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A simple FASTQ toolbox for small to medium size projects without dependencies.

Project description

fastq

A simple FASTQ toolbox for small to medium size projects without dependencies.

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FASTQ files are text-based files for storing nucleotide sequences and its corresponding quality scores. Reading such files is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies.

fastq offers an alternative to this and brings many useful functions without relying on third party packages.

Installation

Using pip / pip3:

pip install fastq

Or by source:

git clone git@github.com:not-a-feature/fastq.git
cd fastq
pip install .

How to use

fastq offers easy to use functions for fastq handling. The main parts are:

  • fastq_object()
    • head
    • body
    • qstr
    • info
    • toFasta()
    • len() / str() / eq()
  • read()
  • write()

fastq_object()

The core component of fastq is the fastq_object().

This object represents an FASTQ entry and consists of a head and body.

import fastq as fq
fo = fq.fastq_object("@M01967:23:0", "GATTTGGGG", "!''*((((*")
fo.getHead() or fo.head # @M01967:23:0
fo.getSeq()  or fo.body # GATTTGGGG
fo.getQual() or fo.qstr # !''*((((*

When fastq_object(..).info is requested, some summary statistics are computed and returned as dict. This computation is "lazy". I.e. the first query takes longer than the second. If the body or qstr is changed manually, info is automatically reset.

fo.getInfo() or fo.info
{'a_num': 1, 'g_num': 5,             # Absolute counts of ACTG
 't_num': 3, 'c_num': 0,             #
 'gc_content': 0.5555555555555556,   # Relatice GC content
 'at_content': 0.4444444444444444,   # Relative AT content
 'qual': 6.444444444444445,          # Mean quality (Illumina Encoding)            
 'qual_median': 7,                   # Median quality
 'qual_variance': 7.027777777777778, # Variance of quality
 'qual_min': 0, 'qual_max': 9}       # Min / Max quality

Following functions are defined on a fastq_object():

str(fo) # will return:
# @M01967:23:0
# GATTTGGGG
# +
# !''*((((*


# Body length
len(fo) # will return 10, the length of the body

# Equality 
print(fo == fo) # True
    
fo_b = fq.fastq_object("@different header", "GATTTGGGG", "!!!!!!!!!")
print(fo == fo_b) # True

fo_c = fq..fastq_object(">Different Body", "ZZZZ", "!--!")
print(fo == fo_c) # False

Reading FASTQ files

read() is a fastq reader which is able to handle compressed and non-compressed files. Following compressions are supported: zip, tar, tar.gz, gz. If multiple files are stored inside an archive, all files are read. This function returns a list of fastq_objects.

fos = fq.read("dolphin.fastq") # List of fastq entries.
fos = fq.read("reads.tar.gz") # Is able to handle compressed files.

Writing FASTA files

write() is a basic fastq writer. It takes a single or a list of fastq_objects and writes it to the given path.

The file is usually overwritten. Set write(fo, "path.fastq", mode="a") to append file.

fos = fq..read("dolphin.fastq") # List of fastq entries
fq..write(fos, "new.fastq")

License

Copyright (C) 2022 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0
TLDR:

| Permissions      | Conditions                   | Limitations |
| ---------------- | ---------------------------- | ----------- |
| ✓ Commercial use | Disclose source              | ✕ Liability |
| ✓ Distribution   | License and copyright notice | ✕ Warranty  |
| ✓ Modification   | Same license                 |             |
| ✓ Patent use     | State changes                |             |
| ✓ Private use    |                              |             |

Go to LICENSE.md to see the full version.

Dependencies

In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version. Go to DEPENDENCIES.md to see all dependencies and licenses.

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