68 tests passing

src/hostile/aligner.py

@@ -31,7 +31,8 @@ class Aligner:
     single_unindexed_cmd: str
     paired_cmd: str
     paired_unindexed_cmd: str
-    paired_interleaved_cmd: str
+    interleaved_cmd: str
+    interleaved_unindexed_cmd: str
 
     def __post_init__(self):
         Path(self.data_dir).mkdir(exist_ok=True, parents=True)
@@ -115,14 +116,15 @@ def check_index(self, index: str, airplane: bool = False) -> Path:
 
     def gen_clean_cmd(
         self,
-        fastq: Path,
+        fastq: Path | str,
         index_path: Path,
         invert: bool,
         rename: bool,
         reorder: bool,
         casava: bool,
+        stdin: bool,
         stdout: bool,
-        output: Path,
+        output: Path | str,
         aligner_args: str,
         aligner_threads: int,
         compression_threads: int,
@@ -202,15 +204,16 @@ def gen_clean_cmd(
 
     def gen_paired_clean_cmd(
         self,
-        fastq1: Path,
-        fastq2: Path,
+        fastq1: Path | str,
+        fastq2: Path | str,
         index_path: Path,
         invert: bool,
         rename: bool,
         reorder: bool,
         casava: bool,
+        stdin: bool,
         stdout: bool,
-        output: Path,
+        output: Path | str,
         aligner_args: str,
         aligner_threads: int,
         compression_threads: int,
@@ -273,20 +276,20 @@ def gen_paired_clean_cmd(
             )
 
         if self.name == "Minimap2":
-            if not mmi_path.is_file():
-                if str(fastq1) == "-" and str(fastq2) == "-":  # Interleaved input
-                    alignment_cmd = self.single_unindexed_cmd  # Same as single
-                else:
+            if not mmi_path.is_file():  # No MMI, make one
+                if stdin:  # Interleaved stdin
+                    alignment_cmd = self.interleaved_unindexed_cmd
+                else:  # Separate fastq1 and fastq2 file input
                     alignment_cmd = self.paired_unindexed_cmd
-            else:
-                if str(fastq1) == "-" and str(fastq2) == "-":
-                    alignment_cmd = self.single_cmd
-                else:
+            else:  # MMI exists
+                if stdin:  # Interleaved stdin
+                    alignment_cmd = self.interleaved_cmd
+                else:  # Separate fastq1 and fastq2 file input
                     alignment_cmd = self.paired_cmd
         else:  # Bowtie2
-            if str(fastq1) == "-" and str(fastq2) == "-":
-                alignment_cmd = self.paired_interleaved_cmd
-            else:
+            if stdin:  # Interleaved stdin
+                alignment_cmd = self.interleaved_cmd
+            else:  # Separate fastq1 and fastq2 file input
                 alignment_cmd = self.paired_cmd
 
         for k in cmd_template.keys():
@@ -333,12 +336,13 @@ def gen_paired_clean_cmd(
                 "{BIN_PATH} -x '{INDEX_PATH}' -1 '{FASTQ1}' -2 '{FASTQ2}'"
                 " -k 1 --mm -p {ALIGNER_THREADS} {ALIGNER_ARGS}"
             ),
-            paired_interleaved_cmd=(
+            interleaved_cmd=(
                 "{BIN_PATH} -x '{INDEX_PATH}' --interleaved -"
                 " -k 1 --mm -p {ALIGNER_THREADS} {ALIGNER_ARGS}"
             ),
             single_unindexed_cmd="",
             paired_unindexed_cmd="",
+            interleaved_unindexed_cmd="",
         ),
         "minimap2": Aligner(
             name="Minimap2",
@@ -360,7 +364,14 @@ def gen_paired_clean_cmd(
                 "'{BIN_PATH}' -ax sr --secondary no -t {ALIGNER_THREADS} {ALIGNER_ARGS}"
                 " -d '{MMI_PATH}' '{INDEX_PATH}' '{FASTQ1}' '{FASTQ2}'"
             ),
-            paired_interleaved_cmd="",
+            interleaved_cmd=(
+                "'{BIN_PATH}' -ax sr --secondary no -t {ALIGNER_THREADS}"
+                " {ALIGNER_ARGS} '{MMI_PATH}' '{FASTQ1}'"
+            ),
+            interleaved_unindexed_cmd=(
+                "'{BIN_PATH}' -ax sr --secondary no -t {ALIGNER_THREADS}"
+                " {ALIGNER_ARGS} -d '{MMI_PATH}' '{INDEX_PATH}' '{FASTQ1}'"
+            ),
         ),
     },
 )

src/hostile/lib.py

@@ -39,17 +39,19 @@ class SampleReport:
 
 
 def gather_stats(
-    fastqs: list[Path],
+    fastqs: list[Path | None],
     aligner: str,
     index: str,
     invert: bool,
     rename: bool,
     reorder: bool,
     casava: bool,
+    stdin: bool,
     stdout: bool,
     output: Path,
 ) -> list[dict[str, str | int | float | list[str]]]:
     stats = []
+    logging.debug(f"gather_stats() {fastqs=}")
     for fastq1 in fastqs:
         fastq1_stem = util.fastq_path_to_stem(fastq1)
         fastq1_out_path = output / f"{fastq1_stem}.clean.fastq.gz"
@@ -71,6 +73,8 @@ def gather_stats(
                 "rename": rename,
                 "reorder": reorder,
                 "casava": casava,
+                "stdin": stdin,
+                "stdout": stdout,
             }.items()
             if v
         ]
@@ -79,8 +83,8 @@ def gather_stats(
             aligner=aligner,
             index=index,
             options=options,
-            fastq1_in_name=Path(fastq1).name,
-            fastq1_in_path=str(fastq1),
+            fastq1_in_name=Path(fastq1).name if not stdin else None,
+            fastq1_in_path=str(fastq1) if not stdin else None,
             fastq1_out_name=fastq1_out_path.name if not stdout else None,
             fastq1_out_path=str(fastq1_out_path) if not stdout else None,
             reads_in=n_reads_in,
@@ -93,13 +97,14 @@ def gather_stats(
 
 
 def gather_stats_paired(
-    fastqs: list[tuple[Path, Path]],
+    fastqs: list[tuple[Path | None, Path | None]],
     aligner: str,
     index: str,
     invert: bool,
     rename: bool,
     reorder: bool,
     casava: bool,
+    stdin: bool,
     stdout: bool,
     output: Path,
 ) -> list[dict[str, str | int | float | list[str]]]:
@@ -128,6 +133,8 @@ def gather_stats_paired(
                 "rename": rename,
                 "reorder": reorder,
                 "casava": casava,
+                "stdin": stdin,
+                "stdout": stdout,
             }.items()
             if v
         ]
@@ -136,10 +143,10 @@ def gather_stats_paired(
             aligner=aligner,
             index=index,
             options=options,
-            fastq1_in_name=Path(fastq1).name,
-            fastq2_in_name=Path(fastq2).name,
-            fastq1_in_path=str(fastq1),
-            fastq2_in_path=str(fastq2),
+            fastq1_in_name=Path(fastq1).name if not stdin else None,
+            fastq2_in_name=Path(fastq2).name if not stdin else None,
+            fastq1_in_path=str(fastq1) if not stdin else None,
+            fastq2_in_path=str(fastq2) if not stdin else None,
             fastq1_out_name=fastq1_out_path.name if not stdout else None,
             fastq2_out_name=fastq2_out_path.name if not stdout else None,
             fastq1_out_path=str(fastq1_out_path) if not stdout else None,
@@ -168,27 +175,27 @@ def clean_fastqs(
     force: bool = False,
     airplane: bool = False,
 ):
-    output = Path(output)
+    stdin = str(fastqs[0]) == "-"
     stdout = str(output) == "-"
+    output = Path(util.CWD) if stdout else Path(output)
     aligner_threads, compression_threads = util.allocate_threads(threads, stdout=stdout)
     logging.debug(
         f"clean_fastqs() {threads=} {aligner_threads=} {compression_threads=}"
+        f" {util.CACHE_DIR=} {util.INDEX_REPOSITORY_URL=}"
     )
-    logging.debug(f"{util.CACHE_DIR=}")
-    logging.debug(f"{util.INDEX_REPOSITORY_URL=}")
     if aligner == ALIGNER.bowtie2:
-        logging.info(f"Hostile v{__version__}. Mode: short read (Bowtie2)")
+        logging.info(
+            f"Hostile v{__version__}. Mode: short read {'from stdin ' if stdin else ''}(Bowtie2)"
+        )
     elif aligner == ALIGNER.minimap2:
-        logging.info(f"Hostile v{__version__}. Mode: long read (Minimap2)")
-    if len(fastqs) == 1 and fastqs[0] == "-":
-        stdin = True
-    else:
-        stdin = False
+        logging.info(
+            f"Hostile v{__version__}. Mode: long read {'from stdin ' if stdin else ''}(Minimap2)"
+        )
+    if not stdin:
         fastqs = [Path(path).absolute() for path in fastqs]
         if not all(fastq.is_file() for fastq in fastqs):
             logging.debug(f"{fastqs=}")
             raise FileNotFoundError("One or more fastq files do not exist")
-    output.mkdir(exist_ok=True, parents=True)
     index_path = aligner.value.check_index(index, airplane=airplane)
     backend_cmds = [
         aligner.value.gen_clean_cmd(
@@ -198,6 +205,7 @@ def clean_fastqs(
             rename=rename,
             reorder=reorder,
             casava=casava,
+            stdin=stdin,
             stdout=stdout,
             output=output,
             aligner_args=aligner_args,
@@ -211,7 +219,7 @@ def clean_fastqs(
     logging.info("Cleaning…")
     if stdin:
         util.run_bash(backend_cmds[0], stdin=True)
-        fastqs[0] = Path("stdin")
+        fastqs[0] = "stdin"
     else:
         util.run_bash_parallel(backend_cmds, description="Cleaning")
     stats = gather_stats(
@@ -222,6 +230,7 @@ def clean_fastqs(
         rename=rename,
         reorder=reorder,
         casava=casava,
+        stdin=stdin,
         stdout=stdout,
         output=output,
     )
@@ -244,28 +253,28 @@ def clean_paired_fastqs(
     force: bool = False,
     airplane: bool = False,
 ):
-    output = Path(output)
+    stdin = str(fastqs[0][0]) == "-"
     stdout = str(output) == "-"
+    output = Path(util.CWD) if stdout else Path(output)
     aligner_threads, compression_threads = util.allocate_threads(threads, stdout=stdout)
     logging.debug(
         f"clean_paired_fastqs() {threads=} {aligner_threads=} {compression_threads=}"
+        f" {util.CACHE_DIR=} {util.INDEX_REPOSITORY_URL=}"
     )
-    logging.debug(f"{util.CACHE_DIR=}")
-    logging.debug(f"{util.INDEX_REPOSITORY_URL=}")
     if aligner == ALIGNER.bowtie2:
-        logging.info(f"Hostile v{__version__}. Mode: paired short read (Bowtie2)")
+        logging.info(
+            f"Hostile v{__version__}. Mode: paired short read {'from stdin ' if stdin else ''}(Bowtie2)"
+        )
     elif aligner == ALIGNER.minimap2:
-        logging.info(f"Hostile v{__version__}. Mode: paired short read (Minimap2)")
-    if len(fastqs) == 1 and fastqs[0][0] == "-":
-        stdin = True
-    else:
-        stdin = False
+        logging.info(
+            f"Hostile v{__version__}. Mode: paired short read {'from stdin ' if stdin else ''}(Minimap2)"
+        )
+    if not stdin:
         fastqs = [
             (Path(path1).absolute(), Path(path2).absolute()) for path1, path2 in fastqs
         ]
         if not all(path.is_file() for fastq_pair in fastqs for path in fastq_pair):
             raise FileNotFoundError("One or more fastq files do not exist")
-    output.mkdir(exist_ok=True, parents=True)
     index_path = aligner.value.check_index(index, airplane=airplane)
     backend_cmds = [
         aligner.value.gen_paired_clean_cmd(
@@ -276,6 +285,7 @@ def clean_paired_fastqs(
             rename=rename,
             reorder=reorder,
             casava=casava,
+            stdin=stdin,
             stdout=stdout,
             output=output,
             aligner_args=aligner_args,
@@ -300,6 +310,7 @@ def clean_paired_fastqs(
         rename=rename,
         reorder=reorder,
         casava=casava,
+        stdin=stdin,
         stdout=stdout,
         output=output,
     )