Package: fastq
A simple FASTQ toolbox for small to medium size projects without dependencies.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.InstallationUsing pip  / pip3:pipinstallfastqOr by source:gitclonegit@github.com:not-a-feature/fastq.gitcdfastq
pipinstall.How to usefastq offers easy to use functions for fastq handling.
The main parts are:read()write()fastq_object()headbodyqstrinfotoFasta()len() / str() / eq()Reading FASTQ filesread()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 iterator of fastq_objects.fos=fq.read("dolphin.fastq")# Iterator of fastq entries.fos=list(fos)# Cast to listfos=fq.read("reads.tar.gz")# Is able to handle compressed files.Writing FASTA fileswrite()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. Setwrite(fo, "path.fastq", mode="a")to append file.fos=fq.read("dolphin.fastq")# Iterator of fastq entriesfos=list(fos)fq.write(fos,"new.fastq")fastq_object()The core component of fastq is thefastq_object().This object represents an FASTQ entry and consists of a head and body.importfastqasfqfo=fq.fastq_object("@M01967:23:0","GATTTGGGG","!''*((((*")fo.getHead()orfo.head# @M01967:23:0fo.getSeq()orfo.body# GATTTGGGGfo.getQual()orfo.qstr# !''*((((*Whenfastq_object(..).infois 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()orfo.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 qualityFollowing methods are defined on afastq_object():str(fo)# will return:# @M01967:23:0# GATTTGGGG# +# !''*((((*# Body lengthlen(fo)# will return 10, the length of the body# Equality# Checks only the body, not the header and not the quality stringprint(fo==fo)# Truefo_b=fq.fastq_object("@different header","GATTTGGGG","!!!!!!!!!")print(fo==fo_b)# Truefo_c=fq..fastq_object(">Different Body","ZZZZ","!--!")print(fo==fo_c)# FalseLicenseCopyright (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 toLICENSE.mdto see the full version.DependenciesIn 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 toDEPENDENCIES.mdto see all dependencies and licenses.