4 samtools fastq threads, restores space before /1, decontaminating--…

…>cleaning, +1 test

src/hostile/aligner.py

@@ -95,7 +95,7 @@ def gen_clean_cmd(
         for k in cmd_template.keys():
             alignment_cmd = alignment_cmd.replace(k, cmd_template[k])
         rename_cmd = (
-            ' | awk \'BEGIN{{FS=OFS="\\t"}} {{$1=int((NR+1)/2)" "; print $0}}\''
+            ' | awk \'BEGIN{{FS=OFS="\\t"}} {{$1=int(NR)" "; print $0}}\''
             if rename
             else ""
         )
@@ -108,10 +108,10 @@ def gen_clean_cmd(
             f" | samtools view -f 4 -"
             # Count reads in stream after filtering
             f" | tee >(samtools view -F 256 -c - > '{count_after_path}')"
-            # Optionally replace paired read headers with integers
+            # Optionally replace read headers with integers
             f"{rename_cmd}"
             # Stream remaining records into fastq files
-            f" | samtools fastq --threads 2 -c 6 -0 '{fastq_out_path}'"
+            f" | samtools fastq --threads 4 -c 6 -0 '{fastq_out_path}'"
         )
         return cmd
 
@@ -153,7 +153,7 @@ def gen_paired_clean_cmd(
         for k in cmd_template.keys():
             alignment_cmd = alignment_cmd.replace(k, cmd_template[k])
         rename_cmd = (
-            f' | awk \'BEGIN{{FS=OFS="\\t"}} {{$1=int((NR+1)/2)""; print $0}}\''
+            f' | awk \'BEGIN{{FS=OFS="\\t"}} {{$1=int((NR+1)/2)" "; print $0}}\''
             if rename
             else ""
         )
@@ -169,6 +169,6 @@ def gen_paired_clean_cmd(
             # Optionally replace paired read headers with integers
             f"{rename_cmd}"
             # Stream remaining records into fastq files
-            f" | samtools fastq --threads 2 -c 6 -N -1 '{fastq1_out_path}' -2 '{fastq2_out_path}'"
+            f" | samtools fastq --threads 4 -c 6 -N -1 '{fastq1_out_path}' -2 '{fastq2_out_path}'"
         )
         return cmd

src/hostile/lib.py

@@ -224,11 +224,11 @@ def clean_fastqs(
         for fastq in fastqs
     ]
     logging.info("Cleaning…")
-    util.run_bash_parallel(backend_cmds, description="Decontaminating…")
+    util.run_bash_parallel(backend_cmds, description="Cleaning…")
     stats = gather_stats(
         rename=rename, fastqs=fastqs, out_dir=out_dir, aligner=aligner.name, index=index
     )
-    logging.info("Finished decontamination")
+    logging.info("Finished cleaning")
     return stats
 
 
@@ -263,12 +263,12 @@ def clean_paired_fastqs(
         for pair in fastqs
     ]
     logging.debug(f"{backend_cmds=}")
-    logging.info("Started decontamination")
-    util.run_bash_parallel(backend_cmds, description="Decontaminating…")
+    logging.info("Cleaning…")
+    util.run_bash_parallel(backend_cmds, description="Cleaning")
     stats = gather_stats_paired(
         rename=rename, fastqs=fastqs, out_dir=out_dir, aligner=aligner.name, index=index
     )
-    logging.info("Finished decontamination")
+    logging.info("Finished cleaning")
     return stats
 
 

tests/data/tuberculosis_2.fastq

@@ -0,0 +1,8 @@
+@Mycobacterium_tuberculosis_1
+TCCCGTCGTAAGCATCGATTCCGACGCGCTGGATGCTGCCCGCATGCTCGCAGAGCATCGTCTGCCTGGACTATTGGTCACCGCCGGAGCGGGCAAACAGTATGCGGTACTCCCTGCCTCACAGGTCGTGCGCTTCATCGTGCCCCGCTG
++
+5430361214022-5224244425513232342544661102331222222/0231322106422524012261/22022/32253121.4240226412221023435/3264252222142422302224322324/222224/2322
+@Mycobacterium_tuberculosis_2
+CCCGTCGTAAGCATCGATTCCGACGCGCTGGATGCTGCCCGCATGCTCGCAGAGCATCGTCTGCCTGGACTATTGGTCACCGCCGGAGCGGGCAAACAGTATGCGGTACTCCCTGCCTCACAGGTCGTGCGCTTCATCGTGCCCCGCTAA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

tests/test_all.py

@@ -17,9 +17,12 @@ def run(cmd: str, cwd: Path = Path()):  # Helper for CLI testing
     )
 
 
-def get_first_line_of_gzip_file(file_path):
+def get_nth_line_of_gzip_file(file_path, line_number=1):
     with gzip.open(file_path, "rt") as fh:
-        return fh.readline().strip()
+        for i, line in enumerate(fh, start=1):
+            if i == line_number:
+                return line.strip()
+    return None
 
 
 def test_version_cli():
@@ -234,10 +237,26 @@ def test_rename():
         rename=True,
         out_dir=out_dir,
     )
-    first_line = get_first_line_of_gzip_file(
-        out_dir / "tuberculosis_1_1.clean.fastq.gz"
+    first_line = get_nth_line_of_gzip_file(out_dir / "tuberculosis_1_1.clean.fastq.gz")
+    assert first_line == "@1"
+    assert stats[0]["rename"] == True
+    shutil.rmtree(out_dir, ignore_errors=True)
+
+
+def test_rename_two_records():
+    stats = lib.clean_fastqs(
+        fastqs=[data_dir / "tuberculosis_2.fastq"],
+        aligner=lib.ALIGNER.bowtie2,
+        index=data_dir / "sars-cov-2/sars-cov-2",
+        rename=True,
+        out_dir=out_dir,
+    )
+    first_line = get_nth_line_of_gzip_file(out_dir / "tuberculosis_2.clean.fastq.gz")
+    fifth_line = get_nth_line_of_gzip_file(
+        out_dir / "tuberculosis_2.clean.fastq.gz", line_number=5
     )
     assert first_line == "@1"
+    assert fifth_line == "@2"
     assert stats[0]["rename"] == True
     shutil.rmtree(out_dir, ignore_errors=True)
 
@@ -255,10 +274,10 @@ def test_paired_rename():
         rename=True,
         out_dir=out_dir,
     )
-    first_line = get_first_line_of_gzip_file(
+    first_line = get_nth_line_of_gzip_file(
         out_dir / "tuberculosis_1_2.clean_1.fastq.gz"
     )
-    assert first_line == "@1/1"
+    assert first_line == "@1 /1"
     assert stats[0]["rename"] == True
     shutil.rmtree(out_dir, ignore_errors=True)
 
@@ -306,7 +325,7 @@ def test_no_rename():
         out_dir=out_dir,
         force=True,
     )
-    first_line = get_first_line_of_gzip_file(
+    first_line = get_nth_line_of_gzip_file(
         (out_dir / "tuberculosis_1_2.clean_1.fastq.gz").resolve()
     )
     assert first_line == "@Mycobacterium_tuberculosis/1"