Metadata-Version: 2.1
Name: pywgsim
Version: 0.5.1
Summary: pywgsim
Home-page: https://github.com/ialbert/pywgsim
Author: Istvan Albert
Author-email: istvan.albert@gmail.com
License: UNKNOWN
Description: ## pywgsim
        
        pywgsim is a modified version of the wgsim short read simulator. 
        
        * https://github.com/lh3/wgsim
        
        The code for `wgsim` has been modified to allow visualizing the simulated mutations as a GFF file.
        
        ![IGV Screenshot](test/igv-example.png)
        
        The package provides both a python wrapper and standalone compiled executables for Linux and MacOS.
        
        ## Installation
        
            pip install pywgsim
        
        PyPI page: https://pypi.org/project/pywgsim/
         
        ## Usage
        
            $ pywgsim -h
            
        prints:
            
            usage: pywgsim [-h] [-e 0.02] [-D 500] [-s 50] [-N 1000] [-1 70] [-2 70]
                           [-r 0.001] [-R 0.15] [-X 0.25] [-S 0] [-A 0.05] [-f]
                           genome [read1] [read2]
            
            positional arguments:
              genome                FASTA reference sequence
              read1                 FASTQ file for first in pair
              read2                 FASTQ file for second in pair
            
            optional arguments:
              -h, --help            show this help message and exit
              -e 0.02, --err 0.02   the base error rate
              -D 500, --dist 500    outer distance between the two ends
              -s 50, --stdev 50     standard deviation
              -N 1000, --num 1000   number of read pairs
              -1 70, --L1 70        length of the first read
              -2 70, --L2 70        length of the second read
              -r 0.001, --mut 0.001
                                    rate of mutations
              -R 0.15, --frac 0.15  fraction of indels
              -X 0.25, --ext 0.25   probability an indel is extended
              -S 0, --seed 0        seed for the random generator
              -A 0.05, --amb 0.05   disregard if the fraction of ambiguous bases higher
                                    than FLOAT
              -f, --fixed           each chromosome gets N sequences
        
        ## Changes compared to wgsim
        
        The original code for wgsim has been modified as follows:
        
        1. The output describing the mutations introduced by `wgsim` are generated in GFF format.
        1. The separator character in the read name has been changed from `_` to `|`. 
        1. There is a new flag called `--fixed` that generates the same `N` number of reads for each chromosome.
        
        ### Read naming
        
        The read naming now follows a more widely accepted convention (i.e. NCBI) and allows for contigs with underscores in them. In addition the visual inspection of the read names is easier: 
        
        `@NC_002945.4|1768156|1768694|0:0:0|4:0:0|4`
        
        ### Fixed mode
        
        In the default operation of wgsim the `N` reads are distributed such to create a uniform coverage across all chromosomes (longer chromosomes get a larger fraction of N). 
        
        When the `--fixed` mode is enabled `N` reads will be generated for each chromosome. The `--fixed` mode was introduced to simplify the evaluation of classifiers. Since the same number of reads is generated from each input sequence it makes it much simpler to assess the quality of classifications. 
         
        ## Mutation output
        
        The tool simulates mutations assuming a diploid genome. The output generated by `pywgsim` will look like this:
        
        ```
        ##gff-version 3
        #
        # N=10000 err_rate=0 mut_rate=0.001 indel_frac=0.15000001 indel_ext=0.25 size=500 std=50 len1=70 len2=70 seed=1607013056
        #
        NC_001416.1    wgsim    snp    89      89      .    +    .    Name=A/R;Ref=A;Alt=R;Type=het
        NC_001416.1    wgsim    snp    2825    2825    .    +    .    Name=-/A;Ref=-;Alt=A;Type=het
        NC_001416.1    wgsim    snp    3712    3712    .    +    .    Name=G/A;Ref=G;Alt=A;Type=hom
        NC_001416.1    wgsim    snp    4622    4622    .    +    .    Name=G/-;Ref=G;Alt=-;Type=hom
        ```
        
        Interpretation: 
        
        * `A/R` means heterozygous mutations with `A/A` and `A/G` alleles.
        * `-/A` means an insertion of a `A` relative to the reference, the type field indicates heterozygous mutation.
        * `G/A` means homozygous mutations with `G/A` alleles in both copies.
        * `G/-` means a deletion of a `G` from the reference, the type field indicates homozygous mutation.
        
        ## Ambiguity codes
        
            A           A           T
            C           C           G
            G           G           C
            T/U         T           A
            M         A or C        K
            R         A or G        Y
            W         A or T        W
            S         C or G        S
            Y         C or T        R
            K         G or T        M
            V      A or C or G      B
            H      A or C or T      D
            D      A or G or T      H
            B      C or G or T      V
            N    G or A or T or C   N
        
        ## Read name conventions
           
        The read names are now of the form:
        
               @NC_002945.4|1768156|1768694|0:0:0|4:0:0|4
        
        Where:
        
           * `NC_002945.4` is the contig name that the fragment was generated from.
           * `1768156` is the left-most position of the fragment.
           * `1768694` is the right-most position of the fragment.
           * `0:0:0` are the number of errors, substitutions and indels in the left-most read of the pair.
           * `4:0:0` are the number of errors, substitutions and indels in the right-most read of the pair.
           * `4` is the read pair number, unique, per contig.
        
        
        ## API
        
        The C interface to `wgsim` is accessible as a single function call 
        
            from pywgsim import wgsim
        
            wgsim.core(r1="read1.fq", r2="read2.fq", ref="genome.fa", err_rate=0.02, mut_rate=0.001, indel_frac=0.15, indel_ext=0.25, max_n=0.05, is_hap=0, N=100000,  dist=500, stdev=50, size_l=100, size_r=100, is_fixed=0, seed=0)
            
        The function creates the files `r1` and `r2`.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: C
Classifier: Programming Language :: Cython
Requires-Python: >=3.6
Description-Content-Type: text/markdown
