Source code for flowcraft.templates.spades

#!/usr/bin/env python3


This module is intended execute Spades on paired-end FastQ files.

Expected input

The following variables are expected whether using NextFlow or the
:py:func:`main` executor.

- ``sample_id`` : Sample Identification string.
    - e.g.: ``'SampleA'``
- ``fastq_pair`` : Pair of FastQ file paths.
    - e.g.: ``'SampleA_1.fastq.gz SampleA_2.fastq.gz'``
- ``kmers`` : Setting for Spades kmers. Can be either ``'auto'``, \
    ``'default'`` or a user provided list.
    - e.g.: ``'auto'`` or ``'default'`` or ``'55 77 99 113 127'``
- ``opts`` : List of options for spades execution.
    1. The minimum number of reads to consider an edge in the de Bruijn \
    graph during the assembly.
        - e.g.: ``'5'``
    2. Minimum contigs k-mer coverage.
        - e.g.: ``['2' '2']``
- ``clear`` : If 'true', remove the input fastq files at the end of the

Generated output

- ``contigs.fasta`` : Main output of spades with the assembly
    - e.g.: ``contigs.fasta``
- ``spades_status`` :  Stores the status of the spades run. If it was \
    successfully executed, it stores ``'pass'``. Otherwise, it stores the\
    ``STDERR`` message.
    - e.g.: ``'pass'``

Code documentation


__version__ = "1.0.2"
__build__ = "29062018"
__template__ = "spades-nf"

import os
import sys
import re
import subprocess

from subprocess import PIPE

from flowcraft_utils.flowcraft_base import get_logger, MainWrapper

logger = get_logger(__file__)

def __get_version_spades():


        cli = ["", "--version"]
        p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE)
        stdout, _ = p.communicate()

        version = stdout.strip().split()[-1][1:].decode("utf8")

    except Exception as e:
        version = "undefined"

    return {
        "program": "SPAdes",
        "version": version,

if __file__.endswith(""):
    SAMPLE_ID = '$sample_id'
    FASTQ_PAIR = '$fastq_pair'.split()
    MAX_LEN = int('$max_len'.strip())
    KMERS = '$kmers'.strip()
    CLEAR = '$clear'
    DISABLE_RR = '$disable_rr'
    OPTS = [x.strip() for x in '$opts'.strip("[]").split(",")]
    CLEAR = '$clear'
    logger.debug("Running {} with parameters:".format(
    logger.debug("SAMPLE_ID: {}".format(SAMPLE_ID))
    logger.debug("FASTQ_PAIR: {}".format(FASTQ_PAIR))
    logger.debug("MAX_LEN: {}".format(MAX_LEN))
    logger.debug("KMERS: {}".format(KMERS))
    logger.debug("OPTS: {}".format(OPTS))
    logger.debug("CLEAR: {}".format(CLEAR))
    logger.debug("DISABLE_RR: {}".format(DISABLE_RR))

[docs]def set_kmers(kmer_opt, max_read_len): """Returns a kmer list based on the provided kmer option and max read len. Parameters ---------- kmer_opt : str The k-mer option. Can be either ``'auto'``, ``'default'`` or a sequence of space separated integers, ``'23, 45, 67'``. max_read_len : int The maximum read length of the current sample. Returns ------- kmers : list List of k-mer values that will be provided to Spades. """ logger.debug("Kmer option set to: {}".format(kmer_opt)) # Check if kmer option is set to auto if kmer_opt == "auto": if max_read_len >= 175: kmers = [55, 77, 99, 113, 127] else: kmers = [21, 33, 55, 67, 77] logger.debug("Kmer range automatically selected based on max read" "length of {}: {}".format(max_read_len, kmers)) # Check if manual kmers were specified elif len(kmer_opt.split()) > 1: kmers = kmer_opt.split() logger.debug("Kmer range manually set to: {}".format(kmers)) else: kmers = [] logger.debug("Kmer range set to empty (will be automatically " "determined by SPAdes") return kmers
[docs]def clean_up(fastq): """ Cleans the temporary fastq files. If they are symlinks, the link source is removed Parameters ---------- fastq : list List of fastq files. """ for fq in fastq: # Get real path of fastq files, following symlinks rp = os.path.realpath(fq) logger.debug("Removing temporary fastq file path: {}".format(rp)) if re.match(".*/work/.{2}/.{30}/.*", rp): os.remove(rp)
@MainWrapper def main(sample_id, fastq_pair, max_len, kmer, opts, clear, disable_rr): """Main executor of the spades template. Parameters ---------- sample_id : str Sample Identification string. fastq_pair : list Two element list containing the paired FastQ files. max_len : int Maximum read length. This value is determined in :py:class:`templates.integrity_coverage` kmer : str Can be either ``'auto'``, ``'default'`` or a sequence of space separated integers, ``'23, 45, 67'``. opts : List of options for spades execution. See above. clear : str Can be either 'true' or 'false'. If 'true', the input fastq files will be removed at the end of the run, IF they are in the working directory disable_rr : str Can either be 'true' or 'false'. If 'true', disables repeat resolution stage of assembling """"Starting spades") min_coverage, min_kmer_coverage = opts"Setting SPAdes kmers") kmers = set_kmers(kmer, max_len)"SPAdes kmers set to: {}".format(kmers)) cli = [ "", "--careful", "--only-assembler", "--threads", "$task.cpus", "--cov-cutoff", min_coverage, "-o", "." ] # Add kmers, if any were specified if kmers: cli += ["-k {}".format(",".join([str(x) for x in kmers]))] # Add FastQ files cli += [ "-1", fastq_pair[0], "-2", fastq_pair[1] ] # Disable RR? if disable_rr == 'true': cli += ['--disable-rr'] logger.debug("Running SPAdes subprocess with command: {}".format(cli)) p = subprocess.Popen(cli, stdout=PIPE, stderr=PIPE) stdout, stderr = p.communicate() # Attempt to decode STDERR output from bytes. If unsuccessful, coerce to # string try: stderr = stderr.decode("utf8") stdout = stdout.decode("utf8") except (UnicodeDecodeError, AttributeError): stderr = str(stderr) stdout = str(stdout)"Finished SPAdes subprocess with STDOUT:\\n" "======================================\\n{}".format(stdout))"Fished SPAdes subprocess with STDERR:\\n" "======================================\\n{}".format(stderr))"Finished SPAdes with return code: {}".format( p.returncode)) with open(".status", "w") as fh: if p.returncode != 0: fh.write("error") sys.exit(p.returncode) else: fh.write("pass") # Change the default contigs.fasta assembly name to a more informative one if "_trim." in fastq_pair[0]: sample_id += "_trim" # Get spades version for output name info = __get_version_spades() assembly_file = "{}_spades{}.fasta".format( sample_id, info["version"].replace(".", "")) os.rename("contigs.fasta", assembly_file)"Setting main assembly file to: {}".format(assembly_file)) # Remove input fastq files when clear option is specified. # Only remove temporary input when the expected output exists. if clear == "true" and os.path.exists(assembly_file): clean_up(fastq_pair) if __name__ == '__main__': main(SAMPLE_ID, FASTQ_PAIR, MAX_LEN, KMERS, OPTS, CLEAR, DISABLE_RR)