从基于行的文件中awk匹配模式并输出为CSV [英] awk matching patterns from row based file and output as CSV
问题描述
我有一个文件，其中记录的格式如下:
I've a file with records in this type of format:
LOCUS NG_029783 19834 bp DNA linear PRI 03-OCT-2014 DEFINITION Homo sapiens long intergenic non-protein coding RNA 1546
(LINC01546), RefSeqGene on chromosome X. ACCESSION NG_029783 VERSION NG_029783.1 KEYWORDS RefSeq; RefSeqGene. SOURCE Homo sapiens (human) ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo. COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
AC004616.1.
This sequence is a reference standard in the RefSeqGene project. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-19834 AC004616.1 8636-28469 FEATURES Location/Qualifiers
source 1..19834
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="X"
/map="Xp22.33"
variation 4
/replace="c"
/replace="t"
/db_xref="dbSNP:1205550"
variation 17
/replace="c"
/replace="t"
/db_xref="dbSNP:1205551"
gene 5001..5948
/gene="OR6K3"
/gene_synonym="OR1-18"
/note="olfactory receptor family 6 subfamily K member 3"
/db_xref="GeneID:391114"
/db_xref="HGNC:HGNC:15030"
mRNA 5001..5948
/gene="OR6K3"
/gene_synonym="OR1-18"
/product="olfactory receptor family 6 subfamily K member
//
LOCUS NG_032962 70171 bp DNA linear PRI 17-JUN-2016 DEFINITION Homo sapiens death domain containing 1 (DTHD1), RefSeqGene on
chromosome 4. ACCESSION NG_032962 VERSION NG_032962.1 KEYWORDS RefSeq; RefSeqGene. SOURCE Homo sapiens (human) ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo. COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from AC104078.3.
This sequence is a reference standard in the RefSeqGene project.
Summary: This gene encodes a protein which contains a death domain.
Death domain-containing proteins function in signaling pathways and
formation of signaling complexes, as well as the apoptosis pathway.
Alternative splicing results in multiple transcript variants.
[provided by RefSeq, Oct 2012]. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-70171 AC104078.3 59395-129565 FEATURES Location/Qualifiers
source 1..70171
/organism="Homo sapiens"
/mol_type="genomic DNA"
/db_xref="taxon:9606"
/chromosome="4"
/map="4p14"
gene 5001..129091
/gene="REEP1"
/gene_synonym="C2orf23; HMN5B; SPG31; Yip2a"
/note="receptor accessory protein 1"
/db_xref="GeneID:65055"
/db_xref="HGNC:HGNC:25786"
/db_xref="MIM:609139"
mRNA join(5001..5060,60842..60914,79043..79119,88270..88390,
91014..91127,110282..110459,125974..129091)
/gene="REEP1"
/gene_synonym="C2orf23; HMN5B; SPG31; Yip2a"
/product="receptor accessory protein 1, transcript variant
1"
/transcript_id="NM_001164730.1"
我一直在使用此工作流程:
Ive been using this workflow:
-
删除空格
gawk '{$1=$1}1' raw_file.text > temp_file.txt
remove spaces
gawk '{$1=$1}1' raw_file.text > temp_file.txt
匹配摘要"内容gawk /Summary/,/\]/{print} temp_file.text > summary_temp.txt
删除新行gawk 'BEGIN {RS=""}{gsub(/\n/,"",$0); print $0}' summary_temp.text > summary.txt
我有几个问题. 首先，我如何结合这三个步骤. 其次，如何选择一个或多个其他匹配项，例如匹配项'/gene ="AP3B2"'(需要匹配"gene"之后的"/gene"的第一个实例)，以便我可以在其中输出内容形式:
I've a couple of questions. First, how could I combine those 3 steps. Second, how could I also select one or more additional matches, for example match '/gene="AP3B2"' (which requires matching the first instance of "/gene" after "gene") so that I could output the contents in this form:
基因，摘要
推荐答案
$ cat tst.awk
BEGIN{RS="//"}
{
match($0, /\/gene="([^"]+)"/, a)
print a[1] ", ",
gensub(/\s\s+/, "", "g", gensub(/.*Summary:\s([^\[]+).*/, "\\1", "g"))
}
说明:
match($0, /\/gene="([^"]+)"/, a)
捕获数组a中的所有"\ gene"部分.根据您的问题，只需要第一次出现，即a [1](而不是AP3B2，btw).
catches all "\gene" parts in array a. According to your question only the first occurrence is needed, which is a[1] (and is not AP3B2, btw).
gensub(/.*Summary:\s([^\[]+).*/, "\\1", "g")
捕获摘要:"之后的所有内容，直到找到"["为止. 最后的结果包含空格和换行符.让我们摆脱它们:
catches everything after "Summary: " until you find a "[". This last result has spaces and newlines. Let's get rid of them:
gensub(/\s\s+/, "", "g", <<result of 1st gensub>>)
并非每条记录都包含一个摘要"
Not every record contains a "Summary"
将脚本更改为:
$ cat tst.awk
BEGIN{RS="//"}
{
match($0, /\/gene="([^"]+)"/, a)
match($0, /Summary:\s([^\[]+)/, b)
print a[1] ",",
gensub(/\s\s+/, " ", "g", b[1])
}
使用OP提供的输入来运行脚本:
Running the script with input provided by OP:
awk -f tst.awk tst.txt
OR6K3,
REEP1, This gene encodes a protein which contains a death domain.Death
domain-containing proteins function in signaling pathways andformation
of signaling complexes, as well as the apoptosis pathway.Alternative
splicing results in multiple transcript variants.
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