ngslite

Light-weight functions for next-generation sequencing (NGS) data analysis

Install

pip install ngslite

Common tools

Common wrapper functions for command-line tools. samtools needs to be installed.

import ngslite as ngs

ngs.sam_to_bam('path/to/sam')
ngs.sort_bam('path/to/bam')
ngs.index_bam('path/to/bam')

# Or simply combine the three steps above
ngs.sam_to_indexed_bam('path/to/sam')

Trimming reads. trim_galore needs to be installed.

ngs.trim_galore(fq1='reads.1.fq', fq2='reads.2.fq', gzip=True)

Mapping reads. bowtie2 needs to be installed.

ngs.bowtie2_mapping(ref='ref.fa', fq1='reads.1.fq', fq2='reads.2.fq', sam='output.sam')

Handling files

Fasta

Read fasta files:

from ngslite import FastaParser

with FastaParser('file.fa') as parser:
    for header, sequence in parser:
        print(header, sequence)

Read the whole fasta file at once:

from ngslite import read_fasta

fasta_data = read_fasta('file.fa')
header, sequence = fasta_data[0]
print(header, sequence)

Write fasta files:

from ngslite import FastaWriter

with FastaWriter('file.fa') as writer:
    writer.write(header, sequence)

Genbank

Read Genbank files:

from ngslite import read_genbank

chromosomes = read_genbank('file.gbk')
for chromosome in chromosomes:
    print(chromosome.seqname)
    for feature in chromosome.features:
        print(feature)

GFF

Read GFF files:

from ngslite import GffParser

with GffParser('file.gff') as parser:
   for feature in parser:
       print(feature.start,
             feature.end,
             feature.strand,
             feature.attributes)

Write GFF files:

from ngslite import GffFeature, GffWriter

feature = GffFeature(
    seqid='chr1',
    source='.',
    type='CDS',
    start=1,
    end=99,
    score='.',
    strand='+',
    phase='.',
    attributes='name=...'
)

with GffWriter('file.gff') as writer:
    writer.write(feature)