OLC NAS Tools

Install

pip install olcnastools

Usage

This program can either be used from the command line or imported directly in Python

Command Line:

usage: nastools.py [-h] --file FILE --outdir OUTDIR --type {fasta,fastq}
                   [--copy] [--verbose]

optional arguments:
  -h, --help            show this help message and exit
  --file FILE, -f FILE  File containing list of SEQ IDs to extract
  --outdir OUTDIR, -o OUTDIR
                        Out directory to link files to
  --type {fasta,fastq}, -t {fasta,fastq}
                        Type of files to retrieve, i.e. fasta or fastq
  --copy, -c            Setting this flag will copy the files instead of
                        creating symlinks
  --verbose, -v         Setting this flag will enable more verbose output

Accessing module in Python

from nastools.nastools import retrieve_nas_files

def retrieve_nas_files(seqids, outdir, filetype, copyflag=False, verbose_flag=False):
    """
    :param seqids: LIST containing strings of valid OLC Seq IDs
    :param outdir: STRING path to directory to dump requested files
    :param filetype: STRING of either 'fastq' or 'fasta' to determine where to search for files
    :param copyflag: BOOL flag to determine if files should be copied or symlinked. Default False.
    :param verbose_flag: BOOL flag to determine logging level. Default False.
    """

Local OLC Testing

To make sure that nothing has broken on this before pushing new versions:

Test FASTA retrieve:

nastools.py -f seqids.txt -o fastas -t fasta

There should be five FASTA files in fastas folder, and the following warning messages:

Located multiple copies of 2018-MER-0103 at the following locations: /mnt/nas2/processed_sequence_data/merged_assemblies/merged_38/BestAssemblies, /mnt/nas2/processed_sequence_data/merged_assemblies/merged_14285_Assembled/BestAssemblies.
Please ensure that only a single copy is present on the NAS

Files for the following SEQ IDs could not be located: 2019-FAKE-2222

Test FASTQ retrieve:

nastools.py -f seqids.txt -o fastqs -t fastq

There should be ten FASTQ files in fastqs folder, and the following warning message:

Files for the following SEQ IDs could not be located: 2019-FAKE-2222