Genomic Summary

Genomic summary statistics is available for FASTQ reads and contiguous sequences.

Genomic FASTQ Read Summary

Install PySEGUL using pip if you haven't done it yet

pip install pysegul

Create a new Python script, import the library, and write python code.

import pysegul

def summarize_reads():
    input_dir = 'tests/raw-data'
    input_format = 'auto'
    summary_mode = 'default'
    prefix = 'read_summary'
    output_dir = 'tests/output'
    summary = pysegul.ReadSummary(
        input_format,  
        summary_mode,
        output_dir,
        prefix
        )
    summary.from_dir(input_dir)

You can also input the alignment paths in a list directly instead of using a directory. Replace the input_dir with input_files and provide a list of paths. Then, call the from_files method instead of from_dir.

import pysegul

def summarize_reads():
    input_path = ['tests/raw-data/read1.fastq', 'tests/raw-data/read2.fastq']
    input_format = 'auto'
    # Available values for summary_mode: 'default', 'complete', 'minimal'.
    summary_mode = 'default'
    prefix = 'read_summary'
    output_dir = 'tests/output'
    summary = pysegul.ReadSummary(
        input_format,  
        summary_mode,
        output_dir,
        prefix
        )
    summary.from_files(input_path)

Genomic Contiguous Sequence Summary

Install PySEGUL using pip if you haven't done it yet

pip install pysegul

Create a new Python script, import the library, and write python code.

import pysegul

def summarize_contigs():
    input_dir = 'tests/contig-data'
    input_format = 'auto'
    prefix = 'contig_summary'
    output_dir = 'tests/output'
    summary = pysegul.ContigSummary(
        input_format,  
        output_dir,
        prefix
        )
    summary.from_dir(input_dir)

You can also input the alignment paths in a list directly instead of using a directory. Replace the input_dir with input_files and provide a list of paths. Then, call the from_files method instead of from_dir.

import pysegul

def summarize_contigs():
    input_path = ['tests/contig-data/contig1.fasta', 'tests/contig-data/contig2.fasta']
    input_format = 'auto'
    prefix = 'contig_summary'
    output_dir = 'tests/output'
    summary = pysegul.ContigSummary(
        input_format,  
        output_dir,
        prefix
        )
    summary.from_files(input_path)