hpviewer's Introduction

HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA

Description

HPViewer is a tool for genotyping and quantification of HPV from metagenomic or human genomic shotgun sequencing data. We designed it to improve performance by masking nonspecific sequences from reference genomes and directly identifying HPV short DNA reads. It contains two HPV databases with different masking strategies, repeat-mask and homology-mask and one homology distance matrix to choose between those two databases.

If you use the HPViewer software, please cite our manuscript:

Yuhan Hao, Liying Yang, Antonio Galvao Neto, Milan R Amin, Dervla Kelly, Stuart M Brown, Ryan C Branski, Zhiheng Pei; HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA, Bioinformatics, bty037, https://doi.org/10.1093/bioinformatics/bty037

Installation

$ git clone https://github.com/yuhanH/HPViewer.git

Pre-requisites

Python (2.7+)

Python packages (sys, getopt, subprocess)

Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

SAMtools: http://www.htslib.org/

Bedtools: http://bedtools.readthedocs.io/en/latest/

Parameters

Required

a) input files (-U or -1 -2): fastq files (or fastq.gz), unpaired (-U unpaired.fastq) or R1,R2 paired (-1 R1.fastq -2 R2.fastq)

b) output file name (-o)

Optional

a) database mask type (-m): hybrid-mask(default), repeat-mask, homology-mask.

If you set -m, it should be in front of reads input (-m repeat-mask -1 R1.fastq -2 R2.fastq). Repeat-mask is a more sensitive mode; and homology-mask is suggested when some types of HPV are present in large abundance which may lead to false positive of other types of HPV.

b) number of threaded used in bowtie2 alignment (-p)

c) minimal coverage threshold to determine HPV present (-c), default is 150 bp (1.5 x average length of your reads).

Results

a) output_HPV_summary.txt has three coloumns with types of HPV present, number of reads per kilobase (RPK) for the matching HPV, and number of reads of the matching HPV.

b) alignment results after bowtie2: output.sam, output.bam

Basic Usage (demo)

python HPViewer.py -U test_unpaired.fastq -o TEST

more TEST/TEST_HPV_profile.txt

Work Flow

hpviewer's People

Contributors

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hpviewer's Issues

aaa

test

https://github.com/yuhanH/uwot/blob/16ea4043954cad33b1e9822e03eddc9d28af5e4f/R/uwot.R#L1656-L1658

error in lines 317, 310

this is the error I got when trying to run HPViewer on a sample metagenomic data -
Traceback (most recent call last):
File "/home/tirosho/HPViewer/HPViewer.py", line 317, in
quant_HPV(outprefix,min_cov)
File "/home/tirosho/HPViewer/HPViewer.py", line 310, in quant_HPV
coverage=str("%.4f" % (1000*float(d2[hpv])/float(d3[hpv])))
KeyError: 'HPV131'

I checked and saw HPV131 is not in the distant matrix database. does this cause the problem? or something else?

updating - I just tried it with another file and got the same error for HPV150, I guess it's not the HPV type that is the problem. Am I missing a python module?

Script/pipeline to update the database?

There are currently 182 types in the pre-built database, however PaVE now has >220, and so I was wondering if there was a script to re-generate the necessary input databases?

cov option does not work

-cov option does not work, will be interpreted as -o v
resulting in a 'v' directory wherein all your output is continuously overwritten.

fix hint: replace cov by single character option c:

print("   -c    <INT>    minimal coverage threshold to determine HPV present, default is 150 bp.")
...
getopt.getopt( sys.argv[1:], "U:1:2:m:o:p:c:h", ["help" ] )
...
if opt in ( "-c", ):
            min_cov = str(val)

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