Package: kmerexplor
KmerExploRDescriptionInstallationOption 1: install with pipOption 2: install with gitInputOutputExamplesUsageOptions-k --keep-counts--tags tags_file--config config.yamlDescriptionFrom a bunch of fastq or countTags output files, KmerExploR provides information on RNA-sequencing datasets :wether the analysis is based on poly-A selection protocol or ribo-depletion,whether the analysis is based on oriented or non-oriented sequencing,gender,whether there is a read coverage bias from 5' to 3' 	long transcriptswether the data are contamined by HeLa, mycoplasma is present or not, or other viruses such as hepatitis B virusspecieKmerExploRuses a set of reference specific kmers designed with Kmerator (https://github.com/Transipedia/kmerator).For general usage, we will use the provided set of kmers. Howerver, it is also possible to create your own kmers reference file to have specific informations on you samples such as request on a particular specie.This code is underGPL3licence.Testing with datasetYou can use the following dataset to test the software and to illustrate the different categories, which contains 5 paired-end human RNA-seq samples:PolyA/RiboDHeLaMycoplasmaStrandedSexfastq1fastq2SRR12010285PolyA+-yesfemalelinklinkENCFF322RPTPolyA-+yesmalelinklinkENCFF001RMXRiboD--yesfemalelinklinkSRR1957703PolyA--yesNAlinklinkSRR1957706PolyA--noNAlinklinkInstallationKmerExploRneedsyamlandmarkdownpython module,
We recommand tu use ``pip` as it install everything you need automatically.Option 1: install KmerExploR with pippip install kmerexplorNota: make sure your PATH variable include~/.local/bin.Option 2: install KmerExploR with git by cloning repository# clone the repository
git clone https://github.com/Transipedia/kmerexplor.git

# create link somewhere in your PATH
sudo ln -s $PWD/kmerexplor/kmerexplor/core.py /usr/local/bin/kmerexplorInputrequired:fastq or outputs from countTags (gzipped or not).For paired samples, fastq names must be in illumina format (_R1_001and_R2_001), or they must end by_1.fastq[.gz]and2.fastq[.gz].countTagsfiles must end bytsv[.gz].countTagsfiles can be aggregated in a single multi-culumn file.optional:yaml configuration file.tags file.Both must match (see below).OutputBy default, outputs are produced in directorykmerexplor-results.table.tsv: tab separated table of results.kmerexplor.html: graphical results.libdirectory contains css and javascript code associated withkmerexplor.html.if--keep-countsoption is specifiedcountTagsdirectory containscountTagsoutput.kmerexplor-results
├── countTags			# with '--keep' option
├── kmerTool.html
├── lib
│   ├── echarts-en.min.js
│   ├── scripts.js
│   └── styles.css
└── table.tsvUsageWithout options or with--help,KmerExploRreturns Helpusage: kmerexplor [-h] (-s | -p) [-k <int>] [-K] [-d] [-o <output_dir>] 
                  [--tmp-dir <tmp_dir>] [--config <file_name>] [-t <tag_file>] 
                  [--dump-config [file_name]] [--show-tags]
                  [--title <string>] [-y] [-c <int>] [-v]
                  <file1> ... [<file1> ... ...]

positional arguments:
  <file1> ...           fastq or fastq.gz or tsv countTags output files.

optional arguments:
  -h, --help            show this help message and exit
  -s, --single          when samples are single.
  -p, --paired          when samples are paired.
  -k <int>, --kmer-size <int>
                        kmer size (default 31).
  -K, --keep-counts     keep countTags outputs.
  -d, --debug           debug.
  -o <output_dir>, --output <output_dir>
                        output directory (default: "./kmerexplor-results").
  --tmp-dir <tmp_dir>   temporary files directory.
  --title <string>      title to be displayed in the html page.
  -y, --yes, --assume-yes
                        assume yes to all prompt answers.
  -c <int>, --cores <int>
                        specify the number of files which can be processed 
                        simultaneously by countTags. (default: 1). Valid when 
                        inputs are fastq files.
  -v, --version         show program's version number and exit

advanced features:
  --config <file_name>  alternate config yaml file.
  -t <tag_file>, --tags <tag_file>
                        alternate tag file.

extra features:
  --dump-config [file_name]
                        dump builtin config file as specified name to current 
                        directory and exit (default name: config.yaml).
  --show-tags           print builtin categories and predictors and exit.Options-k --keep-countsBy default,KmerExploRdeletes intermediate files, particularly countTags output (when input files are fastq files). You could keep countTags output files by using--keep-countsoption. The location of the countTags output files will then be displayed on the standard output.countTags outputs are located in a directory namedcountTags, located inkmerexplor-resultsby default or specified by-ooption.If you want to run again KmerExploR with the same input dataset, you can directly use  this directory (kmerexplor-results/countTags/*.tsv). CountTags step will be bypassed which is saving a lot of time.--tags tags_fileKmerExploR uses an internal default tag file. You can specify another tags file using--tagsoption with an alternate tags file (compressed or not).Tags file formatTags file format is tabuled in 2 columns.column 1 : kmer sequencecolumn 2 : description with dashes "-" are separator, The dashes are very important to define the structure.Example :AACGCCGCGCGTGACAACAAGAAGACCAGGA Histone-H2AFJ-ENST00000501744.2.fa.kmer58AACGCCGCGCGTGACAACAAGAAGACCAGGA: kmerHistone: categoryH2AFJ: seq_idENST00000501744.2.fa.kmer58: seq_def (not used)Warning:config.yamlfile must refer to the same categories than tags file, otherwise KmerExploR does not display results (Histonein the example).Notice: the description of a set of tags can can be displayed on the main home page by creating a markdown file of the same name, suffixed with.md(eg: my-tags.tsv -> my-tags.md).--config config.yamlAssociated to the tags file, KmerExploR includes a configuration file. It is used to reference kmers by categories (ex: Orientation, Mycoplasma) and display some parameters for graphs. It is strongly linked to the tags file.
When you set your own tag file, you also have to specify you own matching config file.Example for one categorie :Basic_features:   # Meta category, show in left sidenav (underscores are replaced by blank)
  Histone:        # Must match with first item (characters before first dash) of the second column
                  # in the tabuled tags file. Also, they will be used for Javascript function names.
                  # They must be unique, and contain uniquely letters, digits and underscores
    sidenav : Poly A / Ribo D
                  # Show in the left sidebar
    title: Poly A and Ribo depletion by Histone detection
                  # Title of the graph, in the main page.
    threshold: 350
                  # Leave blank if threshold is not needed.
                  # More than one threshold possible by adding multiple values separated by coma (ex: 350,450).
    chart_type: bar
                  # Only bar is admitted at this time.
    chart_theme: light
                  # light, dark, or nothing
    desc:         # More details on the graph, located under it
      - Short description of Poly A and Ribodepletion (show as title)
      - A paragraph of explanations.
      - Another paragraph.Using an alternative tag file, you probably have to redefine theconfig.yamlfile,--configoption specifies the location of an alternative yaml configuration file.Nota:if you addas_percent:to a category (empty or not), results will be in percentage (take a look atRead biasesresults).Examples:Mandatory:-pfor paired-end or-sfor single:kmerexplor -p path/to/*.fastq.gz-cfor multithreading,-Kto keep counts (input must be fastq):kmerexplor -p -c 16 -K path/to/*.fastq.gzYou can skip the counting step thanks to countTags output (see-Koption):kmerexplor -p path/to/countTags/files/*.tsv-oto choose your directory output (directory will be created),--titleto show title in results:kmerexplor -p -o output_dir --title 'Title in html page dir/*.fastq.gz'Advanced: using your own tag file and associated config.yaml file:kmerexplor -p -tags my_tags.tsv --config my_config.yaml dir/*.fast.gz