metasnek 0.0.3

Misc functions for metagenomics pipelines

MetaSnek

Misc functions for metagenomic pipelines

Examples

fastq_finder

Return a python dictionary of sample names and fasta/q files from a directory or a TSV file. If given a directory, sample names will be everything upto the first match for "_R1|_R2".

samples.tsv

sample1     reads/sample1_R1.fastq.gz   reads/sample1_R2.fastq.gz
sample2     reads/sample1_R2.fastq      reads/sample2_R2.fastq
sample3     reads/sample3.fasta.gz      None

reads/

reads
  ├── sample1_R1.fastq.gz
  ├── sample1_R2.fastq.gz
  ├── sample2_R1.fastq
  ├── sample2_R2.fastq
  └── sample3.fasta.gz

from metasnek import fastq_finder

samples = fastq_finder.parse_samples_to_dictionary("reads")
samples = fastq_finder.parse_samples_to_dictionary("samples.tsv")
samples

{
'sample1': 
    {
    'R1': 'reads/sample1_R1.fastq.gz', 
    'R2': 'reads/sample1_R2.fastq.gz', 
    }, 
'sample2': 
    {
    'R1': 'reads/sample2_R1.fastq', 
    'R2': 'reads/sample2_R2.fastq'
    }
'sample3': 
    {
    'R1': 'reads/sample3.fasta.gz', 
    'R2': None
    }
}