我正在编写一个脚本，它结合了snakemake和python代码来自动化大量成对出现的文件。更准确地说，我正在将读取与 BWA MEM 与配对末端读取 ( http://bio-bwa.sourceforge.net/bwa.shtml ) 对齐。在脚本的第一部分，我遍历了我的文件中的名称列表（它们是fastq bunzip文件），然后在列表中相应地对它们进行排序。以下是一些文件的快速浏览：
['NG-8653_ 1A _lib95899_4332_7_ 1 ', 'NG-8653_ 1A _lib95899_4332_7_ 2 ', 'NG-8653_ 1B _lib95900_4332_7_ 1 ', 'NG-8653_ 1B _lib95900_4332_7_ 2 ', 'NG-8653_ 1N _lib95898_4332_7_ 1 ', 'NG-8653_ 1N_lib95898_4332_7_2 ' ] _
如您所见，读取按两两排序（1A_... 1 和 1A ..._2 等...）。现在使用子进程，我想通过使用 bunzip2 解压缩它们然后将它们通过 stdin 传递给 bwa mem 来对齐它们。bwa mem 命令将 fastq 格式文件转换为 .sam 文件，然后我必须使用 samtools 将它们转换为 .bam 格式。这是到目前为止的脚本：
import re, os, subprocess, bz2
WDIR = "/home/alaa/Documents/snakemake"
workdir: WDIR
SAMPLESDIR = "/home/alaa/Documents/snakemake/fastq/"
REF = "/home/alaa/Documents/inputs/reference/hg19_ref_genome.fa"
FILE_FASTQ = glob_wildcards("fastq/{samples}.fastq.bz2")
LIST_FILE_SAMPLES = []
for x in FILE_FASTQ[0]:
LIST_FILE_SAMPLES.append(x)
LIST_FILE_SAMPLES = sorted(LIST_FILE_SAMPLES)
print(LIST_FILE_SAMPLES)
rule fastq_to_bam:
run:
for x in range(0, len(LIST_FILE_SAMPLES), 2):
# get the name of the sample (1A, 1B ...)
samp = ""
samp += LIST_FILE_SAMPLES[x].split("_")[1]
# get the corresponding read (1 or 2)
r1 = SAMPLESDIR + LIST_FILE_SAMPLES[x] + ".fastq.bz2"
r2 = SAMPLESDIR + LIST_FILE_SAMPLES[x+1] + ".fastq.bz2"
# gunzipping the files and pipping them
p1 = subprocess.Popen(['bunzip2', '-kc', r1], stdout=subprocess.PIPE)
p2 = subprocess.Popen(['bunzip2', '-kc', r2], stdout=subprocess.PIPE)
# now write the output file to .bam format after aligning them
with open("sam/" + samp + ".bam", "w") as stdout:
fastq2sam = subprocess.Popen(["bwa", "mem", "-T 1", REF, p1.stdout, p2.stdout], stdout=subprocess.PIPE)
fastq2samOutput = subprocess.Popen(["samtools", "view", "-Sb", "-"], shell = True, stdin=fastq2sam.stdout, stdout=stdout)
我试图通过逐行尝试来调试脚本。将 bunzip2 写入输出文件时，它工作正常。现在，如果我尝试通过管道传输它，我会收到一个错误：
Error in job fastq_to_bam while creating output file .
RuleException:
TypeError in line 39 of /home/alaa/Documents/snakemake/Snakefile:
Can't convert '_io.BufferedReader' object to str implicitly
File "/home/alaa/Documents/snakemake/Snakefile", line 39, in __rule_fastq_to_bam
File "/usr/lib/python3.5/subprocess.py", line 947, in __init__
File "/usr/lib/python3.5/subprocess.py", line 1490, in _execute_child
File "/usr/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Exiting because a job execution failed. Look above for error message
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
你能告诉我脚本有什么问题吗？从今天早上开始，我一直在寻找问题，但我似乎无法弄清楚。任何帮助深表感谢。提前致谢。
编辑1：
在阅读了来自@bli 和@Johannes 的更多反馈之后，我已经做到了这一点：
import re, os, subprocess, bz2, multiprocessing
from os.path import join
from contextlib import closing
WDIR = "/home/alaa/Documents/snakemake"
workdir: WDIR
SAMPLESDIR = "fastq/"
REF = "/home/alaa/Documents/inputs/reference/hg19_ref_genome.fa"
FILE_FASTQ = glob_wildcards("fastq/{samples, NG-8653_\d+[a-zA-Z]+_.+}")
LIST_FILE_SAMPLES = []
for x in FILE_FASTQ[0]:
LIST_FILE_SAMPLES.append("_".join(x.split("_")[0:5]))
LIST_FILE_SAMPLES = sorted(LIST_FILE_SAMPLES)
print(LIST_FILE_SAMPLES)
rule final:
input:
expand('bam/' + '{sample}.bam', sample = LIST_FILE_SAMPLES)
rule bunzip_fastq:
input:
r1 = SAMPLESDIR + '{sample}_1.fastq.bz2',
r2 = SAMPLESDIR + '{sample}_2.fastq.bz2'
output:
o1 = SAMPLESDIR + '{sample}_r1.fastq.gz',
o2 = SAMPLESDIR + '{sample}_r2.fastq.gz'
shell:
"""
bunzip2 -kc < {input.r1} | gzip -c > {output.o1}
bunzip2 -kc < {input.r2} | gzip -c > {output.o2}
"""
rule fastq_to_bam:
input:
r1 = SAMPLESDIR + '{sample}_r1.fastq.gz',
r2 = SAMPLESDIR + '{sample}_r2.fastq.gz',
ref = REF
output:
'bam/' + '{sample}.bam'
shell:
"""
bwa mem {input.ref} {input.r1} {input.r2} | samtools -b > {output}
"""
非常感谢您的帮助！我想我可以从这里开始。
最好的问候，阿拉