Python read_chrom_sizes示例

示例#1

    ############################################################

    ## Simulation tag names, assembly to select from.
    batch_name = args.short
    assembly = args.assembly

    ## files & variables
    ## fasta segment lengths; number of segments / sims.
    L = args.L
    N = args.N

    ############################################################
    ########################      ##############################

    ## Read chrom_sizes file to decide where to sample files from.
    chrom_sizes = read_chrom_sizes(assembly, size_dir=chrom_sizes_dir)

    ## Sample fasta.
    ##
    fasta = fastas_dir + assembly + '.fa.gz'
    rseqs = region_samplev2(L, chrom_sizes, N, fasta)

    from tools.SLiM_pipe_tools import SLiM_dispenserv2

    ## Perform Simulations
    ## I. get cookfunction and args:
    selected_book = 'cook_constants_' + args.cookbook

    import tools.cookbook
    book = getattr(tools.cookbook, selected_book)

示例#2

文件： SLiM_cluster.py 项目： SantosJGND/fine-scale-mutation-spectrum-master

## Simulation tag names, assembly to select from.
batch_name= 'Gravel'
assembly= 'hg38'

## files & variables
## fasta segment lengths; number of segments / sims.
L= int(1e4)
N= 4


############################################################
########################      ##############################


## Read chrom_sizes file to decide where to sample files from. 
chrom_sizes= read_chrom_sizes(assembly)

## Sample fasta.
##
fasta= fastas_dir + assembly + '.fa.gz'
rseqs= region_samplev1(L, chrom_sizes,N, fasta)

from tools.SLiM_pipe_tools import SLiM_dispenserv1
from tools.cookbook import cook_constants_Gravel2sampleRange

## Perform Simulations
print('launch SLiM jobs.')

cookargs= {
    "nrange": [.05,.5], 
    "step": N,