Awk 计算每个转录本的平均外显子数_Awk_Average

Awk 计算每个转录本的平均外显子数

awk

Awk 计算每个转录本的平均外显子数,awk,average,Awk,Average,我希望能够计算文件中每个转录本的平均外显子数仅供参考：我使用的文件格式称为文件要查找每个转录本的外显子数量，我们必须在字段9（$9）的分号分隔列表中进行搜索，但仅搜索外显子特征行（字符串“外显子”位于制表符分隔文件的字段3（$3）中的行）每个唯一的转录本id都有一系列相关的外显子特征线，字段9（$9）内的“外显子编号n”数量不断增加：要获得每个转录本的平均外显子数，只需将每个唯一的trasnscript\u id中的最大外显子数相加，然后除以使用的唯一转录本id的总数以下是我的文件中

我希望能够计算文件中每个转录本的平均外显子数
仅供参考：我使用的文件格式称为文件
要查找每个转录本的外显子数量，我们必须在字段9（
$9
）的分号分隔列表中进行搜索，但仅搜索外显子特征行（字符串“
外显子
”位于制表符分隔文件的字段3（
$3
）中的行）
每个唯一的
转录本id
都有一系列相关的外显子特征线，字段9（
$9
）内的“
外显子编号n
”数量不断增加：
要获得每个转录本的平均外显子数，只需将每个唯一的
trasnscript\u id
中的最大
外显子数
相加，然后除以使用的唯一
转录本id
的总数

以下是我的文件中任何给定行的10种可能格式：

chr19 HAVANA gene 405438 409170 . - . gene_id "ENSG00000183186.7"; gene_type "protein_coding"; gene_name "C2CD4C"; level 2; havana_gene "OTTHUMG00000180534.3"; chr19 HAVANA transcript 405438 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA exon 409006 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 1; exon_id "ENSE00001322986.5"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA exon 405438 408401 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA CDS 407099 408361 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA start_codon 408359 408361 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA stop_codon 407096 407098 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 409006 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 1; exon_id "ENSE00001322986.5"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 405438 407098 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 408362 408401 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3";

6.66667
注：字符串“
exon\u number n
”出现在除“
gene
”和“
transcript
”之外的所有特征类型（字段3）的行中，因此计算应仅针对字段3中带有“
exon
”的行

我的实际文件中的样本行：

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 "DDX11L1-002"; 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 "DDX11L1-002"; 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 "DDX11L1-002"; 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 "DDX11L1-002"; 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"; transcript_name "DDX11L1-001"; 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 "DDX11L1-001"; 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 "DDX11L1-001"; 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_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; exon_number 3; exon_id "ENSE00001758273.2"; 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 12975 13052 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; exon_number 4; exon_id "ENSE00001799933.2"; 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 13221 13374 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; exon_number 5; exon_id "ENSE00001746346.2"; 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 13453 13670 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000450305.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; exon_number 6; exon_id "ENSE00001863096.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2"; chr1 HAVANA gene 14404 29570 . - . gene_id "ENSG00000227232.5"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; level 2; havana_gene "OTTHUMG00000000958.1"; chr1 HAVANA transcript 14404 29570 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 29534 29570 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 1; exon_id "ENSE00001890219.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 24738 24891 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 2; exon_id "ENSE00003507205.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 18268 18366 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 3; exon_id "ENSE00003477500.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 17915 18061 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 4; exon_id "ENSE00003565697.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 17606 17742 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 5; exon_id "ENSE00003475637.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 17233 17368 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 6; exon_id "ENSE00003502542.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 16858 17055 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 7; exon_id "ENSE00003553898.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 16607 16765 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 8; exon_id "ENSE00003621279.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 15796 15947 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 9; exon_id "ENSE00002030414.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 15005 15038 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 10; exon_id "ENSE00001935574.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 HAVANA exon 14404 14501 . - . gene_id "ENSG00000227232.5"; transcript_id "ENST00000488147.1"; gene_type "unprocessed_pseudogene"; gene_name "WASH7P"; transcript_type "unprocessed_pseudogene"; transcript_name "WASH7P-001"; exon_number 11; exon_id "ENSE00001843071.1"; level 2; transcript_support_level "NA"; ont "PGO:0000005"; tag "basic"; havana_gene "OTTHUMG00000000958.1"; havana_transcript "OTTHUMT00000002839.1"; chr1 ENSEMBL gene 17369 17436 . - . gene_id "ENSG00000278267.1"; gene_type "miRNA"; gene_name "MIR6859-1"; level 3;
基于我的样本的所需输出：

chr19 HAVANA gene 405438 409170 . - . gene_id "ENSG00000183186.7"; gene_type "protein_coding"; gene_name "C2CD4C"; level 2; havana_gene "OTTHUMG00000180534.3"; chr19 HAVANA transcript 405438 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA exon 409006 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 1; exon_id "ENSE00001322986.5"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA exon 405438 408401 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA CDS 407099 408361 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA start_codon 408359 408361 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA stop_codon 407096 407098 . - 0 gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 409006 409170 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 1; exon_id "ENSE00001322986.5"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 405438 407098 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3"; chr19 HAVANA UTR 408362 408401 . - . gene_id "ENSG00000183186.7"; transcript_id "ENST00000332235.7"; gene_type "protein_coding"; gene_name "C2CD4C"; transcript_type "protein_coding"; transcript_name "C2CD4C-001"; exon_number 2; exon_id "ENSE00001290344.6"; level 2; protein_id "ENSP00000328677.4"; transcript_support_level "2"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS45890.1"; havana_gene "OTTHUMG00000180534.3"; havana_transcript "OTTHUMT00000451789.3";

6.66667
因为

ENST0000456328.2有3个外显子，ENST0000450305.2有6个外显子，ENST0000488147.1有11个外显子
~（3+6+11）/3=6.66667


尝试的解决方案
（i）我试图打印一个列表字段9，用于所有在字段3中有“外显子”
”的行。以下输出基因id 1194547
：
if [ $3 == "exon" ]; then
    awk '{a[$9]++}END{for(i in a){print i, a[i]}}' file
fi

我相信这意味着我的代码只计算第9列的第一部分：gene\u id
。不幸的是，我不能得到一个数字的平均值
（ii）我试图打印字段3中所有带有“exon
”的行，然后计算一个唯一的“transcript\u id
”出现的次数，但我对awk
的知识目前非常薄弱，所以我觉得脚本太离谱了。以下输出唯一的基因id
s列表及其各自的计数，以便输出文件的每一行看起来像这样的“ENSG0000242201.3”；1
，“ENSG0000132478.9”；41
，“ENG00000155099.7”；34
：
awk '$3=="exon" {print $0}' file | awk '{count[$10]++} END {for (word in count) print word, count[word]}'

产生的计数是不准确的，因为它们只是将所有相同的gene\u id
s作为外显子相加。这意味着ENSG0000183186.7
可能在该文件中被发现/计数47次，但由于选择性剪接（该问题的生物学相关性），该基因实际上产生了许多大小不同的转录本，而代码忽略了这一点。它应该特定于“转录本id
”，而不是“基因id
”
（iii）此代码正在进行中，需要大量返工。我试图（1）仅当字段3包含字符串exon
时提取字段9，（2）拆分“；
”分隔列表，仅提取每个唯一“转录本id
”的最高值外显子数n
，然后（3）计算每个转录本的平均外显子数
awk '$3 == "exon" {print $9}' file
#step needed here to split the “;” separated fields $9 to extract the max exon_number
awk '{ total += $1 } END { print total/NR }' file

嗯，我还是不明白整个故事的来龙去脉。所以不管怎样：
# extract the lines with 3rd column equal to "exon"
awk '$3 == "exon"' |
# Extract the interesting parts with a regex. I like `sed` more, so I'll use it.
# extract the transcript_id and exon number
# separator is ';'
sed -n 's/.*transcript_id \([^;]*\).*exon_number \([^;]*\).*/\1;\2/p' |
# because I noticed that number is equal to count of lines
# just count the lines with the same transcript_id
# (actually exon_number is ignored)
# and then calculate the average of the array
awk -F';' '{a[$1]++} END{for (i in a) {cnt++; sum += a[i]} print sum/cnt}'
# or you could also like get the highest number from exon_number with like
# awk ... '{ if (a[$1] < $2) a[$1]=$2 } ...'

我在上面留下了3个命令，所以看起来很冗长，同样的工作可以用一个awk脚本来完成，这将比3个进程链更快。只需使用awk
中的gensub
而不是sed
和awk
中的split
将输入拆分为awk中的一个数组。
请将该示例输入的所需输出（无描述）添加到您的问题中（无注释）。输出应该是…
请显示预期的输出？对于呈现的输入，该数字是多少？你能解释一下如何计算这个数字或者如何解析输入吗？这里有很多熟练的bash程序员，但大多数（像我一样）都不知道什么是GTF文件以及如何解析它。所以我的理解是：“exonic特性”是一个包含$3==“exon”
的行。如何确定一个“外显子特征”有多少“外显子”？也就是说，外显子409006
的第一行有4个外显子，对吗？为什么是4？我看到带有外显子409006
的一行有外显子1号
，值1
是否以某种方式乘以某个值？所以<代码>通过查看第9列，您可以确定“外显子特征”有多少“外显子”这是我不明白的部分。外显特征如何分组/识别？通过基因识别？从新输入：带有基因的外显子特征_id=“ENSG000027232.5”有11个外显子<代码>“ENSG000022972.5”
有6个<代码>“ENSG000022972.5”
有3个？Avarage是11+3+6/3？我在问题中添加了一个更详细的示例（我正在处理的GTF文件中的一个实际片段）。希望这样更容易理解。我总是愿意接受更多的建议来改进我的问题，以方便您的访问，所以请立即回答。这太完美了！谢谢你@KamilCuk！！是的，计算转录本id出现的次数比计算最大的外显子id要容易得多。但愿我自己能想到这一点。