wildcards - 腾讯云开发者社区

文章/答案/技术大牛

发布

workflow04-用snakemake处理复杂命名

different wildcards you can do like: wildcards.sample = "s002" # print that value: wildcards.sample..., "fastq2"] # here we use it on our spoofed wildcards object fq2_from_sample(wildcards) 因为snakemake...(wildcards): return samples_table.loc[wildcards.sample, "fastq2"] rule trim_awesome: input:...[wildcards.sample, "fastq2"] } # make sure our spoofed wildcards variable is set: wildcards.sample...= "s003" # Now see what that function returns on that wildcards input: fq_dict_from_sample(wildcards

1.6K2 0

snakemake杂记：多个转录组比对到多个基因组得到多个bam文件然后合并

/rnaseq/01.clean.reads/{sample}_clean_1.fq") GENOMES, = glob_wildcards("{genome}.fa.masked") GENOMES...' is not defined 然后又换成下面的写法 def getGenomes(wildcards): return wildcards.genome rule samtools_merge...这里面提到 'wildcards' is not "directly" defined in the input of a rule....安装这个思路我写我自己的 def getGenome01(wildcards): return expand(rules.samtools_sort.output.bam,genome=wildcards.genome...,sample=SAMPLES) def getGenome02(wildcards): return expand(rules.samtools_index.output,genome=wildcards.genome

5951 0

您找到你想要的搜索结果了吗？

是的

没有找到

snakemake 学习笔记3

3 [Tue Apr 2 21:09:19 2019] rule adda: input: 3.txt output: 3_add_a.txt jobid: 2 wildcards...done [Tue Apr 2 21:11:09 2019] rule adda: input: 1.txt output: 1_add_a.txt jobid: 1 wildcards...2 21:13:57 2019] rule addb: input: 2_add_a.txt output: 2_add_a_add_b.txt jobid: 0 wildcards...2 21:13:57 2019] rule addb: input: 1_add_a.txt output: 1_add_a_add_b.txt jobid: 1 wildcards...2 21:13:57 2019] rule addb: input: 3_add_a.txt output: 3_add_a_add_b.txt jobid: 2 wildcards

1K2 0

workflow05-snakemake的进阶操作一

: config["samples"][wildcards.sample] output: "mapped_reads/{sample}.bam" threads: 8...: config["samples"][wildcards.sample] 我们可以像字典一样去访问它，比如当我们传入A 时，即传给了通配符对应的{sample}，并可以获得对应的值data/samples...rule bwa_map: input: "data/genome.fa", lambda wildcards: config["samples"][wildcards.sample...5-临时与保护文件比如在下面流程中： rule bwa_map: input: "data/genome.fa", lambda wildcards: config...["samples"][wildcards.sample] output: temp("mapped_reads/{sample}.bam") params:

1.4K3 1

Logstash写入Elasticsearch发生的metadata通配异常问题

caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards...caused_by"=>{"type"=>"illegal_state_exception", "reason"=>"There are no external requests known to support wildcards

3.9K35 23

使用sonarqube需要注意版本差异

Wildcards can be used : sonar.java.test.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory...Wildcards can be used : sonar.java.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory...Wildcards can be used : sonar.libraries=path/to/specific/Library.jar,path/to/libs/*.jar,directory/**/

7463 0

hive之路10-show命令

Wildcards in the regular expression can only be ‘’ for any character(s) or ‘|’ for a choice....显示所有的数据库通配符只有两种： * 和 | * 表示所有 | 表示或 SHOW DATABASES [LIKE 'identifier_with_wildcards']; Show Tables/...Wildcards in the regular expression can only be ‘*’ for any character(s) or ‘|’ for a choice....SHOW TABLES [IN database_name] ['identifier_with_wildcards']; Show Views SHOW VIEWS;...显示的信息更全面 SHOW TABLE EXTENDED [IN|FROM database_name] LIKE 'identifier_with_wildcards' [PARTITION(partition_spec

1.6K2 0

workflow01-初探snakemake

WorkflowError: Target rules may not contain wildcards....Please specify concrete files or a rule without wildcards at the command line, or have a rule without...wildcards at the very top of your workflow (e.g. the typical "rule all" which just collects all results...data/raw/002_R2.fq output: results/awesome/002_R1.fq, results/awesome/002_R2.fq jobid: 2 wildcards...data/raw/003_R2.fq output: results/awesome/003_R1.fq, results/awesome/003_R2.fq jobid: 0 wildcards

2K3 1

流程管理工具snakemake学习笔记杂记02

samples/" output_folder = "/home/myan/scratch/private/practice_data/RNAseq/20220511/" SRR,FRR = glob_wildcards...}_%j.out -e logs_errors/{rule}/{rule}_{wildcards}_%j.err --mail-type=ALL --mail-user=mingyan24@126.com...)] print(fq_list) inputs = [(dir,file) for dir,files in fq_list.items() for file in files] #glob_wildcards...pomeRTD/00.raw.fastq/" output_folder = "/home/myan/scratch/private/pomeRTD/" #Folder,SRR,FRR = glob_wildcards...print(list_fastq) inputs = [(dir,file) for dir,files in list_fastq.items() for file in files] #glob_wildcards

1.4K1 0

Snakemake+RMarkdown定制你的分析流程和报告

): return config["sample"][wildcards.sample][wildcards.end] rule rename: input: get_fq...): return config["diffGroup"][wildcards.dgroup]["control"] def get_diff_case_sn(wildcards):...return config["diffGroup"][wildcards.dgroup]["case"] def get_diff_control_bam(wildcards): sn =...get_diff_case_bam(wildcards): sn = get_diff_case_sn(wildcards) bams = [f"03align/{i}.filter.bam..." for i in sn] return bams def get_diff_control_peak(wildcards): sn = get_diff_control_sn(wildcards

4.4K3 0

Snakemake — 可重复数据分析框架

output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...output: mapped_reads/B.bam jobid: 6 reason: Missing output files: mapped_reads/B.bam wildcards...output: mapped_reads/A.bam jobid: 4 reason: Missing output files: mapped_reads/A.bam wildcards...Missing output files: sorted_reads/B.bam; Input files updated by another job: mapped_reads/B.bam wildcards...Missing output files: sorted_reads/A.bam; Input files updated by another job: mapped_reads/A.bam wildcards

1.8K1 0

Elasticsearch 的 Close 索引快照：6.8 不支持，7.2 就行了？

It also changes snapshot requests in v8.0.0 to automatically expand wildcards to closed indices...For v7.1.0 and above, wildcards are by default only expanded to open indices, which can be changed...by explicitly setting the expand_wildcards option either to all or closed....创建包含所有索引（包括 close 的）的快照 PUT /_snapshot/my_backup/snapshot_all { "indices": "*", "expand_wildcards...只快照 close 的索引 PUT /_snapshot/my_backup/snapshot_closed_only { "indices": "*", "expand_wildcards":

43252 57

Elasticsearch-py 2.3版本的API翻译文档（一）

6.5K5 0

workflow03-用snakemake制作比对及变异查找流程

output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...我们在snakemake 中使用的{sample}，实际上是创建的wildcards 对象的一个属性。因此在shell 中需要写为{wildcards.sample}。...output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...output: "sorted_reads/{sample}.bam" shell: "samtools sort -T sorted_reads/{wildcards.sample...https://archive.fastgit.org/snakemake/snakemake-tutorial-data/archive/refs/tags/v7.4.2.tar.gz tar --wildcards

1.8K5 1

UBports安装Arduino记录

exclusion) --no-ignore-case case sensitive matching (default) --no-wildcards...verbatim string matching --no-wildcards-match-slash wildcards do not match '/'...--wildcards use wildcards (default for exclusion) --wildcards-match-slash wildcards

9811 0

elasticsearch API约定(一)

expand_wildcards expand_wildcards表示查询索引的范围，open表示查询所有匹配并open的索引，closed则表示查询所有匹配的索引，如下：假设bank关闭，bank2...pretty&expand_wildcards=open" 此时，只会展示open的索引信息，如下： ?...pretty&expand_wildcards=closed" 结果如下： ?

1.1K3 0

<? extends T> 和 <? super T> 的使用

super T> 是Java泛型中的“通配符（Wildcards）” 和 “边界（Bounds）”的概念是指 “上界通配符（Upper Bounds Wildcards）” 是指 “下界通配符（Lower Bounds Wildcards）” 1....下面代码就是“上界通配符（Upper Bounds Wildcards）”： Plate 翻译成人话就是：一个能放水果以及一切是水果派生类的盘子。...相对应的，“下界通配符（Lower Bounds Wildcards）”： Plate 表达的就是相反的概念：一个能放水果以及一切是水果基类的盘子。Plate<？

1.3K3 2

Oraccle SQL调优系列之ASH简介

target specified: Specify SQL_ID (eg: from V$SQL.SQL_ID) report target: Defaults to NULL: (% and _ wildcards...specified: Specify MODULE name (eg: from V$SESSION.MODULE) report target: Defaults to NULL: (% and _ wildcards...specified: Specify ACTION name (eg: from V$SESSION.ACTION) report target: Defaults to NULL: (% and _ wildcards...Specify CLIENT_ID (eg: from V$SESSION.CLIENT_IDENTIFIER) report target: Defaults to NULL: (% and _ wildcards...specified: Specify PLSQL_ENTRY name (eg: "SYS.DBMS_LOB.*") report target: Defaults to NULL: (% and _ wildcards

1.3K1 0

python和pygame游戏开发指南

= os.path.join(*args) return os.path.normpath(path) def find_data_files(self, srcdir, *wildcards...也可以加进来 if '.svn' in dirname: return names = [] lst, wildcards...= arg for wc in wildcards: wc_name = self.opj(dirname, wc)...('recursive', True) if recursive: os.path.walk(srcdir, walk_helper, (file_list, wildcards...)) else: walk_helper((file_list, wildcards), srcdir,

1.1K2 0

python+pygame游戏开发之使用Py2exe打包游戏

1.6K2 0

点击加载更多

workflow04-用snakemake处理复杂命名

snakemake杂记：多个转录组比对到多个基因组得到多个bam文件然后合并

snakemake 学习笔记3

workflow05-snakemake的进阶操作一

Logstash写入Elasticsearch发生的metadata通配异常问题

使用sonarqube需要注意版本差异

hive之路10-show命令

workflow01-初探snakemake

流程管理工具snakemake学习笔记杂记02

Snakemake+RMarkdown定制你的分析流程和报告

Snakemake — 可重复数据分析框架

Elasticsearch 的 Close 索引快照：6.8 不支持，7.2 就行了？

Elasticsearch-py 2.3版本的API翻译文档（一）

workflow03-用snakemake制作比对及变异查找流程

UBports安装Arduino记录

elasticsearch API约定(一)

<? extends T> 和 <? super T> 的使用

Oraccle SQL调优系列之ASH简介

python和pygame游戏开发指南

python+pygame游戏开发之使用Py2exe打包游戏

相关资讯

热门标签

活动推荐

运营活动

社区

活动

圈层

关于

腾讯云开发者

热门产品

热门推荐

更多推荐