Generating JSON File
Can be generated from Excel spreadsheet template, or for simple cases, directly from multifasta file. The Excel template is located on aspen at /scratch/dlemmer/ASAP/assay_data/ASAP_assay_template.xltx (monsoon is: /scratch/dl765/ASAP/assay_data/ASAP_assay_template.xltx)
prepareJSONInput -x <EXCEL_FILE> -o <OUTPUT_JSON_FILE>
Full usage details:
usage: prepareJSONInput [-h] (-f FILE | -x FILE) -o FILE [-w WORKSHEET] [-V]
asap.prepareJSONInput -- Create a JSON input file for ASAP from a multifasta or Excel spreadsheet
optional arguments:
-h, --help show this help message and exit
-w WORKSHEET, --worksheet WORKSHEET
Excel worksheet to use, the first one in the file will be used if not specified
-V, --version show program's version number and exit
required arguments:
-f FILE, --fasta FILE
fasta file containing amplicon sequences.
-x FILE, --excel FILE
Excel file of assay data.
-o FILE, --out FILE output JSON file to write. [REQUIRED]
Running ASAP
analyzeAmplicons -n <RUN_NAME> -j <PATH_TO_JSON_FILE> -r <DIRECTORY_OF_READ_FILES> -o <OUTPUT_DIRECTORY> <other options>
<RUN_NAME> can be whatever you want, the final output file will be: <OUTPUT_DIRECTORY>/<RUN_NAME>_analysis.xml
You can also change the depth (default 100), proportion (default 0.1), breadth (default 0.8) filters using the -d and -p and -b options
Pre-made JSON files are located on aspen at /scratch/dlemmer/ASAP/assay_data/*.json (monsoon: /scratch/dl765/ASAP/assay_data/*.json)
Full usage details:
usage: analyzeAmplicons [-h] -n NAME -j JSON [-r DIR | -b DIR] [-o DIR]
[--trim | --no-trim] [-s ADAPTERS] [-q [QUAL]]
[-m LEN] [-a ALIGNER] [--aligner-args ARGS] [-d DEPTH]
[--breadth BREADTH] [-p PROPORTION] [-V]
asap.analyzeAmplicons -- Align and interpret amplicon sequencing reads
optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
required arguments:
-n NAME, --name NAME name for this run. [REQUIRED]
-j JSON, --json JSON JSON file of assay descriptions. [REQUIRED]
optional arguments:
-r DIR, --read-dir DIR
directory of read files to analyze.
--bam-dir DIR directory of bam files to analyze.
-o DIR, --out-dir DIR
directory to write output files to. [default: `pwd`]
-s JOB_MANAGER, --submitter JOB_MANAGER
cluster job submitter to use (PBS, SLURM, SGE, none). [default: PBS]
--submitter-args ARGS
additional arguments to pass to the job submitter, enclosed in "".
--smor perform SMOR analysis with overlapping reads. [default: False]
read trimming options:
--trim perform adapter trimming on reads. [default: True]
--no-trim do not perform adapter trimming.
-s ADAPTERS, --adapter-sequences ADAPTERS
location of the adapter sequence file to use for trimming. [default:
<ASAP install dir>/asap/illumina_adapters_all.fasta]
-q [QUAL], --qual [QUAL]
perform quality trimming [default: False], optional parameter can be used to
customize quality trimming parameters to trimmomatic.
[default: SLIDINGWINDOW:5:20]
-m LEN, --minlen LEN minimum read length to keep after trimming. [default: 80]
read mapping options:
-a ALIGNER, --aligner ALIGNER
aligner to use for read mapping, supports bowtie2, novoalign, and bwa.
[default: bowtie2]
--aligner-args ARGS additional arguments to pass to the aligner, enclosed in "".
-d DEPTH, --depth DEPTH
minimum read depth required to consider a position covered. [default: 100]
-b BREADTH, --breadth BREADTH
minimum breadth of coverage required to consider an amplicon as present.
[default: 0.8]
-p PROPORTION, --proportion PROPORTION
minimum proportion required to call a SNP at a given position. [default: 0.1]
-i PERCID, --identity PERCID
minimum percent identity required to align a read to a reference amplicon
sequence. [default: 0]
This command will ultimately generate the xml file. To convert this into more better things, run:
Formatting Output
formatOutput -s <XSLT_FILE> -x <XML_OUTPUT_FILE> -o <MAIN_OUTPUT_FILE_TO_WRITE>
This will generate all the html files, which you can open directly in your web browser. XSLT files are located on aspen at /scratch/dlemmer/ASAP/output_transforms/*.xsl (monsoon: /scratch/dl765/ASAP/output_transforms/*.xsl)
Full usage details:
usage: formatOutput [-h] -s FILE -x FILE [-o FILE] [-V]
asap.formatOutput -- Apply an XSLT transformation on the XML output to generate a more user-friendly output
optional arguments:
-h, --help show this help message and exit
-t, --text output plain text
-V, --version show program's version number and exit
required arguments:
-s FILE, --stylesheet FILE
XSLT stylesheet to use for transforming the output. [REQUIRED]
-x FILE, --xml FILE XML output file to transform. [REQUIRED]
-o FILE, --out FILE output file to write. [REQUIRED]