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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.

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  • $\begingroup$ No documentation is a major reason to not use this tool and to start looking for something else. The website seems to be in a poor state towards content, everything says "coming soon", I would be careful to build your analysis on this. $\endgroup$ – ATpoint Jun 13 '20 at 16:15
  • $\begingroup$ agree, while unfortunately, this is the only tool that I have found yet, that is dedicated to defective genomes analysis. $\endgroup$ – Dmitrii Trubetskoy Jun 13 '20 at 16:37
  • $\begingroup$ If you download the script and then type python DI-tector_06.py -h into the command line then you see explanations on the parameters. Maybe that helps getting started. $\endgroup$ – ATpoint Jun 13 '20 at 18:51
  • $\begingroup$ true, it says I have to do it this way: 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 Just cannot figure out what are Virus_Ref Input_Data might be just a .fastq and .gtf files? $\endgroup$ – Dmitrii Trubetskoy Jun 13 '20 at 19:36
  • $\begingroup$ Regardless it is a stylish (and fashionable) question $\endgroup$ – M__ Jun 14 '20 at 19:54
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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.
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