SAMTOOLS FASTX

Converts a SAM, BAM or CRAM into FASTQ or FASTA format.

URL: http://www.htslib.org/doc/samtools-fasta.html

Example

This wrapper can be used in the following way:

rule samtools_fastq:
    input:
        "{prefix}.sam",
    output:
        read1="{prefix}.1.fasta",
        read2="{prefix}.2.fasta",
        read0="{prefix}.0.fasta",
    log:
        "{prefix}.log",
    # Samtools takes additional threads through its option -@
    threads: 2  # This value - 1 will be sent to -@
    params:
        outputtype="fasta",
        extra="",
    message:
        ""
    wrapper:
        "v9.15.0/bio/samtools/fastx/"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• samtools=1.24

• snakemake-wrapper-utils=0.9.0

Input/Output

Input:

• bam or sam file (.bam, .sam)

Output:

• read1: FASTA or FASTQ file for read 1

• read2: FASTA or FASTQ file for read 2

• reado: FASTA or FASTQ file for both reads 1 and 2

• reads: FASTA or FASTQ file for singleton reads (both reads 1 and 2, where the pair is not present)

• read0: FASTA or FASTQ file for other reads (marked as both/none read 1 and 2)

Params

• extra: additional program arguments (not -@/–threads, -o, -1, -2, -s, or -0).

Authors

• William Rowell

• Filipe G. Vieira

Code

__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"


from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts

samtools_opts = get_samtools_opts(
    snakemake, parse_write_index=False, parse_output=False, parse_output_format=False
)
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)


# Parse outputs
fq_out = ""
for label, out_file in snakemake.output.items():
    if label.startswith("read"):
        fq_out += f" -{label.removeprefix('read')} {out_file}"

shell(
    "samtools {snakemake.params.outputtype} {samtools_opts} {fq_out} {extra} {snakemake.input} {log}"
)