Rename --offline to --airplane to free up -o for --output

README.md

@@ -87,7 +87,7 @@ hostile clean --fastq1 short.r1.fq.gz --fastq2 short.r2.fq.gz --stdout > clean.f
 ```bash
 $ hostile clean -h
 usage: hostile clean [-h] --fastq1 FASTQ1 [--fastq2 FASTQ2] [--aligner {bowtie2,minimap2,auto}] [--index INDEX] [--invert] [--rename] [--reorder] [--out-dir OUT_DIR] [-s] [-t THREADS] [--force]
-                     [--aligner-args ALIGNER_ARGS] [--offline] [-d]
+                     [--aligner-args ALIGNER_ARGS] [--airplane] [-d]
 
 Remove reads aligning to an index from fastq[.gz] input files.
 
@@ -120,7 +120,7 @@ options:
   --aligner-args ALIGNER_ARGS
                         additional arguments for alignment
                         (default: )
-  --offline             disable automatic index download
+  --airplane             disable automatic index download
                         (default: False)
   -d, --debug           show debug messages
                         (default: False)

src/hostile/aligner.py

@@ -35,7 +35,7 @@ class Aligner:
     def __post_init__(self):
         Path(self.data_dir).mkdir(exist_ok=True, parents=True)
 
-    def check_index(self, index: str, offline: bool = False) -> Path:
+    def check_index(self, index: str, airplane: bool = False) -> Path:
         """Test aligner and check/download a ref/index if necessary, returning genome or index path"""
         try:
             util.run(f"{self.bin_path} --version", cwd=self.data_dir)
@@ -49,7 +49,7 @@ def check_index(self, index: str, offline: bool = False) -> Path:
             elif (self.data_dir / f"{index}.1.bt2").is_file():
                 index_path = self.data_dir / index
                 logging.info(f"Found cached standard index {index}")
-            elif not offline and util.fetch_manifest(util.INDEX_REPOSITORY_URL).get(
+            elif not airplane and util.fetch_manifest(util.INDEX_REPOSITORY_URL).get(
                 index
             ):
                 file_name = f"{index}.tar"
@@ -70,10 +70,8 @@ def check_index(self, index: str, offline: bool = False) -> Path:
                 logging.info(f"Downloaded standard index {index_path}")
             else:
                 message = f"{index} is neither a valid custom Bowtie2 index path nor a valid standard index name. Mode: short read (Bowtie2)"
-                if offline:
-                    message += (
-                        ". Disable offline mode to enable discovery of standard indexes"
-                    )
+                if airplane:
+                    message += ". Disable airplane mode to enable discovery of standard indexes"
                 raise FileNotFoundError(message)
 
         elif self.name == "Minimap2":
@@ -88,7 +86,7 @@ def check_index(self, index: str, offline: bool = False) -> Path:
                     logging.info(
                         f"Found cached standard index {index} (MMI file will be generated)"
                     )
-            elif not offline and util.fetch_manifest(util.INDEX_REPOSITORY_URL).get(
+            elif not airplane and util.fetch_manifest(util.INDEX_REPOSITORY_URL).get(
                 index
             ):
                 file_name = f"{index}.fa.gz"
@@ -108,10 +106,8 @@ def check_index(self, index: str, offline: bool = False) -> Path:
                 logging.info(f"Downloaded standard index {index_path}")
             else:
                 message = f"{index} is neither a valid custom FASTA path, nor a valid standard index name. Mode: long read (Minimap2)"
-                if offline:
-                    message += (
-                        ". Disable offline mode to enable discovery of standard indexes"
-                    )
+                if airplane:
+                    message += ". Disable airplane mode to enable discovery of standard indexes"
                 raise FileNotFoundError(message)
 
         return index_path

src/hostile/cli.py

@@ -34,18 +34,18 @@ def clean(
     aligner_args: str = "",
     threads: int = util.CPU_COUNT,
     force: bool = False,
-    offline: bool = False,
+    airplane: bool = False,
     debug: bool = False,
 ) -> None:
     """
-    Remove reads aligning to an index from fastq[.gz] input files.
+    Remove reads aligning to an index from fastq[.gz] input files or stdin.
 
     :arg fastq1: path to forward fastq[.gz] file
     :arg fastq2: optional path to reverse fastq[.gz] file (short reads only)
     :arg aligner: alignment algorithm. Defaults to minimap2 (long read) given fastq1 only or bowtie2 (short read)
         given fastq1 and fastq2. Override with bowtie2 for single/unpaired short reads
     :arg index: name of standard index or path to custom genome (Minimap2) or Bowtie2 index
-    :arg invert: keep only reads aligning to the target genome (and their mates if applicable)
+    :arg invert: keep only reads aligning to the index (and their mates if applicable)
     :arg rename: replace read names with incrementing integers
     :arg reorder: ensure deterministic output order
     :arg casava: use Casava 1.8+ read header format
@@ -54,7 +54,7 @@ def clean(
     :arg aligner_args: additional arguments for alignment
     :arg threads: number of alignment threads. A sensible default is chosen automatically
     :arg force: overwrite existing output files
-    :arg offline: disable automatic index download
+    :arg airplane: disable automatic index download
     :arg debug: show debug messages
     """
 
@@ -84,7 +84,7 @@ def clean(
             aligner_args=aligner_args,
             threads=threads,
             force=force,
-            offline=offline,
+            airplane=airplane,
         )
     else:
         stats = lib.clean_fastqs(
@@ -100,7 +100,7 @@ def clean(
             aligner_args=aligner_args,
             threads=threads,
             force=force,
-            offline=offline,
+            airplane=airplane,
         )
     print(json.dumps(stats, indent=4), file=sys.stderr if stdout else sys.stdout)
 

src/hostile/lib.py

@@ -168,7 +168,7 @@ def clean_fastqs(
     aligner_args: str = "",
     threads: int = util.CPU_COUNT,
     force: bool = False,
-    offline: bool = False,
+    airplane: bool = False,
 ):
     aligner_threads, compression_threads = util.allocate_threads(threads, stdout=stdout)
     logging.debug(
@@ -189,7 +189,7 @@ def clean_fastqs(
             logging.info(f"{fastqs=}")
             raise FileNotFoundError("One or more fastq files do not exist")
     Path(out_dir).mkdir(exist_ok=True, parents=True)
-    index_path = aligner.value.check_index(index, offline=offline)
+    index_path = aligner.value.check_index(index, airplane=airplane)
     backend_cmds = [
         aligner.value.gen_clean_cmd(
             fastq=fastq,
@@ -246,7 +246,7 @@ def clean_paired_fastqs(
     aligner_args: str = "",
     threads: int = util.CPU_COUNT,
     force: bool = False,
-    offline: bool = False,
+    airplane: bool = False,
 ):
     aligner_threads, compression_threads = util.allocate_threads(threads, stdout=stdout)
     logging.debug(
@@ -264,7 +264,7 @@ def clean_paired_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")
     Path(out_dir).mkdir(exist_ok=True, parents=True)
-    index_path = aligner.value.check_index(index, offline=offline)
+    index_path = aligner.value.check_index(index, airplane=airplane)
     backend_cmds = [
         aligner.value.gen_paired_clean_cmd(
             fastq1=fastq_pair[0],

tests/test_all.py

@@ -710,25 +710,25 @@ def test_mismatched_number_of_reads_bowtie2(tmp_path):
         )
 
 
-def test_offline_invalid_mm2_standard_index_name(tmp_path):
+def test_airplane_invalid_mm2_standard_index_name(tmp_path):
     with pytest.raises(FileNotFoundError):
         lib.clean_fastqs(
             fastqs=[data_dir / "sars-cov-2_1_1.fastq"],
             index="invalid_index_name",
             aligner=lib.ALIGNER.minimap2,
             out_dir=tmp_path,
-            offline=True,
+            airplane=True,
         )
 
 
-def test_offline_invalid_bt2_standard_index_name(tmp_path):
+def test_airplane_invalid_bt2_standard_index_name(tmp_path):
     with pytest.raises(FileNotFoundError):
         lib.clean_fastqs(
             fastqs=[data_dir / "sars-cov-2_1_1.fastq"],
             index="invalid_index_name",
             aligner=lib.ALIGNER.bowtie2,
             out_dir=tmp_path,
-            offline=True,
+            airplane=True,
         )