我有一个看起来像这样的JSON
{
"barcodes": {
"0004F--0004R": {
"Barcode UID": "4",
"Sample ID": "10887581",
"For Barcode Name": "0004F",
"For Barcode Sequence": "GGTAGTGTGTATCAGTACATG",
"Rev Barcode Name": "0004R",
"Rev Barcode Sequence": "GGTAGTGTGTATCAGTACATG",
"Genes Sequenced": "",
"Ethnicity": "",
"laa_params": {
"--minLength": "3000",
"--ignoreEnds": "60",
"--maxReads": "2500",
"--maxPhasingReads": "500"
}
},
"0014F--0014R": {
"Barcode UID": "14",
"Sample ID": "10895675",
"For Barcode Name": "0014F",
"For Barcode Sequence": "GGTAGCGTCTATATACGTATA",
"Rev Barcode Name": "0014R",
"Rev Barcode Sequence": "GGTAGCGTCTATATACGTATA",
"Genes Sequenced": "A/B/C",
"Ethnicity": "British/Irish",
"laa_params": {
"--minLength": "3000",
"--ignoreEnds": "60",
"--maxReads": "2500",
"--maxPhasingReads": "500"
}
},
"0018F--0018R": {
"Barcode UID": "18",
"Sample ID": "10896709",
"For Barcode Name": "0018F",
"For Barcode Sequence": "GGTAGCATCACTACGCTAGAT",
"Rev Barcode Name": "0018R",
"Rev Barcode Sequence": "GGTAGCATCACTACGCTAGAT",
"Genes Sequenced": "B/C",
"Ethnicity": "British/Irish",
"laa_params": {
"--minLength": "3000",
"--ignoreEnds": "60",
"--maxReads": "2500",
"--maxPhasingReads": "500"
}
}
}
}
我使用此JSON创建一个fasta文件,在其中我将条形码“ 0014F--0014R”的名称分为两半。每个部分都放在一个文件中,然后在其下面的相关顺序如下:
>0014F
GGTAGCGTCTATATACGTATA
>0014R
GGTAGCGTCTATATACGTATA
我使用Groovy进行此操作,其代码为:
// Load JSON
// cfg_file is the JSON
def analysis_config = jsonSlurper.parse(cfg_file)
// Create Keyset of "barcodes"
barcodes = Channel.from(analysis_config.barcodes.keySet())
// Create fasta:
new File('barcodes.fasta').withOutputStream { out ->
analysis_config.barcodes.each { barcode ->
def (fname, revname) = barcode.key.split('--')
out << ">$fname\n${barcode.value['For Barcode Sequence']}\n"
out << ">$revname\n${barcode.value['Rev Barcode Sequence']}\n"
}
}
我想更改此逻辑,以便如果“已排序的基因”为空,请跳过该条形码。
在“ 0004F--0004R”中,没有基因测序。如何实现此逻辑?
在Python中,您可以简单地做:
if not barcode['genessequenced']:
continue
...,它将跳过该条形码。我本质上是一名Python程序员,并且正在使用Nextflow,它使用Groovy作为其基本语言。帮助将不胜感激。
我感觉我的整个逻辑都必须改变。当前流是:
现在,流程应为:1.使用“基因排序”创建条形码的keySet()2.用序列填充每个序列
所以,barcodes = Channel.from(analysis_config.barcodes.keySet())
知道如何将逻辑添加到其中吗?
类似:
barcodes = Channel.from(analysis_config.barcodes.[if "Genes Sequenced"].keySet())
在常规情况下将是这样:
analysis_config.barcodes.findAll{b-> b.value."Genes Sequenced"}.keySet()
或
analysis_config.barcodes.findAll{k,v-> v."Genes Sequenced"}.keySet()
或
analysis_config.barcodes.findAll{k,v-> v["Genes Sequenced"]}.keySet()