添加gtf文件答案

【问题标题】：Additing gtf file添加gtf文件
【发布时间】：2018-11-19 23:36:23
【问题描述】：

我必须从给定的 gtf 文件中仅获取 ENSEMBLE 非染色体假基因为每个带注释的假基因添加附加属性字段“过滤”，其值为“手动”，并另存为新文件。所以我必须通过包含“ENSEMBLY”“pseudogenes”而不包含“Chr”来过滤给定的文件，将其保存在新文件中并添加到最后一列附加属性（手动过滤）。您能告诉我如何最好使用 awk 或 sed 来做到这一点吗？

    ##description: evidence-based annotation of the human genome (GRCh38), version 29 (Ensembl 94)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2018-08-30
chr1    HAVANA  gene    11869   14409   .       +       .       gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2";
chr1    HAVANA  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name 
"DDX11L1-202"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    11869   12227   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    12613   12721   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  exon    13221   14409   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1
-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1    HAVANA  transcript      12010   13670   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; tr
anscript_name "DDX11L1-201"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12010   12057   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12179   12227   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript
_name "DDX11L1-201"; exon_number 2; exon_id "ENSE00001671638.2"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
chr1    HAVANA  exon    12613   12697   .       +       .       gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unp

【问题讨论】：

你已经尝试了什么？
预期输出是什么？
示例中的哪几行描述了ENSEMBLE non-chromosomal pseudogene？为什么（相关字符串是什么）？
这是匹配模式的行：ENSEMBL exon 169224 169502 。 - 。基因ID“ENSG00000284215.2”；成绩单ID“ENST00000639764.2”；基因类型“假基因”；基因名称“AC245056.4”；转录类型“假基因”；成绩单名称“AC245056.4-201”；外显子编号 2； exon_id "ENSE00003804365.1"; 3级；标签“基本”；过滤：手动；
实际上我已经做到了，但也许只使用 awk 有更好的解决方案？

标签： regex bash awk sed bioinformatics

【解决方案1】：

如果您仍然使用 Awk，则根本不需要 grep。

另外，不太重要的是，修改$0 有点浪费。 print 可让您准确指定要打印的内容。

awk '!/##/ && !/chr/ && /pseudogene/ && /ENSEMBL/ {
       print $0" Filtered: manually;"}' gencode.v29.chr_patch_hapl_scaff.basic.annotation.gtf > gencode.v29.filtered.gtf

【讨论】：