kspham / rnavariantcalling

RNAvariantcalling

RNAvariantcalling is a powerful tool for calling variants from RNA sequences to provide high quality variants, which were filter by a recently-published database about editing sites in human genome.

• RNA sequences were mapped by 2 mapper STAR and HISAT2, which can handle splice junction problem very well
• Variants were called by Freebayes, then only variants called from both STAR and HISAT2 were stored for the next step
• Such reliable variants were filtered one more time with a database of humnan editing sites

Version

1.0

Author

[email protected]

Dependencies

RNAvariantcalling uses a number of materials to work properly:

• hg19 genome indexed by STAR
• hg19 genome indexed by HISAT2
• hg19 genome un-indexed - for variant calling
• hg19 gene annotation file
• Python 2.7+
• vcftools
• STAR aligner
• HISAT2 aligner
• Freebayes variant calling

These will be downloaded automatically at the very first time you run rnavariantcalling.

And also, rnavariantcalling need these tools below have to be installed on your computer:

• samtools
• tabix
• bgzip
• GNU-parallel
• Set::IntervalTree (perl)
• URI::Escape (perl)

Installation

1. $git clone https://github.com/kspham/rnavariantcalling.git
2. $cd rnavariantcalling
3. $python setup.py install
4. $./configure (generate config.yaml)
At the very first time you run rnavariantcalling, you have to download the indexed human genome for STAR Aligner and HISAT2 Aligner, and also the gene annotation of human genome.

3. $./initial.sh

4.Done! Now you rnavariantcalling can work properly.

Usage

$ rnavariantcalling.py [-h] [--ThreadsN N] [--reads read1 read2 ... readN] [--outdir OUTDIR] --config yamlFile

-h, --helps help message and exit
--reads READS [READS ...], -U READS [READS ...] Input RNA reads
---outdir OUTDIR, -o OUTDIR Where the final result will be stored
--ThreadsN N Number of threads
--config yamlFile configuration file as yaml format

Example

- Paired-ends reads:

$ rnavariantcalling.py --ThreadsN 32 --reads 1.fastq.gz 2.fastq.gz -o /output/directory/ --config /path/to/your/config.yaml

-Single-end read:

$ rnavariantcalling.py --ThreadsN 32 -U unpaired_read.fastq.gz -o /output/directory/ --config /path/to/your/config.yaml

License

MIT

Free Software, Hell Yeah!

rnavariantcalling's Issues

rs_id

It turns out that RSID has real problems, can you turn off the part that convert rs_id in the pipeline?
Thanks.

resource management

Seems that the rna pipeline cause a 32-cores, 128 GB RAM system to halt. Please check the resource (threads/memory) usage.

Chay xong variant calling va khong co ket qua

HI Tan,
Sau khi chay xong variant calling thi khong co ket qua gi.

/home/hoabo/smartpipe/rnavariantcalling/src/rnavariantcalling.py --ThreadsN 20 -U /media/proj3/easyrna/download/6abb83bad6243f7940813af0911f8790.fastq.gz -o /media/proj3/easyrna/output/a/b/8/d/6abb83bad6243f7940813af0911f8790/vcl

-rw-r--r-- 1 root root 525121146 Nov 16 22:35 /media/proj3/easyrna/download/6abb83bad6243f7940813af0911f8790.fastq.gz

Thanks !!!

navariantcalling.py error

Hi Tan,
Co 1 so loi trong code PYTHON navariantcalling.py vi chua remove mot so line conflict cua GIT

Em check lai nhe. Thanks em !!

trong file VCF annotate có xuất hiện SNP nhưng trong BamViewer nhìn không thấy

readme

how to use the pipeline.

Can logging xuong file

Hi Tan,

Em nen output tien trinh pipeline bang log file

import logging
import import logging.handlers

Create Logger instance

def initLogger():
oLogger = logging.getLogger("RNAVARIANTCALLING")
oLogger.setLevel(logging.DEBUG)
oLoggerHandler = logging.handlers.RotatingFileHandler("./debug.log", maxBytes=10485760, backupCount=10)
oFormatter = logging.Formatter("%(levelname)s : [%(asctime)s] - [%(filename)s at line (%(lineno)d) of (%(funcName)s) function] - [%(message)s]")
oLoggerHandler.setFormatter(oFormatter)
oLogger.addHandler(oLoggerHandler)

Main function handler

def main():
###Khoi tao LOGGER
initLogger()

###COI logging tren python (search di nhe)
oLogger = logging.getLogger("RNAVARIANTCALLING")
oLogger.info("AAAAA")

Thanks em !!!

freebayes for rna-seq

RNA-seq in some areas have very high coverage or very low coverage (very different from DNA). This causes the memory intensive scenario that we observed.
We should subsample these high coverage regions before moving to freebayes.

snpEff

Integrate snpEff to the pipeline to annotate the effect of variants.

Log file tao ngay thu muc chay tool

Hi Tan,

hien tai co van de la log files khi chay pipeline tao tu dong tai thu muc hien tai

VD : anh dang thu muc /home/hoa, chay pipeline thi file logs se duoc tao tai day (du git clone vao thu muc rnavariantcalling

Em add them 1 param do add log directory nua nhe.

Thanks !!!

Code dùng os.system, để execute 1 command như vcftool, hisat2 ...

Hi Tân,
Code pipeline dùng os.system để execute 1 external command có 2 vấn đề :

• ko security vì chưa escape shell command

• ko handle được trạng thái của external command
  Anh suggestion dùng thêm 2 hàm này :

  1/ execute a command

  def executeCommand(sCommand):
  ###Get all output data
  outData, errData = subprocess.Popen(sCommand, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True).communicate()

  ###Get all response data
  for lineData in outData.splitlines():
      if(self.RUNNING_DEBUG_FLAG == 1):
          outStringData = str(lineData)
          print("%s" % (outStringData))
  
  ###If there is error
  if((errData != None) and (len(errData) > 0)):
      print("Command has error:{0}".format(errData))
  

  ---

2/ escape shell script

def shellEscape(s):

return s.replace("(","(").replace(")",")")

Thanks !!!

Pipeline chi support paired-end files

Hi Tan,
Pipeline co support single-pair file ko em ?
Trong Readme, em cho example command line thi ro hon em nhe.
Thanks em !!!

Can chay voi param: --unset 9 ??

Hi Tan,
Sau khi anh git pull ve, bay gio anh co can chay voi param : --unset 9 , nua khogn em?
Thanks !!!

Annotated 0 bytes

Hi Tan,

Sau khi git pull code ve, anh da chay tuan tu cac lenh sau :

• sudo python setup.py install
• ./configure
• ./initial.sh

Va sau do, submit lai workspace, data output 0 byte

Thanks !!!