fastqtools

Introduction

fastq is used to clean raw fastq data…

Authors

Status

Note

not reviewed yet.

Installation

use git to clone code:

git clone git@192.168.1.251:/home/git/fastqtools.git

Attention

if you want to run fastqtools on local server without docker , try to add config.py.

Usage

just type command:

/path/to/fastqClean.py -h
/path/to/fastqStat.py -h
/path/to/fastqSplit.py -h

developments followed by Dcer rules, script will need a yaml file,which shoud contain following key and values

must_args

  • args1
    desc of args2
  • args2
    desc of args2

optinal args

  • args3
    desc of args3

here is a sample yaml file:

args1: value of args1
args2: value of args2

RUN

cli way

copy and paste to your input yaml file and call script:

/path/of/ctpips.py -c your.yml

serer way

send request to jbios with /start/ctpips/:

req = requests.get("http://<server>:port/ctpips/",data=json.dumps(indict))

for jbios detail information check api documentation here

Code

latest

fastqtools package

Subpackages
fastqtools.fastqReader package
Submodules
fastqtools.fastqReader.fastqReader module
class fastqtools.fastqReader.fastqReader.fastqReader(fq1, fq2)[source]
next()[source]
class fastqtools.fastqReader.fastqReader.fq(id, seq, flag, qual)[source]
fastqtools.fastqReader.fastqWriter module
fastqtools.fastqReader.fastqWriter.fastqWriter(read, prefix)[source]

write reads to fastqs

Module contents
fastqtools.fastqSplit package
Submodules
fastqtools.fastqSplit.fastqMerge module
fastqtools.fastqSplit.fastqMerge.fastqMerge(fqs, prefix)[source]
fastqtools.fastqSplit.fastqSplit module
fastqtools.fastqSplit.fastqSplit.fastqSplit(fq1, fq2, splitNum, prefix)[source]

split Fastq in to small ones to accelerate downstreaming analysis…

fastqtools.fastqSplit.getfileNum module
fastqtools.fastqSplit.getfileNum.getfileNum(afile)[source]
Module contents
fastqtools.fastqStat package
Submodules
fastqtools.fastqStat.fastqStat module
fastqtools.fastqStat.fastqStat.code2score(code)[source]
fastqtools.fastqStat.fastqStat.fastqStat(fq1, fq2, prefix)[source]
fastqtools.fastqStat.fastqStat.qual20(scores)[source]
fastqtools.fastqStat.fastqStat.score2code(score)[source]
fastqtools.fastqStat.getfileNum module
fastqtools.fastqStat.getfileNum.getfileNum(afile)[source]
Module contents
fastqtools.readprocess package
Submodules
fastqtools.readprocess.readprocess module
class fastqtools.readprocess.readprocess.readprocess(read)[source]
autoadaptremove(flag)[source]
length(lenMin)[source]
nbase(percent)[source]
qual(q, percent)[source]
trim(head1, tail1, head2, tail2)[source]
umi(umis)[source]
fastqtools.readprocess.tools module
fastqtools.readprocess.tools.autocutadaptor(seq1, seq2)[source]
fastqtools.readprocess.tools.checkN(seq, percent)[source]
fastqtools.readprocess.tools.checking_adaptor(seq1, seq2, common, threadhold=0.95)[source]
fastqtools.readprocess.tools.checkqual(qual, q_thread, percent)[source]
fastqtools.readprocess.tools.checkumi(seq, umis)[source]
fastqtools.readprocess.tools.code2score(code)[source]
fastqtools.readprocess.tools.diffstr(str1, str2)[source]
class fastqtools.readprocess.tools.dnaseq[source]
static complent(seq)[source]
static reverse(seq)[source]
fastqtools.readprocess.tools.enlong_and_find_common(seq1, seq2, seed_choosed, mismatchMax=5)[source]

return best common sequences.

fastqtools.readprocess.tools.score2code(score)[source]
fastqtools.readprocess.tools.seeding(seq1, seq2, seed_len=10, seed_max=3, seed_step=1)[source]

find seed candidates return seeds and locus.

Module contents
Module contents

setup module

Setup file for jbiot.

setup.find_bins()[source]
setup.readfile(filename)[source]
setup.setup_package()[source]