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Fastq API Usage

Import package

from pyBioTools import Fastq
from pyBioTools.common import jhelp

index_reads

jhelp(Fastq.Filter)

Filter (input_fn, output_fn, min_len, min_qual, remove_duplicates, qual_offset, verbose, quiet, progress, kwargs)

Filter fastq reads based on their length, mean quality and the presence of duplicates. Can also be used to concatenate reads from multiple files in a single one.

  • input_fn (required) [list(str)]

Fastq file path or directory containing fastq files or list of files, or regex or list of regex. It is quite flexible.

  • output_fn (required) [str]

Destination fastq file. Automatically gzipped if the .gz extension is found

  • min_len (default: None) [int]

Minimal reads length

  • min_qual (default: None) [float]

Minimal mean read PHRED quality

  • remove_duplicates (default: False) [bool]

If true duplicated reads with the same read id are discarded

  • qual_offset (default: 33) [int]

Quality scoring system off set. Nowadays pretty much everyone uses +33

  • verbose (default: False) [bool]

  • quiet (default: False) [bool]

  • progress (default: False) [bool]

  • kwargs

Basic usage

Fastq.Filter ("./data/sample_1.fastq", "./output/sample_1_filtered.fastq", min_len=100, min_qual=7, remove_duplicates=True, verbose=True)

## Running Fastq Filter ##
    Parsing reads
    [DEBUG]: Reading file ./data/sample_1.fastq
    [DEBUG]: End of file ./data/sample_1.fastq
    Read counts summary
     total_reads: 12,000
     valid_reads: 10,882
     low_qual_reads: 643
     short_reads: 474
     source files: 1
     duplicate_reads: 1

All fastq from a directory instead and write to compressed fastq

Fastq.Filter ("./data/", "./output/sample_1_filtered.fastq.gz", min_len=100, min_qual=7, verbose=True)

## Running Fastq Filter ##
    Parsing reads
    [DEBUG]: Reading file ./data/sample_1.fastq
    [DEBUG]: End of file ./data/sample_1.fastq
    [DEBUG]: Reading file ./data/sample_2.fastq
    [DEBUG]: End of file ./data/sample_2.fastq
    Read counts summary
     total_reads: 24,000
     valid_reads: 21,809
     low_qual_reads: 1,304
     short_reads: 887
     source files: 2