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Merged
sejooning merged 2 commits into from
Aug 15, 2023
Merged

Incorporate bug fixes and update version number #46

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116b893
Update ncm.py
Jul 6, 2023
51e2634
Update README.md
Jul 6, 2023
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11 changes: 8 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,8 @@ NGSCheckMate is a software package for identifying next generation sequencing (N

NGSCheckMate paper is now published in [_Nucleic Acids Research_](https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx193).


* pdf documentation is included in the package. [Documentation.pdf](Documentation.pdf)



## Table of contents
* [Requirements](#requirements)
* [Installation](#installation)
Expand Down Expand Up @@ -96,6 +93,14 @@ cd $NCM_HOME
source install_ncmfastq.sh
```

#### Containers
The tool is available through software containers for ease of installation:
* Docker: https://quay.io/repository/biocontainers/ngscheckmate?tab=tags&tag=latest
* Singularity/Apptainer: https://depot.galaxyproject.org/singularity/ngscheckmate:1.0.0--py27r41hdfd78af_3
* Conda: `bioconda::ngscheckmate=1.0.0`

Additionally, there is a Nextflow subworkflow for use on bam files available as part of the nf-core project, https://github.com/nf-core/modules/blob/master/subworkflows/nf-core/bam_ngscheckmate/main.nf.

## Usage
#### 1) BAM/VCF mode
```
Expand Down
28 changes: 16 additions & 12 deletions ncm.py
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Expand Up @@ -56,7 +56,9 @@ def pearson_def(x, y):
xdiff2 += xdiff * xdiff
ydiff2 += ydiff * ydiff

return diffprod / math.sqrt(xdiff2 * ydiff2)
sqrt_xdiff2_ydiff2 = math.sqrt(xdiff2 * ydiff2)

return diffprod / sqrt_xdiff2_ydiff2 if sqrt_xdiff2_ydiff2 != 0.0 else 0.0

# createDataSet
# base_dir : directory of files, bedFile: name of the bedFile
Expand Down Expand Up @@ -251,7 +253,7 @@ def createDataSetFromList(base_list, bedFile):
link = line.strip()
f = open(link, "r")
dbsnpf= open(bedFile,"r")
file = link[link.rindex("/")+1:]
file = os.path.basename(link)
depth = dict()
depth[file] = 0
real_count[file] = 0
Expand Down Expand Up @@ -909,7 +911,7 @@ def classifying():
training_flag =0
####0715 Append

output_matrix_f = open(outdir + "/output_corr_matrix.txt","w")
output_matrix_f = open(outdir + "/" + out_tag + "_output_corr_matrix.txt","w")
output_matrix = dict()

if out_tag!="stdout":
Expand Down Expand Up @@ -1118,17 +1120,20 @@ def generate_R_scripts():
if len(feature_list)==0:
r_file.close()
else :
cmd = "output_corr_matrix <- read.delim(\"" + outdir + "/output_corr_matrix.txt\")\n"
cmd = "output_corr_matrix <- read.delim(\"" + outdir + "/" + out_tag + "_output_corr_matrix.txt\")\n"
cmd = cmd + "data = output_corr_matrix\n"
cmd = cmd + "d3 <- as.dist((1 - data[,-1]))\n"
cmd = cmd + "clust3 <- hclust(d3, method = \"average\")\n"
if len(feature_list) < 5:
cmd = cmd + "pdf(\"" +outdir+ "/" + pdf_tag + ".pdf\", width=10, height=7)\n"
else:
cmd = cmd + "pdf(\"" +outdir+ "/" + pdf_tag + ".pdf\", width="+str(math.log10(len(feature_list))*10) +", height=7)\n"
cmd = cmd + "op = par(bg = \"gray85\")\n"
cmd = cmd + "par(plt=c(0.05, 0.95, 0.2, 0.9))\n"
cmd = cmd + "plot(clust3, lwd = 2, lty = 1,cex=0.8, xlab=\"Samples\", sub = \"\", ylab=\"Distance (1-Pearson correlation)\",hang = -1, axes = FALSE)\n"
cmd = cmd + "pdf(\"" +outdir+ "/" + pdf_tag + ".pdf\", width="+str(math.log10(7*len(feature_list))*10) +", height=7)\n"
cmd = cmd + "op = par(bg = \"white\")\n"
cmd = cmd + "par(plt=c(0.05, 0.95, 0.25, 0.9))\n"
if len(feature_list) < 3:
cmd = cmd + "plot(as.dendrogram(clust3), lwd = 2, lty = 1,cex=0.8, xlab=\"Samples\", sub = \"\", ylab=\"Distance (1-Pearson correlation)\", axes = FALSE)\n"
else:
cmd = cmd + "plot(clust3, lwd = 2, lty = 1,cex=0.8, xlab=\"Samples\", sub = \"\", ylab=\"Distance (1-Pearson correlation)\",hang = -1, axes = FALSE)\n"
cmd = cmd + "axis(side = 2, at = seq(0, 1, 0.2), labels = FALSE, lwd = 2)\n"
cmd = cmd + "mtext(seq(0, 1, 0.2), side = 2, at = seq(0, 1, 0.2), line = 1, las = 2)\n"
cmd = cmd + "dev.off()\n"
Expand All @@ -1147,8 +1152,7 @@ def remove_internal_files():
if outdir.find("*"):
sys.exit()


command = "rm -rf " + outdir + "/output_corr_matrix.txt"
command = "rm -rf " + outdir + "/" + out_tag + "_output_corr_matrix.txt"
proc = subprocess.Popen(command, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)
return_code = proc.wait()
command = "rm -rf " + outdir + "/r_script.r"
Expand Down Expand Up @@ -1362,7 +1366,7 @@ def output_filter():
testsamplename = ""

help = """
Ensuring Sample Identity v1.0
Ensuring Sample Identity v1.0.1
Usage: NGSCheckmate

Desc.: Input = the absolute path list of vcf files (samtools mpileup and bcftools)
Expand All @@ -1373,7 +1377,7 @@ def output_filter():
ncm.py -B -d /data/bam/ -bed /data/SNP_hg19.bed -O /data/output -N Matched_list
ncm.py -B -l /data/bam_list.txt -bed /data/SNP_hg19.bed -O /data/output/ -N Matched_list

Sejoon Lee, Soo Lee, Eunjung Lee, 2015
Sejoon Lee, Soo Lee, Eunjung Lee, 2023
"""

parser = argparse.ArgumentParser(description=help, formatter_class=RawTextHelpFormatter)
Expand Down