seismicrna.core.ngs package

Subpackages

• seismicrna.core.ngs.tests package
  • Submodules
    • TestConstants
      • TestConstants.test_phreds()
      • TestConstants.test_quals()
    • TestDecode
      • TestDecode.test_decode()
    • TestEncode
      • TestEncode.test_encode()

Submodules

seismicrna.core.ngs.phred.decode_phred(quality_code: str, phred_encoding: int)

Decode the ASCII character for a Phred quality score to an integer.

Parameters:

• quality_code (str) – The Phred score encoded as an ASCII character.

• phred_encoding (int) – The encoding offset for Phred scores. A Phred score is encoded as the character whose ASCII value is the sum of the phred score and the encoding offset.

Returns:

The Phred quality score represented by the ASCII character.

Return type:

int

seismicrna.core.ngs.phred.encode_phred(phred_score: int, phred_encoding: int)

Encode a numeric Phred quality score as an ASCII character.

Parameters:

• phred_score (int) – The Phred score as an integer.

• phred_encoding (int) – The encoding offset for Phred scores. A Phred score is encoded as the character whose ASCII value is the sum of the phred score and the encoding offset.

Returns:

The character whose ASCII code, in the encoding scheme of the FASTQ file, represents valid quality.

Return type:

str

exception seismicrna.core.ngs.xam.DuplicateSampleReferenceError

Bases: DuplicateValueError

A sample-reference pair occurred more than once.

seismicrna.core.ngs.xam.calc_extra_threads(num_cpus: int)

Calculate the number of extra threads to use (option -@).

seismicrna.core.ngs.xam.collate_xam_cmd(xam_inp: Path | None, xam_out: Path | None, *, tmp_pfx: Path | None = None, fast: bool = False, num_cpus: int = 1)

Collate a SAM or BAM file using samtools collate.

Parameters:

• xam_inp (Path | None) – Input SAM/BAM file; reads from stdin (“-”) if None.

• xam_out (Path | None) – Output SAM/BAM file; writes to stdout if None.

• tmp_pfx (Path | None) – Prefix for temporary files; defaults to xam_out without its extension if xam_out is not None.

• fast (bool = False) – Use fast mode, which outputs primary alignments only.

• num_cpus (int = 1) – Number of threads to use.

Returns:

Shell command string.

Return type:

str

seismicrna.core.ngs.xam.count_single_paired(flagstats: dict)

Count the records in a SAM/BAM file given an output dict from get_flagstats().

seismicrna.core.ngs.xam.count_total_reads(flagstats: dict)

Count the total records in a SAM/BAM file.

seismicrna.core.ngs.xam.flagstat_cmd(xam_inp: Path | None, *, num_cpus: int = 1)

Compute the statistics with samtools flagstat.

seismicrna.core.ngs.xam.idxstats_cmd(xam_inp: Path)

Count the number of reads aligning to each reference.

seismicrna.core.ngs.xam.index_xam_cmd(bam: Path, *, num_cpus: int = 1)

Build an index of a XAM file using samtools index.

seismicrna.core.ngs.xam.parse_flagstat(process: CompletedProcess)

Convert the output into a dict with one entry per line.

seismicrna.core.ngs.xam.parse_idxstats(process: CompletedProcess)

Map each reference to the number of reads aligning to it.

seismicrna.core.ngs.xam.parse_ref_header(process: CompletedProcess)

Map each reference to its header line.

seismicrna.core.ngs.xam.ref_header_cmd(xam_inp: Path, *, num_cpus: int)

Get the header line for each reference.

seismicrna.core.ngs.xam.sort_xam_cmd(xam_inp: Path | None, xam_out: Path | None, *, tmp_pfx: Path | None = None, name: bool = False, num_cpus: int = 1)

Sort a SAM or BAM file using samtools sort.

Parameters:

• xam_inp (Path | None) – Input SAM/BAM file; reads from stdin if None.

• xam_out (Path | None) – Output SAM/BAM file; writes to stdout if None.

• tmp_pfx (Path | None) – Prefix for temporary files; defaults to xam_out without its extension if xam_out is not None.

• name (bool = False) – Sort by read name instead of by coordinate.

• num_cpus (int = 1) – Number of threads to use.

Returns:

Shell command string.

Return type:

str

seismicrna.core.ngs.xam.view_xam_cmd(xam_inp: Path | None, xam_out: Path | None, *, sam: bool = False, bam: bool = False, cram: bool = False, with_header: bool = False, only_header: bool = False, min_mapq: int = 0, flags_req: int = 0, flags_exc: int = 0, ref: str | None = None, end5: int | None = None, end3: int | None = None, refs_file: Path | None = None, num_cpus: int = 1)

Convert between SAM and BAM formats, extract reads aligning to a specific reference/region, and filter by flag and mapping quality using samtools view.

Parameters:

• xam_inp (Path | None) – Input SAM/BAM file; reads from stdin if None.

• xam_out (Path | None) – Output SAM/BAM file; writes to stdout if None.

• sam (bool = False) – Output in SAM format.

• bam (bool = False) – Output in BAM format.

• cram (bool = False) – Output in CRAM format (requires refs_file).

• with_header (bool = False) – Include the header in the output.

• only_header (bool = False) – Output only the header.

• min_mapq (int = 0) – Minimum mapping quality score required.

• flags_req (int = 0) – Bitwise flag; only output reads with all these bits set.

• flags_exc (int = 0) – Bitwise flag; skip reads with any of these bits set.

• ref (str | None) – Only output reads aligning to this reference.

• end5 (int | None) – 5’ coordinate of the region to extract (requires ref and end3).

• end3 (int | None) – 3’ coordinate of the region to extract (requires ref and end5).

• refs_file (Path | None) – FASTA file of reference sequences (required for CRAM output).

• num_cpus (int = 1) – Number of threads to use.

Returns:

Shell command string.

Return type:

str

seismicrna.core.ngs.xam.xam_paired(flagstats: dict)

Determine if the reads are single-end or paired-end.

seismicrna.core.ngs.xam.xam_to_fastq_cmd(xam_inp: Path | None, fq_out: Path | None, *, flags_req: int | None = None, flags_exc: int | None = None, label_12: bool = False, num_cpus: int = 1)

Convert XAM format to FASTQ format, and filter by flags.

Parameters:

• xam_inp (Path | None) – Input SAM/BAM file; reads from stdin if None.

• fq_out (Path | None) – Output FASTQ file; writes to stdout if None.

• flags_req (int | None) – Bitwise flag; only output reads with all these bits set.

• flags_exc (int | None) – Bitwise flag; skip reads with any of these bits set.

• label_12 (bool = False) – Add /1 and /2 suffixes to the names of paired-end reads.

• num_cpus (int = 1) – Number of threads to use.

Returns:

Shell command string.

Return type:

str