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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
1.6K20编辑于 2022-07-07 - 来自专栏小明的数据分析笔记本
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
61610编辑于 2023-08-23 - 来自专栏育种数据分析之放飞自我
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
1.1K20发布于 2019-07-07 - 来自专栏北野茶缸子的专栏
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:
1.4K31编辑于 2022-07-07 - 来自专栏大数据生态
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
3.9K3523发布于 2021-09-26 - 来自专栏johnhuster
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/**/
76130编辑于 2022-03-28 - 来自专栏机器学习/数据可视化
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
1.6K20发布于 2021-03-02 - 来自专栏北野茶缸子的专栏
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
2K31编辑于 2022-07-07 - 来自专栏小明的数据分析笔记本
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
1.4K10编辑于 2022-05-23 - 来自专栏生信技能树
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
4.5K30编辑于 2022-06-27 - 来自专栏生信菜鸟团
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
2K10编辑于 2024-03-25 - 来自专栏大数据生态
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":
4585257编辑于 2025-12-22 - 来自专栏北野茶缸子的专栏
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
1.8K51编辑于 2022-07-07 - 来自专栏机器人课程与技术
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
99010发布于 2021-03-03 - 来自专栏美男的自我修养
Elasticsearch-py 2.3版本的API翻译文档（一）
（这包括_all字符串或未指定索引时）| |expand_wildcards | 是否将通配符表达式扩展为打开，关闭或两者的具体索引。 （这包括_all字符串或未指定索引时）| |expand_wildcards | 是否将通配符表达式扩展为打开，关闭或两者的具体索引。 （这包括_all字符串或未指定索引时）| |expand_wildcards | 是否将通配符表达式扩展为打开，关闭或两者的具体索引。 （这包括_all字符串或未指定索引时）| |expand_wildcards | 是否将通配符表达式扩展为打开，关闭或两者的具体索引。 （这包括_all字符串或未指定索引时） expand_wildcards - 是否将通配符表达式扩展为打开，关闭或两者的具体索引。
6.5K50发布于 2019-05-07 - 来自专栏玩转JavaEE
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： ?
1.1K30发布于 2018-12-13 - 来自专栏Vincent-yuan
<? 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 <? extends T> 是指 “上界通配符（Upper Bounds Wildcards）” <? super T> 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<？ extends Fruit> 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<？ super Fruit> 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<？
1.3K32发布于 2021-06-21 - 来自专栏Nicky's blog
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
1.4K10编辑于 2022-05-07 - 来自专栏Java架构师必看
python和pygame游戏开发指南[python游戏设计与开发]
= 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,
1.1K20编辑于 2022-02-27 - 来自专栏游戏开发那些事
python+pygame游戏开发之使用Py2exe打包游戏
= 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,
1.6K20发布于 2018-09-12
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