text: user6948: I am trying to use a free .py script from this site 
    http://www.di-tector.cyame.eu/
  
  while unfortunately there's neither manual nor any documentation presented.
  I have downloaded the .py script however I have absolutely no idea how it can be started. Can anyone give me an idea of how that can be done?
  The corresponding article (https://pubmed.ncbi.nlm.nih.gov/30012569/) only displays parameters for executing it and there is no way to understand what steps must be performed firstly. Thank you.
  
  user-1: See the help:
  python DI-tector_06.py -h
  usage: DI-tector_06.py [-h] [-g HOST_REF] [-s MIN_SEGMENT] [-m MIN_MAPQ]
                         [-n NB_READS] [-o OUTPUT_DIRECTORY] [-t TAG] [-d]
                         [-l INDEL_LENGTH] [-f] [-p POLARITY] [-q] [-k]
                         [-x NB_THREADS]
                         Virus_Ref Input_Data
  
  positional arguments:
    Virus_Ref             Virus genome reference sequence in FASTA format.
    Input_Data            File containing single reads in FASTQ format.
  
  optional arguments:
    -h, --help            show this help message and exit
    -g HOST_REF, --Host_Ref HOST_REF
                          Host genome reference sequence in FASTA format.
    -s MIN_SEGMENT, --Min_Segment MIN_SEGMENT
                          Minimum segment length. Default is 15.
    -m MIN_MAPQ, --Min_MAPQ MIN_MAPQ
                          Skip alignments with MAPQ smaller than INT. Default is
                          25.
    -n NB_READS, --Nb_Reads NB_READS
                          Show only DVGs with counts reads > or egal to INT.
                          Default is 2.))
    -o OUTPUT_DIRECTORY, --Output_Directory OUTPUT_DIRECTORY
                          Enter a directory name that all compiled output files
                          will be saved in.
    -t TAG, --Tag TAG     Enter a tag name that will be appended before each
                          output file. Default is 'DI-tector'.
    -d, --DVG_sequences   Generate multi-fasta file with DVG sequences. Default
                          is (OFF).
    -l INDEL_LENGTH, --InDel_Length INDEL_LENGTH
                          Skip alignments with size of InDels smaller or egal to
                          INT. Default size is 1.
    -f, --Fasta           Select '-f' if data is in FASTA format fasta. Default
                          is FASTQ.
    -p POLARITY, --Polarity POLARITY
                          [0] Positive strand genome / [1] Negative strand
                          genome. Default is 0.
    -q, --No_Quantification
                          Inactive percentage quantification. Quantification
                          need bedtools Default is (ON).
    -k, --Keep_files      Keep intermediaite files (i.e. alignment etc...).
                          Default is (OFF).
    -x NB_THREADS, --Nb_threads NB_THREADS
                          Number of threads. Default is 1.
  
  
original_text: 6948: <p>I am trying to use a free .py script from this site </p>
  
  <pre><code>  http://www.di-tector.cyame.eu/
  </code></pre>
  
  <p>while unfortunately there's neither manual nor any documentation presented.</p>
  
  <p>I have downloaded the .py script however I have absolutely no idea how it can be started. Can anyone give me an idea of how that can be done?</p>
  
  <p>The corresponding article (<a href="https://pubmed.ncbi.nlm.nih.gov/30012569/" rel="nofollow noreferrer">https://pubmed.ncbi.nlm.nih.gov/30012569/</a>) only displays parameters for executing it and there is no way to understand what steps must be performed firstly. Thank you.</p>
   -1: <p>See the help:</p>
  
  <pre><code>python DI-tector_06.py -h
  usage: DI-tector_06.py [-h] [-g HOST_REF] [-s MIN_SEGMENT] [-m MIN_MAPQ]
                         [-n NB_READS] [-o OUTPUT_DIRECTORY] [-t TAG] [-d]
                         [-l INDEL_LENGTH] [-f] [-p POLARITY] [-q] [-k]
                         [-x NB_THREADS]
                         Virus_Ref Input_Data
  
  positional arguments:
    Virus_Ref             Virus genome reference sequence in FASTA format.
    Input_Data            File containing single reads in FASTQ format.
  
  optional arguments:
    -h, --help            show this help message and exit
    -g HOST_REF, --Host_Ref HOST_REF
                          Host genome reference sequence in FASTA format.
    -s MIN_SEGMENT, --Min_Segment MIN_SEGMENT
                          Minimum segment length. Default is 15.
    -m MIN_MAPQ, --Min_MAPQ MIN_MAPQ
                          Skip alignments with MAPQ smaller than INT. Default is
                          25.
    -n NB_READS, --Nb_Reads NB_READS
                          Show only DVGs with counts reads &gt; or egal to INT.
                          Default is 2.))
    -o OUTPUT_DIRECTORY, --Output_Directory OUTPUT_DIRECTORY
                          Enter a directory name that all compiled output files
                          will be saved in.
    -t TAG, --Tag TAG     Enter a tag name that will be appended before each
                          output file. Default is 'DI-tector'.
    -d, --DVG_sequences   Generate multi-fasta file with DVG sequences. Default
                          is (OFF).
    -l INDEL_LENGTH, --InDel_Length INDEL_LENGTH
                          Skip alignments with size of InDels smaller or egal to
                          INT. Default size is 1.
    -f, --Fasta           Select '-f' if data is in FASTA format fasta. Default
                          is FASTQ.
    -p POLARITY, --Polarity POLARITY
                          [0] Positive strand genome / [1] Negative strand
                          genome. Default is 0.
    -q, --No_Quantification
                          Inactive percentage quantification. Quantification
                          need bedtools Default is (ON).
    -k, --Keep_files      Keep intermediaite files (i.e. alignment etc...).
                          Default is (OFF).
    -x NB_THREADS, --Nb_threads NB_THREADS
                          Number of threads. Default is 1.
  </code></pre>
  