在awk中修改文本文件 [英] modifying the text file in awk
问题描述
我有一个文本文件，如下例所示:
I have a text file like the following small example:
chr1 HAVANA transcript 12010 13670 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; tr
anscript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_tran
script "OTTHUMT00000002844.2";
chr2 HAVANA exon 53 955 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript
_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene
"OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
这个小例子的预期输出是:
the expected output for the small example is:
chr1 HAVANA transcript 11998 12060 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; tr
anscript_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene "OTTHUMG00000000961.2"; havana_tran
script "OTTHUMT00000002844.2";
chr2 HAVANA exon 41 103 . + . gene_id "ENSG00000223972.4"; transcript_id "ENST00000450305.2"; gene_type "pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; transcript
_type "transcribed_unprocessed_pseudogene"; transcript_status "KNOWN"; transcript_name "DDX11L1-001"; exon_number 1; exon_id "ENSE00001948541.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; havana_gene
"OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000002844.2";
输入文件中的
有不同的行.每行以chr开头.每行都有一些列，分隔符可以是制表符或;".
我要从中创建一个新文件，其中仅第4列和第5列会有变化.实际上，新文件中的第4列为((column 4 in original file)-12)，而新文件中的第5列为((column 4 in original file)+50).输入文件和输出文件之间唯一的区别在于第4和第5列中的数字.
我尝试使用以下命令在awk中做到这一点:
in the input file, there are different lines. each line starts with chr. every line has some columns and separators are either tab or ";".
I want to make a new file from this one in which there would be a change only in columns 4 and 5. in fact column 4 in the new file would be ((column 4 in original file)-12) and 5th column in the new file would be ((column 4 in original file)+50). the only difference between input file and output file in the numbers in 4th and 5th column.
I tried to do that in awk using the following command:
awk 'BEGIN { FS="\t;" } {print $1"\t"$2"\t"$3"\t"$4=$4-12"\t"$5=$4+50"\t"$6"\t"$7"\t"$8"\t"$9" "$10";"$11" "$12";"$13" "$14";"$15" "$16";"$17" "$18";"$19" "$20";"$21" "$22";"$23" "$24";"$25" "$26";"$27" "$28";"$29" "$30";"$31" "$32";"$33" "$34";"$35" "$36";"$37" "$38";" }' input.txt > test2.txt
当我运行代码时，它将返回此错误:
when I run the code, it would return this error:
awk: cmd. line:1: BEGIN { FS="\t;" } {print $1"\t"$2"\t"$3"\t"$4=$4-12"\t"$5=$4+50"\t"$6"\t"$7"\t"$8"\t"$9" "$10";"$11" "$12";"$13" "$14";"$15" "$16";"$17" "$18";"$19" "$20";"$21" "$22";"$23" "$24";"$25" "$26";"$27" "$28";"$29" "$30";"$31" "$32 ";" $33" "$34";"$35" "$36";"$37" "$38";" }
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: BEGIN { FS="\t;" } {print $1"\t"$2"\t"$3"\t"$4=$4-12"\t"$5=$4+50"\t"$6"\t"$7"\t"$8"\t"$9" "$10";"$11" "$12";"$13" "$14";"$15" "$16";"$17" "$18";"$19" "$20";"$21" "$22";"$23" "$24";"$25" "$26";"$27" "$28";"$29" "$30";"$31" "$32 ";" $33" "$34";"$35" "$36";"$37" "$38";" }
awk: cmd. line:1: ^ syntax error
您知道如何解决它吗?我想获得一个与输入文件格式完全相同的输出文件.含义相同的定界符.
do you know how to fix it? I want to get the an output file with exactly the same format as input file. meaning the same delimiters.
推荐答案
无需单独输出每列，只需修改现有数据，然后打印修改后的行即可.
There is no need to output every single column individually, it's enough to modify the existing data and then print the modified line.
awk -F '\t' '{ col4 = $4; $4 = col4 - 12; $5 = col4 + 50; print }' OFS='\t' file
这会在打印整行之前修改第四和第五个制表符分隔的列.
This modifies the fourth and fifth tab-delimited column before printing the whole line.
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