit tests

.github/workflows/CI.yml

@@ -15,6 +15,7 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
+
     steps:
 
       - name: Checkout Repository
@@ -43,3 +44,40 @@ jobs:
 
       - name: Run local test
         run: bash test/test_workflow_local.sh
+
+  unit-testing:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v3
+
+      - name: Setup environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          activate-environment: mirflowz
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Update mirflowz env with root packages
+        run: mamba env update -n mirflowz -f environment.root.yml
+
+      - name: Update mirflowz env with dev packages
+        run: mamba env update -n mirflowz -f environment.dev.yml
+
+      - name: run unit tests
+        run: |
+          coverage run --source scripts -m pytest
+          coverage xml
+
+      - name: submit coverage report
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: true
+          verbose: true

environment.dev.yml

@@ -1,5 +1,9 @@
 name: mirflowz
 channels:
   - bioconda
+  - defaults
 dependencies:
+  - coverage>=7.2
+  - pytest>=7.1.2
+  - pytest-cov
   - snakefmt

environment.yml

@@ -5,4 +5,5 @@ channels:
 dependencies:
   - graphviz=7.1.0
   - python=3.9.16
+  - pysam>=0.21.0
   - snakemake=7.24.0

scripts/filter_multimappers.py

@@ -38,6 +38,7 @@
     filter_multimappers.py SAM > SAM
 """
 import argparse
+from itertools import chain
 from pathlib import Path
 import sys
 from typing import List
@@ -67,7 +68,7 @@ def parse_arguments():
     return parser
 
 
-def count_indels(aln: pysam.AlignedSegment) -> int:
+def count_indels(aln: pysam.libcalignedsegment.AlignedSegment) -> int:
     """Count the number of indels in an alignment based on its CIGAR string.
 
     This function counts the number of indels in the alignment based on the
@@ -101,7 +102,7 @@ def find_best_alignments(alns: List[pysam.AlignedSegment]) -> List[pysam.Aligned
     Retrns:
         best_alignments: alignments with the less indels
     """
-    aln_indels = [(aln, count_indels(alignment=aln)) for aln in alns]
+    aln_indels = [(aln, count_indels(aln=aln)) for aln in alns]
     min_indels = min(aln_indels, key=lambda x: x[1])[1]
     best_alignments = [aln for i, (aln, indels) in enumerate(aln_indels) if indels == min_indels]
 
@@ -121,7 +122,7 @@ def write_output(alignments: List[pysam.AlignedSegment]) -> None:
     if len(alignments) == 1:
         sys.stdout.write(alignments[0].to_string() + '\n')
     else:
-        best_alignments = find_best_alignments(alignments=alignments)
+        best_alignments = find_best_alignments(alns=alignments)
         for alignment in best_alignments:
             sys.stdout.write(alignment.to_string() + '\n')
 
@@ -133,13 +134,20 @@ def main(sam_file: Path) -> None:
         sam_file: Path to the input SAM file.
     """
     with pysam.AlignmentFile(sam_file, "r") as samfile:
+
+        try:
+            first_alignment = next(samfile)
+
+        except StopIteration:
+            sys.stdout.write(str(samfile.header))
+            return
 
         sys.stdout.write(str(samfile.header))
 
         current_query = None
         current_alignments: list[pysam.AlignedSegment] = []
 
-        for alignment in samfile:
+        for alignment in chain([first_alignment],samfile):
 
             if alignment.is_secondary or alignment.is_supplementary:
                 continue

scripts/tests/files/in_sam_diff_multimappers.sam

@@ -0,0 +1,4 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+1-1	16	19	77595	255	14M1D8M	*	0	0	GCAGGAGAATCACTGATGTCAG	*	MD:Z:14^T2A1C3	NH:i:2	NM:i:3	XA:Z:Q	XI:i:1
+1-1	0	19	330456	255	4M1D1M1I3M1D13M	*	0	0	CTGACATCAGTGATTCTCCTGC	*	MD:Z:4^G4^A13	NH:i:2	NM:i:3	XA:Z:Q	XI:i:0

scripts/tests/files/in_sam_empty.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+@PG	ID:samtools	PN:samtools	VN:1.16.1	CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam

scripts/tests/files/in_sam_equal_multimappers.sam

@@ -0,0 +1,5 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+1-1	0	19	142777	255	15M1I5M	*	0	0	GCTAGGTGGGAGGCTTGAAGC	*	MD:Z:4C0T14	NH:i:3	NM:i:3	XA:Z:Q	XI:i:0
+1-1	16	19	270081	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14G0G4	NH:i:3	NM:i:3	XA:Z:Q	XI:i:2
+1-1	16	19	545543	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14A0G4	NH:i:3	NM:i:3	XA:Z:Q	XI:i:1

scripts/tests/files/in_sam_multimappers.sam

@@ -0,0 +1,13 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+1-1	0	19	7589	255	24M	*	0	0	ATTTCAAGCCAGGTGGCGTTTTTC	*	MD:Z:13G10	NH:i:1	NM:i:1
+2-1	0	19	63250	255	22M	*	0	0	GAAAGCGCTTCGCTTCAGAGTG	*	MD:Z:11C10	NH:i:1	NM:i:1
+3-1	0	19	63251	255	22M	*	0	0	AAAGCGCTTCCCTTCAGAGTGA	*	MD:Z:21T	NH:i:1	NM:i:1
+4-1	0	19	63250	255	22M	*	0	0	TAAAGCGCTTCCCTTCAGAGTG	*	MD:Z:G21	NH:i:1	NM:i:1
+5-1	0	19	7589	255	24M	*	0	0	CTTTCAAGCCAGGGGGCGTTTTTC	*	MD:Z:A23	NH:i:1	NM:i:1
+6-1	0	19	7590	255	24M	*	0	0	TTTCAAGCCAGGTGGCGTTTTTCT	*	MD:Z:12G11	NH:i:1	NM:i:1
+7-1	0	19	142777	255	15M1I5M	*	0	0	GCTAGGTGGGAGGCTTGAAGC	*	MD:Z:4C0T14	NH:i:3	NM:i:3	XA:Z:Q	XI:i:0
+7-1	16	19	270081	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14G0G4	NH:i:3	NM:i:3	XA:Z:Q	XI:i:2
+7-1	16	19	545543	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14A0G4	NH:i:3	NM:i:3	XA:Z:Q	XI:i:1
+8-1	16	19	77595	255	14M1D8M	*	0	0	GCAGGAGAATCACTGATGTCAG	*	MD:Z:14^T2A1C3	NH:i:2	NM:i:3	XA:Z:Q	XI:i:1
+8-1	0	19	330456	255	4M1D1M1I3M1D13M	*	0	0	CTGACATCAGTGATTCTCCTGC	*	MD:Z:4^G4^A13	NH:i:2	NM:i:3	XA:Z:Q	XI:i:0

scripts/tests/files/out_sam_diff_multimappers.sam

@@ -0,0 +1 @@
+1-1	16	19	77595	255	14M1D8M	*	0	0	GCAGGAGAATCACTGATGTCAG	*	MD:Z:14^T2A1C3	NM:i:3	XA:Z:Q	XI:i:1	NH:i:1	HI:i:1

scripts/tests/files/out_sam_empty.sam

@@ -0,0 +1,3 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+@PG	ID:samtools	PN:samtools	VN:1.16.1	CL:samtools sort -n -o results/test_lib/header_sorted_catMappings.sam results/test_lib/concatenated_header_catMappings.sam

scripts/tests/files/out_sam_equal_multimappers.sam

@@ -0,0 +1,3 @@
+1-1	0	19	142777	255	15M1I5M	*	0	0	GCTAGGTGGGAGGCTTGAAGC	*	MD:Z:4C0T14	NM:i:3	XA:Z:Q	XI:i:0	NH:i:3	HI:i:1
+1-1	16	19	270081	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14G0G4	NM:i:3	XA:Z:Q	XI:i:2	NH:i:3	HI:i:2
+1-1	16	19	545543	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14A0G4	NM:i:3	XA:Z:Q	XI:i:1	NH:i:3	HI:i:3

scripts/tests/files/out_sam_multimappers.sam

@@ -0,0 +1,12 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+1-1	0	19	7589	255	24M	*	0	0	ATTTCAAGCCAGGTGGCGTTTTTC	*	MD:Z:13G10	NH:i:1	NM:i:1
+2-1	0	19	63250	255	22M	*	0	0	GAAAGCGCTTCGCTTCAGAGTG	*	MD:Z:11C10	NH:i:1	NM:i:1
+3-1	0	19	63251	255	22M	*	0	0	AAAGCGCTTCCCTTCAGAGTGA	*	MD:Z:21T	NH:i:1	NM:i:1
+4-1	0	19	63250	255	22M	*	0	0	TAAAGCGCTTCCCTTCAGAGTG	*	MD:Z:G21	NH:i:1	NM:i:1
+5-1	0	19	7589	255	24M	*	0	0	CTTTCAAGCCAGGGGGCGTTTTTC	*	MD:Z:A23	NH:i:1	NM:i:1
+6-1	0	19	7590	255	24M	*	0	0	TTTCAAGCCAGGTGGCGTTTTTCT	*	MD:Z:12G11	NH:i:1	NM:i:1
+7-1	0	19	142777	255	15M1I5M	*	0	0	GCTAGGTGGGAGGCTTGAAGC	*	MD:Z:4C0T14	NM:i:3	XA:Z:Q	XI:i:0	NH:i:3	HI:i:1
+7-1	16	19	270081	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14G0G4	NM:i:3	XA:Z:Q	XI:i:2	NH:i:3	HI:i:2
+7-1	16	19	545543	255	6M1I14M	*	0	0	GCTTCAAGCCTCCCACCTAGC	*	MD:Z:14A0G4	NM:i:3	XA:Z:Q	XI:i:1	NH:i:3	HI:i:3
+8-1	16	19	77595	255	14M1D8M	*	0	0	GCAGGAGAATCACTGATGTCAG	*	MD:Z:14^T2A1C3	NM:i:3	XA:Z:Q	XI:i:1	NH:i:1	HI:i:1

scripts/tests/files/sam_no_multimappers.sam

@@ -0,0 +1,7 @@
+@HD	VN:1.0	SO:queryname
+@SQ	SN:19	LN:600000	M5:f9635dbff42b16049de830a7a121fa12	UR:NA
+1-1	0	19	44414	255	21M	*	0	0	GAAGGCGCTTCCCTTTGGAGT	*	MD:Z:21	NH:i:1	NM:i:0
+2-1	0	19	44377	255	11M3I11M	*	0	0	CTACAAAGGGAGGTAGCACTTTCTC	*	MD:Z:22	NH:i:1	NM:i:3	XA:Z:Q	XI:i:0
+3-1	0	19	7590	255	20M3I3M	*	0	0	TTTCAAGCCAGGGGGCGTTTCCGTTC	*	MD:Z:23	NH:i:1	NM:i:3	XA:Z:Q	XI:i:0
+4-1	0	19	7590	255	23M	*	0	0	TTTCAAGTCAGGGGGCGTTTTTC	*	MD:Z:7C15	NH:i:1	NM:i:1
+5-1	0	19	30893	255	32M2I53M	*	0	0	CTCAAGCTGTGACTCTCCAGAGGGATGCACTTGATCTCTTATGTGAAAAAAAAGAAGGCGCTTCCCTTTAGAGCGTTACGGTTTGGG	*	MD:Z:85	NH:i:1	NM:i:2	XA:Z:Q	XI:i:0