python - scriptExit 1 与 pybedtools venn_mpl - snakemake 5.2.4

Question

我想用 pybedtools 创建 VennDiagramms。有一个使用 matplotlib 的特殊脚本，称为 venn_mpl。当我在我的 jupyter notebook 中试用它时，它工作得很好。您可以使用 python 或使用 shell 命令来完成。

不幸的是，当我想在我的 snakefile 中使用它时出了点问题，我无法真正弄清楚问题是什么。

首先，这是脚本:venn_mpl.py

#!/gnu/store/3w3nz0h93h7jif9d9c3hdfyimgkpx1a4-python-wrapper-3.7.0/bin/python
"""
Given 3 files, creates a 3-way Venn diagram of intersections using matplotlib; \
see :mod:`pybedtools.contrib.venn_maker` for more flexibility.

Numbers are placed on the diagram.  If you don't have matplotlib installed.
try venn_gchart.py to use the Google Chart API instead.

The values in the diagram assume:

    * unstranded intersections
    * no features that are nested inside larger features
"""

import argparse
import sys
import os
import pybedtools

def venn_mpl(a, b, c, colors=None, outfn='out.png', labels=None):
    """
    *a*, *b*, and *c* are filenames to BED-like files.

    *colors* is a list of matplotlib colors for the Venn diagram circles.

    *outfn* is the resulting output file.  This is passed directly to
    fig.savefig(), so you can supply extensions of .png, .pdf, or whatever your
    matplotlib installation supports.

    *labels* is a list of labels to use for each of the files; by default the
    labels are ['a','b','c']
    """
    try:
        import matplotlib.pyplot as plt
        from matplotlib.patches import Circle
    except ImportError:
        sys.stderr.write('matplotlib is required to make a Venn diagram with %s\n' % os.path.basename(sys.argv[0]))
        sys.exit(1)

    a = pybedtools.BedTool(a)
    b = pybedtools.BedTool(b)
    c = pybedtools.BedTool(c)

    if colors is None:
        colors = ['r','b','g']

    radius = 6.0
    center = 0.0
    offset = radius / 2

    if labels is None:
        labels = ['a','b','c']

然后是我的代码:

rule venndiagramm_data:
     input:
         data = expand("bed_files/{sample}_peaks.narrowPeak", sample=config["samples"]["data"])
     output:
         "figures/Venn_PR1_PR2_GUI_data.png"
     run:
         col = ['g','k','b']
         lab = ['PR1_data','PR2_data','GUI_data']
         venn_mpl(input.data[0], input.data[1], input.data[2], colors = col, labels = lab, outfn = output)

错误是:

SystemExit in line 62 of snakemake_generatingVennDiagramm.py:
1

snakemake-log 只给我:

rule venndiagramm_data:
    input: bed_files/A_peaks.narrowPeak,bed_files/B_peaks.narrowPeak, bed_files/C_peaks.narrowPeak
    output: figures/Venn_PR1_PR2_GUI_data.png
    jobid: 2

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

我已经尝试按照文档中的说明添加:

rule error:
  shell:
    """
    set +e
    somecommand ...
    exitcode=$?
    if [ $exitcode -eq 1 ]
    then
        exit 1
    else
        exit 0
    fi
    """

但这并没有改变什么。

然后我的下一个想法是在使用我之前也测试过并且运行良好的 shell 命令的同时执行它。但是后来我得到了一个不同但我认为非常相似的错误消息，我也没有找到合适的解决方案:

rule venndiagramm_data_shell:
    input:
        data = expand("bed_files/{sample}_peaks.narrowPeak", sample=config["samples"]["data"])
    output:
        "figures/Venn_PR1_PR2_GUI_data.png"
    shell:
        "venn_mpl.py -a {input.data[0]} -b {input.data[1]} -c {input.data[2]} --color 'g,k,b' --labels 'PR1_data,PR2_data,GUI_data'"
The snakemake log:

[Thu May 23 16:37:27 2019]
rule venndiagramm_data_shell:
    input: bed_files/A_peaks.narrowPeak, bed_files/B_peaks.narrowPeak, bed_files/C_peaks.narrowPeak
    output: figures/Venn_PR1_PR2_GUI_data.png
    jobid: 1

[Thu May 23 16:37:29 2019]
Error in rule venndiagramm_data_shell:
    jobid: 1
    output: figures/Venn_PR1_PR2_GUI_data.png

RuleException:
CalledProcessError in line 45 of snakemake_generatingVennDiagramm.py:
Command ' set -euo pipefail;  venn_mpl.py -a input.data[0] -b input.data[1] -c input.data[2] --color 'g,k,b' --labels 'PR1_data,PR2_data,GUI_data' ' returned non-zero exit status 1.

有没有人知道这可能是什么原因以及如何解决？

仅供引用:我说过我测试了它，但没有使用 snakemake 运行它。这是我的工作代码:

from snakemake.io import expand
import yaml
import pybedtools
from pybedtools.scripts.venn_mpl import venn_mpl

config_text_real = """ 
samples:
    data:
    - A
    - B
    - C
    control:
    - A_input 
    - B_input
    - C_input
"""
config_vennDiagramm = yaml.load(config_text_real)
config = config_vennDiagramm

data = expand("{sample}_peaks.narrowPeak", sample=config["samples"]["data"])
col = ['g','k','b']
lab = ['PR1_data','PR2_data','GUI_data']
venn_mpl(data[0], data[1], data[2], colors = col, labels = lab, outfn = 'Venn_PR1_PR2_GUI_data.png')

control = expand("{sample}_peaks.narrowPeak", sample=config["samples"]["control"])
lab = ['PR1_control','PR2_control','GUI_control']
venn_mpl(control[0], control[1], control[2], colors = col, labels = lab, outfn = 'Venn_PR1_PR2_GUI_control.png')

在我的 jupyter shell 笔记本中:

!A='../path/to/file/A_peaks.narrowPeak'
!B='../path/to/file/B_peaks.narrowPeak'
!C='../path/to/file/C_peaks.narrowPeak'
!col=g,k,b
!lab='PR1_data, PR2_data, GUI_data'
!venn_mpl.py -a ../path/to/file/A_peaks.narrowPeak -b ../path/to/file/B_peaks.narrowPeak -c ../path/to/file/C_peaks.narrowPeak --color "g,k,b" --labels "PR1_data, PR2_data, GUI_data"

我使用完整路径而不是变量的原因是，由于某些原因代码无法使用 "$A"调用变量。

Answer 1

不确定这是否解决了问题，但我注意到的一件事是:

shell:
    "venn_mpl.py -a input.data[0] -b input.data[1] -c input.data[2]..." 

可能应该是:

shell:
    "venn_mpl.py -a {input.data[0]} -b {input.data[1]} -c {input.data[2]}..."