從基於行的文件中awk匹配模式並輸出為CSV

Question

我有一個帶有這種格式記錄的文件：

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：

1. 刪除空格gawk '{$1=$1}1' raw_file.text > temp_file.txt

2. 匹配“摘要”內容gawk /Summary/,/\\]/{print} temp_file.text > summary_temp.txt

3. 刪除新行gawk 'BEGIN {RS=""}{gsub(/\\n/,"",$0); print $0}' summary_temp.text > summary.txt gawk 'BEGIN {RS=""}{gsub(/\\n/,"",$0); print $0}' summary_temp.text > summary.txt

我有幾個問題。 首先，我如何結合這三個步驟。 其次，如何選擇一個或多個其他匹配項，例如匹配項'/ gene =“ AP3B2”'（需要匹配“ gene”之后的“ / gene”的第一個實例），以便我可以在其中輸出內容形成：

基因，總結

Answer 1

$ cat tst.awk
BEGIN{RS="//"}
{
  match($0, /\/gene="([^"]+)"/, a)
  print a[1] ", ", 
        gensub(/\s\s+/, "", "g", gensub(/.*Summary:\s([^\[]+).*/, "\\1", "g"))
}

說明 ：

match($0, /\\/gene="([^"]+)"/, a)

捕獲數組a中的所有“ \\ gene”部分。 根據您的問題，只需要第一個出現，即a [1]（而不是AP3B2，btw）。

gensub(/.*Summary:\s([^\[]+).*/, "\\1", "g")

捕獲“摘要：”之后的所有內容，直到找到“ [”為止。 最后的結果包含空格和換行符。 讓我們擺脫它們：

gensub(/\s\s+/, "", "g", <<result of 1st gensub>>)

編輯：並非每個記錄都包含一個“摘要”

將腳本更改為：

$ 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提供的輸入來運行腳本：

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.