diff --git a/fgpyo/sam/__init__.py b/fgpyo/sam/__init__.py
index 8290916d..b68ce5e6 100644
--- a/fgpyo/sam/__init__.py
+++ b/fgpyo/sam/__init__.py
@@ -197,13 +197,14 @@ class SamFileType(enum.Enum):
ext (str): The standard file extension for this file type.
"""
- def __init__(self, mode: str, ext: str) -> None:
+ def __init__(self, mode: str, ext: str, index_ext: Optional[str]) -> None:
self.mode = mode
self.extension = ext
+ self.index_extension = index_ext
- SAM = ("", ".sam")
- BAM = ("b", ".bam")
- CRAM = ("c", ".cram")
+ SAM = ("", ".sam", None)
+ BAM = ("b", ".bam", ".bai")
+ CRAM = ("c", ".cram", ".crai")
@classmethod
def from_path(cls, path: Union[Path, str]) -> "SamFileType":
diff --git a/fgpyo/sam/builder.py b/fgpyo/sam/builder.py
index 6209763e..77c62802 100755
--- a/fgpyo/sam/builder.py
+++ b/fgpyo/sam/builder.py
@@ -27,6 +27,7 @@
from pysam import AlignmentHeader
from fgpyo import sam
+from fgpyo import samtools
from fgpyo.sam import SamOrder
@@ -544,7 +545,7 @@ def to_path(
with NamedTemporaryFile(suffix=".bam", delete=True) as fp:
file_handle: IO
- if self.sort_order is SamOrder.Unsorted:
+ if self.sort_order in [SamOrder.Unsorted, SamOrder.Unknown]:
file_handle = path.open("w")
else:
file_handle = fp.file
@@ -555,20 +556,14 @@ def to_path(
for rec in self._records:
if pred(rec):
writer.write(rec)
-
- default_samtools_opt_list = ["-o", str(path), fp.name]
-
file_handle.close()
- if self.sort_order == SamOrder.QueryName:
- # Ignore type hints for now until we have wrappers to use here.
- pysam.sort(*(["-n"] + default_samtools_opt_list)) # type: ignore
- elif self.sort_order == SamOrder.Coordinate:
- # Ignore type hints for now until we have wrappers to use here.
- pysam.sort(*default_samtools_opt_list) # type: ignore
- if index:
- # Ignore type hints for now until we have wrappers to use here.
- pysam.index(str(path)) # type: ignore
-
+ if self.sort_order not in [SamOrder.Unsorted, SamOrder.Unknown]:
+ samtools.sort(
+ input=Path(fp.name),
+ output=path,
+ index_output=index,
+ sort_order=self.sort_order,
+ )
return path
def __len__(self) -> int:
diff --git a/fgpyo/samtools.py b/fgpyo/samtools.py
new file mode 100644
index 00000000..189dbc5b
--- /dev/null
+++ b/fgpyo/samtools.py
@@ -0,0 +1,377 @@
+"""
+Type-Hinted Wrappers around pysam samtools dispatch functions.
+--------------------------------------------------------------
+
+Calls pysam samtools functions, with type hints for relevant parameters and return types.
+
+Examples
+~~~~~~~~
+.. code-block:: python
+
+ >>> from fgpyo import samtools
+ >>> Path("example1.sorted.bam.bai").exists()
+ False
+ >>> samtools.sort(input=Path("example1.bam"), output=Path("example1.sorted.bam"))
+ ''
+ >>> samtools.index(input=Path("example1.sorted.bam"))
+ ''
+ >>> Path("example1.sorted.bam.bai").exists()
+ True
+
+Module Contents
+~~~~~~~~~~~~~~~
+The module contains the following public method definitions:
+ - :class:`~fgpyo.samtools.dict` -- Wrapper around pysam call to samtools dict with type hints
+ on inputs and return type
+ - :class:`~fgpyo.samtools.sort` -- Wrapper around pysam call to samtools sort with type hints
+ on inputs and return type
+ - :class:`~fgpyo.samtools.faidx` -- Wrapper around pysam call to samtools faidx with type hints
+ on inputs and return type
+ - :class:`~fgpyo.samtools.index` -- Wrapper around pysam call to samtools index with type hints
+ on inputs and return type
+"""
+import enum
+from pathlib import Path
+from typing import TYPE_CHECKING
+from typing import List
+from typing import Optional
+from typing import Tuple
+
+from fgpyo.sam import SamFileType
+from fgpyo.sam import SamOrder
+
+
+def pysam_fn(*args: str) -> str:
+ """
+ Type hinted import of an example function from the pysam samtools dispatcher.
+ """
+ pass
+
+
+if TYPE_CHECKING:
+ _pysam_dict = pysam_fn
+ _pysam_sort = pysam_fn
+ _pysam_faidx = pysam_fn
+ _pysam_index = pysam_fn
+else:
+ from pysam import dict as _pysam_dict
+ from pysam import faidx as _pysam_faidx
+ from pysam import index as _pysam_index
+ from pysam import sort as _pysam_sort
+
+
+def dict(
+ input: Path,
+ output: Path,
+ no_header: bool = False,
+ alias: bool = False,
+ assembly: Optional[str] = None,
+ alt: Optional[Path] = None,
+ species: Optional[str] = None,
+ uri: Optional[str] = None,
+) -> str:
+ """
+ Calls the `samtools` function `dict` using the pysam samtools dispatcher.
+
+ Arguments will be formatted into the appropriate command-line call which will be invoked
+ using the pysam dispatcher.
+
+ Returns the stdout of the resulting call to pysam.dict()
+
+ Args:
+ input: Path to the FASTA files to generate a sequence dictionary for.
+ output: Path to the file to write output to.
+ no_header: If true will not print the @HD header line.
+ assembly: The assembly for the AS tag.
+ alias: Adds an AN tag with the same value as the SN tag, except that a 'chr' prefix is
+ removed if SN has one or added if it does not. For mitochondria (i.e., when SN is “M”
+ or “MT”, with or without a “chr” prefix), also adds the remaining combinations of
+ “chr/M/MT” to the AN tag.
+ alt: Add an AH tag to each sequence listed in the specified bwa-style .alt file. These
+ files use SAM records to represent alternate locus sequences (as named in the QNAME
+ field) and their mappings to the primary assembly.
+ species: Specify the species for the SP tag.
+ uri: Specify the URI for the UR tag. Defaults to the absolute path of ref.fasta.
+ """
+
+ args: List[str] = ["--output", str(output)]
+
+ if no_header:
+ args.append("--no-header")
+
+ if alias:
+ args.append("--alias")
+
+ if assembly is not None:
+ args.extend(["--assembly", assembly])
+
+ if alt is not None:
+ args.extend(["--alt", str(alt)])
+
+ if species is not None:
+ args.extend(["--species", species])
+
+ if uri is not None:
+ args.extend(["--uri", uri])
+
+ args.append(str(input))
+
+ return _pysam_dict(*args)
+
+
+@enum.unique
+class FaidxMarkStrand(enum.Enum):
+ RevComp = "rc"
+ No = "no"
+ Sign = "sign"
+ Custom = "custom"
+
+
+def faidx(
+ input: Path,
+ output: Optional[Path] = None,
+ length: int = 60,
+ regions: Optional[List[str]] = None,
+ region_file: Optional[Path] = None,
+ fai_idx: Optional[Path] = None,
+ gzi_idx: Optional[Path] = None,
+ continue_if_non_existent: bool = False,
+ fastq: bool = False,
+ reverse_complement: bool = False,
+ mark_strand: FaidxMarkStrand = FaidxMarkStrand.RevComp,
+ custom_mark_strand: Optional[Tuple[str, str]] = None,
+) -> str:
+ """
+ Calls the `samtools` function `faidx` using the pysam samtools dispatcher.
+
+ Arguments will be formatted into the appropriate command-line call which will be invoked
+ using the pysam dispatcher.
+
+ Returns the stdout of the resulting call to pysam.faidx()
+
+ Args:
+ input: Path to the FAIDX files to index / read from.
+ output: Path to the file to write FASTA output.
+ length: Length of FASTA sequence line.
+ regions: regions to extract from the FASTA file in samtools region format
+ (<chrom>:<1-based start>-<1-based end>)
+ region_file: Path to file containing regions to extract from the FASTA file in samtools
+ region format (<chrom>:<1-based start>-<1-based end>). 1 region descriptor per line.
+ fai_idx: Read/Write to specified FAI index file.
+ gzi_idx: Read/Write to specified compressed file index (used with .gz files).
+ continue_if_non_existent: If true continue qorking if a non-existent region is requested.
+ fastq: Read FASTQ files and output extracted sequences in FASTQ format. Same as using
+ samtools fqidx.
+ reverse_complement: Output the sequence as the reverse complement. When this option is
+ used, “/rc” will be appended to the sequence names. To turn this off or change the
+ string appended, use the mark_strand parameter.
+ mark_strand: Append strand indicator to sequence name. Type to append can be one of:
+ FaidxMarkStrand.RevComp - Append '/rc' when writing the reverse complement. This is the
+ default.
+
+ FaidxMarkStrand.No - Do not append anything.
+
+ FaidxMarkStrand.Sign - Append '(+)' for forward strand or '(-)' for reverse
+ complement. This matches the output of “bedtools getfasta -s”.
+
+ FaidxMarkStrand.Custom - custom,<custom_mark_strand[0]>,<custom_mark_strand[1]>
+ Append string <pos> to names when writing the forward strand and <neg> when writing the
+ reverse strand. Spaces are preserved, so it is possible to move the indicator into the
+ comment part of the description line by including a leading space in the strings
+ <custom_mark_strand[0]> and <custom_mark_strand[1]>.
+ custom_mark_strand: The custom strand indicators to use in in the Custom MarkStrand
+ setting. The first value of the tuple will be used as the positive strand indicator,
+ the second value will be used as the negative strand indicator.
+ """
+
+ mark_strand_str: str
+ if mark_strand == FaidxMarkStrand.Custom:
+ assert custom_mark_strand is not None, (
+ "Cannot use custom mark strand without providing the custom strand indicators to "
+ + "`custom_mark_string`"
+ )
+ mark_strand_str = f"{mark_strand.value},{custom_mark_strand[0]},{custom_mark_strand[1]}"
+ else:
+ mark_strand_str = mark_strand.value
+
+ args: List[str] = ["--length", str(length), "--mark-strand", mark_strand_str]
+
+ if output is not None:
+ args.extend(["--output", str(output)])
+
+ if continue_if_non_existent:
+ args.append("--continue")
+ if reverse_complement:
+ args.append("--reverse-complement")
+ if fastq:
+ args.append("--fastq")
+
+ if fai_idx is not None:
+ args.extend(["--fai-idx", str(fai_idx)])
+
+ if gzi_idx is not None:
+ args.extend(["--gzi-idx", str(gzi_idx)])
+
+ if region_file is not None:
+ args.extend(["--region-file", str(region_file)])
+
+ args.append(str(input))
+
+ if regions is not None:
+ args.extend(regions)
+
+ return _pysam_faidx(*args)
+
+
+@enum.unique
+class SamIndexType(enum.Enum):
+ BAI = "-b"
+ CSI = "-c"
+
+
+def index(
+ input: Path,
+ # See https://github.com/pysam-developers/pysam/issues/1155
+ # inputs: List[Path], Cant currently accept multiple
+ output: Optional[Path] = None,
+ threads: int = 0,
+ index_type: SamIndexType = SamIndexType.BAI,
+ csi_index_size: int = 14,
+) -> str:
+ """
+ Calls the `samtools` function `index` using the pysam samtools dispatcher.
+
+ Arguments will be formatted into the appropriate command-line call which will be invoked
+ using the pysam dispatcher.
+
+ Returns the stdout of the resulting call to pysam.index()
+
+ Args:
+ input: Path to the SAM/BAM/CRAM file to index.
+ output: Path to the file to write output. (Currently may only be used when exactly one
+ alignment file is being indexed.)
+ threads: Number of input/output compression threads to use in addition to main thread.
+ index_type: The type of index file to produce when indexing.
+ csi_index_size: Sets the minimum interval size of CSI indices to 2^INT.
+ """
+
+ # assert len(inputs) >= 1, "Must provide at least one input to samtools index."
+
+ # if len(inputs) != 1:
+ # assert (
+ # output is None
+ # ), "Output currently can only be used if there is exactly one input file being indexed"
+ # args = ["-M"]
+ # else:
+ # args = []
+ args = []
+
+ if index_type != SamIndexType.BAI:
+ args.append(index_type.value)
+
+ if index_type == SamIndexType.CSI:
+ args.extend(["-m", str(csi_index_size)])
+ args.extend(["-@", str(threads)])
+ args.append(str(input))
+ if output is not None:
+ args.extend(["-o", str(output)])
+
+ return _pysam_index(*args)
+
+
+def sort(
+ input: Path,
+ output: Path,
+ index_output: bool = True,
+ sort_unmapped_reads: bool = False,
+ kmer_size: int = 20,
+ compression_level: Optional[int] = None,
+ memory_per_thread: str = "768MB",
+ sort_order: SamOrder = SamOrder.Coordinate,
+ sort_tag: Optional[str] = None,
+ output_format: SamFileType = SamFileType.BAM,
+ tempfile_prefix: Optional[str] = None,
+ threads: int = 1,
+ no_pg: bool = False,
+) -> str:
+ """
+ Calls the `samtools` function sort using the pysam samtools dispatcher.
+
+ Arguments will be formatted into the appropriate command-line call which will be invoked
+ using the pysam dispatcher.
+
+ Returns the stdout of the resulting call to pysam.sort()
+
+ Args:
+ input: Path to the SAM/BAM/CRAM file to sort.
+ output: Path to the file to write output.
+ index_output: If true, creates an index for the output file.
+ sort_unmapped_reads: If true, sort unmapped reads by their sequence minimizer, reverse
+ complementing where appropriate. This has the effect of collating some similar data
+ together, improving the compressibility of the unmapped sequence. The minimiser kmer
+ size is adjusted using the ``kmer_size`` option. Note data compressed in this manner
+ may need to be name collated prior to conversion back to fastq.
+
+ Mapped sequences are sorted by chromosome and position.
+ kmer_size: the kmer-size to be used if sorting unmapped reads.
+ compression_level: The compression level to be used in the final output file.
+ memory_per_thread: Approximately the maximum required memory per thread, specified either
+ in bytes or with a K, M, or G suffix.
+
+ To prevent sort from creating a huge number of temporary files, it enforces a minimum
+ value of 1M for this setting.
+ sort_order: The sort order to use when sorting the file.
+ sort_tag: The tag to use to use to sort the SAM/BAM/CRAM records. Will be sorted by
+ this tag first, followed by position (or name, depending on ``sort_order``
+ provided).
+ output_format: the output file format to write the results as.
+ By default, will try to select a format based on the ``output`` filename extension;
+ if no format can be deduced, bam is selected.
+ tempfile_prefix: The prefix to use for temporary files. Resulting files will be in
+ format PREFIX.nnnn.bam, or if the specified PREFIX is an existing directory, to
+ PREFIX/samtools.mmm.mmm.tmp.nnnn.bam, where mmm is unique to this invocation of the
+ sort command.
+
+ By default, any temporary files are written alongside the output file, as
+ out.bam.tmp.nnnn.bam, or if output is to standard output, in the current directory
+ as samtools.mmm.mmm.tmp.nnnn.bam.
+ threads: The number of threads to use when sorting. By default, operation is
+ single-threaded.
+ no_pg: If true, will not add a @PG line to the header of the output file.
+ """
+
+ output_string = (
+ f"{output}##idx##{output}{output_format.index_extension}"
+ if index_output and output_format.index_extension is not None
+ else str(output)
+ )
+
+ args = ["-m", memory_per_thread, "-O", output_format._name_, "-@", str(threads)]
+
+ if sort_unmapped_reads:
+ args.extend(["-M", "-K", str(kmer_size)])
+
+ if compression_level is not None:
+ args.extend(["-I", str(compression_level)])
+
+ if sort_order == SamOrder.QueryName:
+ args.append("-n")
+ elif sort_order == SamOrder.TemplateCoordinate:
+ args.append("--template-coordinate")
+ else:
+ assert (
+ sort_order == SamOrder.Coordinate
+ ), "Sort order to samtools sort cannot be Unknown or Unsorted"
+
+ if sort_tag is not None:
+ args.extend(["-t", sort_tag])
+
+ if tempfile_prefix is not None:
+ args.extend(["-T", tempfile_prefix])
+
+ if no_pg:
+ args.append("--no-PG")
+
+ args.extend(["-o", output_string, str(input)])
+
+ return _pysam_sort(*args)
diff --git a/fgpyo/tests/test_samtools.py b/fgpyo/tests/test_samtools.py
new file mode 100644
index 00000000..ee0f97a9
--- /dev/null
+++ b/fgpyo/tests/test_samtools.py
@@ -0,0 +1,664 @@
+from pathlib import Path
+from typing import List
+from typing import Optional
+
+import bgzip
+import pytest
+from pysam.utils import SamtoolsError
+
+from fgpyo import sam
+from fgpyo import samtools
+from fgpyo.sam import SamFileType
+from fgpyo.sam import SamOrder
+from fgpyo.sam.builder import SamBuilder
+from fgpyo.samtools import FaidxMarkStrand
+from fgpyo.samtools import SamIndexType
+
+EXAMPLE_DICT_FASTA: str = """\
+>chr1
+GATTACATTTGAGAGA
+>chr2
+CCCCTACCCACCC
+>chr1_alt
+GATTACATGAGAGA
+>chr2_alt
+CCCCTACCACCC
+"""
+
+EXPECTED_DICT: str = """\
+@HD VN:1.0 SO:unsorted
+@SQ SN:chr1 LN:16 M5:0b2bf1b29cf5338d75a8feb8c8a3784b UR:consistent_location
+@SQ SN:chr2 LN:13 M5:87afe3395654b1fe1443b54490c47871 UR:consistent_location
+@SQ SN:chr1_alt LN:14 M5:23ce480f016f77dfb29d3c17aa98f567 UR:consistent_location
+@SQ SN:chr2_alt LN:12 M5:2ee663b21d249ebecaa9ffbdb6e0b970 UR:consistent_location
+"""
+
+HEADERLESS_DICT: str = """\
+@SQ SN:chr1 LN:16 M5:0b2bf1b29cf5338d75a8feb8c8a3784b UR:consistent_location
+@SQ SN:chr2 LN:13 M5:87afe3395654b1fe1443b54490c47871 UR:consistent_location
+@SQ SN:chr1_alt LN:14 M5:23ce480f016f77dfb29d3c17aa98f567 UR:consistent_location
+@SQ SN:chr2_alt LN:12 M5:2ee663b21d249ebecaa9ffbdb6e0b970 UR:consistent_location
+"""
+
+OTHER_TAG_DICT: str = """\
+@HD VN:1.0 SO:unsorted
+@SQ SN:chr1 LN:16 M5:0b2bf1b29cf5338d75a8feb8c8a3784b AN:1 UR:consistent_location AS:test1 SP:test3
+@SQ SN:chr2 LN:13 M5:87afe3395654b1fe1443b54490c47871 AN:2 UR:consistent_location AS:test1 SP:test3
+@SQ SN:chr1_alt LN:14 M5:23ce480f016f77dfb29d3c17aa98f567 AH:* AN:1_alt UR:consistent_location AS:test1 SP:test3
+@SQ SN:chr2_alt LN:12 M5:2ee663b21d249ebecaa9ffbdb6e0b970 AH:* AN:2_alt UR:consistent_location AS:test1 SP:test3
+""" # noqa: E501
+
+
+@pytest.fixture
+def example_dict_fasta(tmp_path: Path) -> Path:
+ outfile = tmp_path / "example.fa"
+
+ with outfile.open("w") as out_fh:
+ out_fh.write(EXAMPLE_DICT_FASTA)
+
+ return outfile
+
+
+def test_dict_produces_sequence_dict(
+ tmp_path: Path,
+ example_dict_fasta: Path,
+) -> None:
+ output_access = tmp_path / "example.dict"
+ assert not output_access.exists()
+ samtools.dict(input=example_dict_fasta, output=output_access, uri="consistent_location")
+ assert output_access.exists()
+
+ output_contents: str
+ with output_access.open("r") as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == EXPECTED_DICT
+
+
+def test_dict_no_header_works(
+ tmp_path: Path,
+ example_dict_fasta: Path,
+) -> None:
+ output_access = tmp_path / "example.dict"
+ assert not output_access.exists()
+ samtools.dict(
+ input=example_dict_fasta, output=output_access, no_header=True, uri="consistent_location"
+ )
+ assert output_access.exists()
+
+ output_contents: str
+ with output_access.open("r") as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == HEADERLESS_DICT
+
+
+ALT_FILE: str = """\
+chr1_alt 0 chr1 1 30 7M2D7M * 0 0 * * NM:i:2
+chr2_alt 0 chr2 1 30 6M1D6M * 0 0 * * NM:i:1
+"""
+
+
+@pytest.fixture
+def bwa_style_alt(tmp_path: Path) -> Path:
+ outfile = tmp_path / "example.alt"
+
+ with outfile.open("w") as out_fh:
+ out_fh.write(ALT_FILE)
+
+ return outfile
+
+
+def test_dict_other_tags_work(
+ tmp_path: Path,
+ example_dict_fasta: Path,
+ bwa_style_alt: Path,
+) -> None:
+ output_access = tmp_path / "example.dict"
+ assert not output_access.exists()
+ samtools.dict(
+ input=example_dict_fasta,
+ output=output_access,
+ alias=True,
+ assembly="test1",
+ alt=bwa_style_alt,
+ species="test3",
+ uri="consistent_location",
+ )
+ assert output_access.exists()
+
+ output_contents: str
+ with output_access.open("r") as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == OTHER_TAG_DICT
+
+
+EXAMPLE_FAIDX_FASTA: str = """\
+>chr1
+GATTACATTTGAGAGA
+>chr2
+CCCCTACCCACCC
+"""
+
+SUBSET_FASTA_TEMPLATE: str = """\
+>chr1:1-7{mark_strand}
+GATTACA
+>chr2:8-13{mark_strand}
+CCACCC
+"""
+SUBSET_FASTA: str = SUBSET_FASTA_TEMPLATE.format(mark_strand="")
+
+WRAPPED_SUBSET_FASTA: str = """\
+>chr1:1-7
+GATTA
+CA
+>chr2:8-13
+CCACC
+C
+"""
+
+
+@pytest.fixture
+def example_faidx_fasta(tmp_path: Path) -> Path:
+ outfile = tmp_path / "example.fa"
+
+ with outfile.open("w") as out_fh:
+ out_fh.write(EXAMPLE_FAIDX_FASTA)
+
+ return outfile
+
+
+def test_faidx_produces_functional_index(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(input=example_faidx_fasta)
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta, output=output_access, regions=["chr1:1-7", "chr2:8-13"]
+ )
+
+ output_contents: str
+ with output_access.open("r") as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == SUBSET_FASTA
+
+
+def test_faidx_fails_if_non_existent_region_requested(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ with pytest.raises(SamtoolsError):
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(input=example_faidx_fasta)
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta, output=output_access, regions=["chr3:1-4", "chr1:1-7"]
+ )
+
+
+def test_faidx_passes_if_non_existent_region_requested_when_continue_passed(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ assert not output_index_expected.exists()
+ samtools.faidx(input=example_faidx_fasta)
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ continue_if_non_existent=True,
+ regions=["chr3:1-4", "chr1:1-7"],
+ )
+
+
+def test_faidx_regions_and_regions_file_result_in_same_thing(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(input=example_faidx_fasta)
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+
+ regions = ["chr1:1-7", "chr2:8-13"]
+
+ region_file = tmp_path / "regions.txt"
+ with region_file.open("w") as region_fh:
+ region_fh.writelines([f"{region}\n" for region in regions])
+
+ samtools.faidx(input=example_faidx_fasta, output=output_access, regions=regions)
+
+ manually_passed_output_contents: str
+ with output_access.open("r") as subset_fasta:
+ manually_passed_output_contents = subset_fasta.read()
+
+ samtools.faidx(input=example_faidx_fasta, output=output_access, region_file=region_file)
+
+ file_passed_output_contents: str
+ with output_access.open("r") as subset_fasta:
+ file_passed_output_contents = subset_fasta.read()
+
+ assert manually_passed_output_contents == file_passed_output_contents
+
+
+def test_length_parameter(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(
+ input=example_faidx_fasta,
+ )
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ regions=["chr1:1-7", "chr2:8-13"],
+ length=5,
+ )
+
+ output_contents: str
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == WRAPPED_SUBSET_FASTA
+
+
+RC_SUBSET_FASTA: str = """\
+>chr1:1-7{mark_strand}
+TGTAATC
+>chr2:8-13{mark_strand}
+GGGTGG
+"""
+
+
+def test_rc_parameter(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(
+ input=example_faidx_fasta,
+ )
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ reverse_complement=True,
+ regions=["chr1:1-7", "chr2:8-13"],
+ )
+
+ output_contents: str
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == RC_SUBSET_FASTA.format(mark_strand="/rc")
+
+
+@pytest.mark.parametrize(
+ argnames=["mark_strand", "expected_fwd_mark_strand", "expected_rev_mark_strand"],
+ argvalues=[
+ (FaidxMarkStrand.RevComp, "", "/rc"),
+ (FaidxMarkStrand.No, "", ""),
+ (FaidxMarkStrand.Sign, "(+)", "(-)"),
+ (FaidxMarkStrand.Custom, "ex1a", "ex1b"),
+ (FaidxMarkStrand.Custom, "ex2a", "ex2b"),
+ ],
+ ids=["rev comp", "no", "sign", "custom1", "custom2"],
+)
+def test_mark_strand_parameters(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+ mark_strand: FaidxMarkStrand,
+ expected_fwd_mark_strand: str,
+ expected_rev_mark_strand: str,
+) -> None:
+ output_index_expected = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(
+ input=example_faidx_fasta,
+ )
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ reverse_complement=False,
+ mark_strand=mark_strand,
+ custom_mark_strand=(expected_fwd_mark_strand, expected_rev_mark_strand),
+ regions=["chr1:1-7", "chr2:8-13"],
+ )
+ output_contents: str
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == SUBSET_FASTA_TEMPLATE.format(mark_strand=expected_fwd_mark_strand)
+
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ reverse_complement=True,
+ mark_strand=mark_strand,
+ custom_mark_strand=(expected_fwd_mark_strand, expected_rev_mark_strand),
+ regions=["chr1:1-7", "chr2:8-13"],
+ )
+
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == RC_SUBSET_FASTA.format(mark_strand=expected_rev_mark_strand)
+
+
+EXAMPLE_FASTQ: str = """\
+@chr1
+GATTACATTTGAGAGA
++
+;;;;;;;;;;;;;;;;
+@chr2
+CCCCTACCCACCC
++
+;;;;;;;;;;;;;
+"""
+
+SUBSET_FASTQ: str = """\
+@chr1:1-7
+GATTACA
++
+;;;;;;;
+@chr2:8-13
+CCACCC
++
+;;;;;;
+"""
+
+
+@pytest.fixture
+def example_fastq(tmp_path: Path) -> Path:
+ outfile = tmp_path / "example.fq"
+
+ with outfile.open("w") as out_fh:
+ out_fh.write(EXAMPLE_FASTQ)
+
+ return outfile
+
+
+def test_fastq_parameter(
+ tmp_path: Path,
+ example_fastq: Path,
+) -> None:
+ output_index_expected = Path(f"{example_fastq}.fai")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ samtools.faidx(
+ input=example_fastq,
+ fastq=True,
+ )
+ assert output_index_expected.exists()
+
+ output_access = tmp_path / "output_subset.fq"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_fastq,
+ output=output_access,
+ regions=["chr1:1-7", "chr2:8-13"],
+ fastq=True,
+ )
+
+ output_contents: str
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+
+ assert output_contents == SUBSET_FASTQ
+
+
+@pytest.fixture
+def example_faidx_fasta_gz(tmp_path: Path) -> Path:
+ outfile = tmp_path / "example.fa.gz"
+
+ with outfile.open(mode="wb") as out_fh:
+ with bgzip.BGZipWriter(out_fh) as fh:
+ fh.write(bytes(EXAMPLE_FAIDX_FASTA, "Utf-8"))
+
+ return outfile
+
+
+def test_index_outputs(
+ tmp_path: Path,
+ example_faidx_fasta: Path,
+ example_faidx_fasta_gz: Path,
+) -> None:
+ example_fai = Path(f"{example_faidx_fasta}.fai")
+
+ # Make sure we're producing the index
+ assert not example_fai.exists()
+ samtools.faidx(
+ input=example_faidx_fasta,
+ fai_idx=example_fai,
+ )
+ assert example_fai.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ regions=["chr1:1-7", "chr2:8-13"],
+ fai_idx=example_fai,
+ )
+
+ output_contents: str
+ with output_access.open() as subset_fasta:
+ output_contents = subset_fasta.read()
+ assert output_contents == SUBSET_FASTA
+
+ example_gzi = Path(f"{example_faidx_fasta_gz}.gzi")
+ assert not example_gzi.exists()
+ samtools.faidx(
+ input=example_faidx_fasta_gz,
+ gzi_idx=example_gzi,
+ )
+ assert example_gzi.exists()
+
+ output_access = tmp_path / "output_subset.fa"
+ # Make sure the index is functional
+ samtools.faidx(
+ input=example_faidx_fasta,
+ output=output_access,
+ regions=["chr1:1-7", "chr2:8-13"],
+ gzi_idx=example_gzi,
+ )
+
+ compressed_output_contents: str
+ with output_access.open() as subset_fasta:
+ compressed_output_contents = subset_fasta.read()
+
+ assert compressed_output_contents == SUBSET_FASTA
+
+
+@pytest.mark.parametrize(
+ argnames=["index_type"],
+ argvalues=[
+ (SamIndexType.BAI,),
+ (SamIndexType.CSI,),
+ ],
+ ids=["BAI", "CSI"],
+)
+def test_index_works_with_one_input(
+ tmp_path: Path,
+ index_type: SamIndexType,
+) -> None:
+ builder = SamBuilder(sort_order=SamOrder.Coordinate)
+ builder.add_pair(name="test1", chrom="chr1", start1=4000, start2=4300)
+ builder.add_pair(
+ name="test2", chrom="chr1", start1=5000, start2=4700, strand1="-", strand2="+"
+ )
+ builder.add_pair(name="test3", chrom="chr2", start1=4000, start2=4300)
+ builder.add_pair(name="test4", chrom="chr5", start1=4000, start2=4300)
+
+ # At the moment sam builder doesnt support generating CRAM and SAM formats, so for now we're
+ # only testing on BAMs
+ input_file = tmp_path / "test_input.bam"
+ builder.to_path(input_file)
+
+ output_index_expected = Path(f"{input_file}.{index_type._name_.lower()}")
+
+ # Make sure we're producing the index
+ assert not output_index_expected.exists()
+ # samtools.index(inputs=[input_file], index_type=index_type)
+ samtools.index(input=input_file, index_type=index_type)
+ assert output_index_expected.exists()
+
+
+# Can't accept multiple inputs at the moment.
+# See https://github.com/pysam-developers/pysam/issues/1155
+# @pytest.mark.parametrize(
+# argnames=["index_type"],
+# argvalues=[
+# (SamIndexType.BAI,),
+# (SamIndexType.CSI,),
+# ],
+# ids=["BAI", "CSI"],
+# )
+# def test_index_works_with_multiple_inputs(
+# tmp_path: Path,
+# index_type: SamIndexType,
+# ) -> None:
+# builder = SamBuilder(sort_order=SamOrder.Coordinate)
+# builder.add_pair(name="test1", chrom="chr1", start1=4000, start2=4300)
+# builder.add_pair(
+# name="test2", chrom="chr1", start1=5000, start2=4700, strand1="-", strand2="+"
+# )
+# builder.add_pair(name="test3", chrom="chr2", start1=4000, start2=4300)
+# builder.add_pair(name="test4", chrom="chr5", start1=4000, start2=4300)
+
+# # At the moment sam builder doesnt support generating CRAM and SAM formats, so for now we're
+# # only testing on BAMs
+# input_file1 = tmp_path / "test_input1.bam"
+# builder.to_path(input_file1)
+# input_file2 = tmp_path / "test_input2.bam"
+# builder.to_path(input_file2)
+
+# inputs = [
+# input_file1,
+# input_file2,
+# ]
+
+# # Make sure we're producing the indices
+# for input in inputs:
+# output_index_expected = Path(f"{input}.{index_type._name_.lower()}")
+# assert not output_index_expected.exists()
+
+# samtools.index(inputs=inputs, index_type=index_type)
+# for input in inputs:
+# output_index_expected = Path(f"{input}.{index_type._name_.lower()}")
+# assert output_index_expected.exists()
+
+
+@pytest.mark.parametrize(
+ argnames=["file_type"],
+ argvalues=[
+ (SamFileType.SAM,),
+ (SamFileType.BAM,),
+ (SamFileType.CRAM,),
+ ],
+ ids=["SAM", "BAM", "CRAM"],
+)
+@pytest.mark.parametrize(
+ argnames=["index_output"],
+ argvalues=[
+ (True,),
+ (False,),
+ ],
+ ids=["indexed", "not_indexed"],
+)
+@pytest.mark.parametrize(
+ argnames=["sort_order", "expected_name_order"],
+ argvalues=[
+ (SamOrder.Coordinate, ["test2", "test3", "test4", "test1"]),
+ (SamOrder.QueryName, ["test1", "test2", "test3", "test4"]),
+ (SamOrder.TemplateCoordinate, ["test2", "test3", "test4", "test1"]),
+ ],
+ ids=["Coordinate sorting", "Query name sorting", "Template Sorted"],
+)
+def test_sort_types(
+ tmp_path: Path,
+ file_type: SamFileType,
+ index_output: bool,
+ sort_order: Optional[SamOrder],
+ expected_name_order: List[str],
+) -> None:
+
+ builder = SamBuilder(sort_order=SamOrder.Unsorted)
+ builder.add_pair(
+ name="test3", chrom="chr1", start1=5000, start2=4700, strand1="-", strand2="+"
+ )
+ builder.add_pair(name="test2", chrom="chr1", start1=4000, start2=4300)
+ builder.add_pair(name="test1", chrom="chr5", start1=4000, start2=4300)
+ builder.add_pair(name="test4", chrom="chr2", start1=4000, start2=4300)
+
+ input_file = tmp_path / "test_input.bam"
+ output_file = tmp_path / f"test_output{file_type.extension}"
+
+ builder.to_path(input_file)
+
+ samtools.sort(
+ input=input_file,
+ output=output_file,
+ index_output=index_output,
+ sort_order=sort_order,
+ )
+ with sam.reader(output_file) as in_bam:
+ for name in expected_name_order:
+ read1 = next(in_bam)
+ assert (
+ name == read1.query_name
+ ), "Position based read sort order did not match expectation"
+ read2 = next(in_bam)
+ assert (
+ name == read2.query_name
+ ), "Position based read sort order did not match expectation"
+
+ if index_output and file_type != SamFileType.SAM:
+ assert Path(f"{output_file}{file_type.index_extension}")
diff --git a/poetry.lock b/poetry.lock
index 30722455..50755d93 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -47,6 +47,14 @@ python-versions = ">=3.6"
[package.dependencies]
pytz = ">=2015.7"
+[[package]]
+name = "bgzip"
+version = "0.4.0"
+description = "Utilities working with blocked gzip streams."
+category = "dev"
+optional = false
+python-versions = "*"
+
[[package]]
name = "black"
version = "20.8b1"
@@ -58,7 +66,6 @@ python-versions = ">=3.6"
[package.dependencies]
appdirs = "*"
click = ">=7.1.2"
-dataclasses = {version = ">=0.6", markers = "python_version < \"3.7\""}
mypy-extensions = ">=0.4.3"
pathspec = ">=0.6,<1"
regex = ">=2020.1.8"
@@ -111,26 +118,18 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
[[package]]
name = "coverage"
-version = "6.2"
+version = "7.0.1"
description = "Code coverage measurement for Python"
category = "dev"
optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
[package.dependencies]
-tomli = {version = "*", optional = true, markers = "extra == \"toml\""}
+tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
[package.extras]
toml = ["tomli"]
-[[package]]
-name = "dataclasses"
-version = "0.8"
-description = "A backport of the dataclasses module for Python 3.6"
-category = "dev"
-optional = false
-python-versions = ">=3.6, <3.7"
-
[[package]]
name = "docutils"
version = "0.17.1"
@@ -607,8 +606,8 @@ docs = ["sphinx"]
[metadata]
lock-version = "1.1"
-python-versions = ">=3.6.1,<4.0"
-content-hash = "2b4e8a884aa17b49f71b3d692d7b9b45c1182d73803a9b28060e28cc0080c91c"
+python-versions = ">=3.7.0,<4.0"
+content-hash = "954260de2d0450920ea4e87211637fc9553c7fcf455c88e6b8e390f55d059c5c"
[metadata.files]
alabaster = [
@@ -619,12 +618,20 @@ appdirs = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
{file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
]
-atomicwrites = []
-attrs = []
+atomicwrites = [
+ {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
+]
+attrs = [
+ {file = "attrs-22.1.0-py2.py3-none-any.whl", hash = "sha256:86efa402f67bf2df34f51a335487cf46b1ec130d02b8d39fd248abfd30da551c"},
+ {file = "attrs-22.1.0.tar.gz", hash = "sha256:29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6"},
+]
babel = [
{file = "Babel-2.11.0-py3-none-any.whl", hash = "sha256:1ad3eca1c885218f6dce2ab67291178944f810a10a9b5f3cb8382a5a232b64fe"},
{file = "Babel-2.11.0.tar.gz", hash = "sha256:5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6"},
]
+bgzip = [
+ {file = "bgzip-0.4.0.tar.gz", hash = "sha256:2562202a99b0cff1777d051cd3ed7ffa9a568ff8486f922935808e1a0478f01c"},
+]
black = [
{file = "black-20.8b1.tar.gz", hash = "sha256:1c02557aa099101b9d21496f8a914e9ed2222ef70336404eeeac8edba836fbea"},
]
@@ -640,65 +647,71 @@ click = [
{file = "click-8.0.4-py3-none-any.whl", hash = "sha256:6a7a62563bbfabfda3a38f3023a1db4a35978c0abd76f6c9605ecd6554d6d9b1"},
{file = "click-8.0.4.tar.gz", hash = "sha256:8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb"},
]
-colorama = []
-coverage = [
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@@ -801,14 +844,26 @@ packaging = [
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diff --git a/pyproject.toml b/pyproject.toml
index d86ba9f9..667926b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,6 +40,7 @@ pytest = ">=5.4.2"
mypy = ">=0.770"
flake8 = ">=3.8.1"
black = ">=19.10b0"
+bgzip = ">=0.4.0"
pytest-cov = ">=2.8.1"
isort = ">=5.10.1"