我希望能够计算每个外显子特征的平均外显子数量。>>
例如，如果您确定一个特征具有6且另一个特征具有4 exons的GTF中仅存在两个外显子特征（即，一个数字是该特征的平均值），则输出应为8 exons。每个外显子特征的外显子数）。我不介意它是否打印到外壳上，或者是否必须在output.txt文件中访问它。
GENCODE GTF文件包含以下布局：
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";关于我实际使用的工具的更详细的示例：
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;尝试的解决方案...
以下第一次尝试产生了gene_id 1194547，我认为这意味着我的代码only正在读取并计算第9列的第一部分：gene_id。我无法获得一个数字的平均值。
if [ $3 == "exon" ]; then awk '{a[$9]++}END{for(i in a){print i, a[i]}}' gencode.v26.annotation.gtf > output.txt fi第二次尝试
[下面的第二次尝试产生了gene_id和它们各自的计数的列表，以使输出文件的每一行看起来像这样"ENSG00000242201.3"; 1，"ENSG00000132478.9"; 41，"ENSG00000155099.7"; 34。
[不幸的是，该计数是不准确的，因为它仅将与gene_ids相同的所有数字都计数为外显子。这意味着ENSG00000183186.7可能在文件中被发现/计数47次，但是ENSG00000183186.7实际上会产生许多不同大小的转录本，作为不同外显子集的一部分，这些外显子集都与该代码集中在一起。我没有尝试汇总此列表。
awk '$3=="exon" {print $0}' gencode.v26.annotation.gtf | awk '{count[$10]++} END {for (word in count) print word, count[word]}' > output.txt第三尝试
我的第三次也是最后一次尝试是正在进行的工作。我希望（1）如果第3列包含exon，则将GTF的第9列提取到另一个文件，（2）拆分“;”分离列表并为每个外显子集提取最高值exon_number，然后（3）计算每个外显子特征的平均外显子数。我不确定该去哪里。awk '$3 == "exon" {print $9}' gencode.v26.annotation.gtf > output1.txt
#another step here to split the “;” separated fields of column 9 to extract the max exon_number
awk '{ total += $1 } END { print total/NR }' output1 > output2.txt
附加说明：exon_number 1，exon_number 2...exon_number 8等出现在GTF文件的所有功能类型（第3列）中，gene除外。
BACKGROUND ...我希望能够使用bash代码计算GENCODE GTF文件中每个外显子特征的平均外显子数。例如，如果您确定一个...
# 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 } ...'