我正在嘗試解析 antismash 的輸出來計算 BGC 的數量。我發現人們使用 python 編寫的腳本我一無所知,所以我試圖使用 bash 腳本來解決這個問題。
具有預測簇的基因庫格式檔案如下所示:
head -30 sca_11_chr8_3_0.region001.gbk
LOCUS sca_11_chr8_3_0 45390 bp DNA linear UNK 01-JAN-1980
DEFINITION sca_11_chr8_3_0.
ACCESSION sca_11_chr8_3_0
VERSION sca_11_chr8_3_0
KEYWORDS .
SOURCE
ORGANISM
.
COMMENT ##antiSMASH-Data-START##
Version :: 6.0.1-a859617(changed)
Run date :: 2021-10-31 18:00:02
NOTE: This is a single cluster extracted from a larger record!
Orig. start :: 169481
Orig. end :: 214871
##antiSMASH-Data-END##
FEATURES Location/Qualifiers
protocluster 1..45390
/aStool="rule-based-clusters"
/contig_edge="False"
/core_location="join{[194767:194871](-),
[194650:194652](-), [191596:194619](-),
[189481:191503](-)}"
/cutoff="20000"
/detection_rule="cds(Condensation and (AMP-binding or
A-OX))"
/neighbourhood="20000"
/product="NRPS"
/protocluster_number="1"
/tool="antismash"
proto_core complement(join(20001..22022,22116..25138,25170..25171,
尾 sca_11_chr8_3_0.region001.gbk
44881 ggagcttgtg gagagaagtg agacgtatcg cacgaatgct cttcagcaga tgctgggcag
44941 ttagaggatt tgcactttag tttcatagag ttgatgtgtc gaggagataa tttgagatac
45001 cagtatatgt aatttaccta cctacctagt cgagattgga cattgtacaa gagaaataac
45061 aactaactat acgagacaag cctgatgtgt tgatagtttc attcatgtct ggtgtttgtg
45121 gcatgtttat gttggagtag ctgtacagaa gataccgcgc tattcccagt gatcatggcc
45181 cccacgcctc caactcggca cctgaccttg atcccctttg ggaagcatgt ctcagtgtct
45241 cagccgtgag ccgtagaggc tgcacagcat ggagaagctg tcctgtcaat tcaggggatt
45301 tgcccacggg ggctatcata tgatgaatct cggacaccct acacgttgtt accgcctttc
45361 ttagctcctg ctggtagccg tcccctgaac
//
首先,我將 gbk 檔案連接成一個,以便它包含所有預測的簇,然後 grep 給出軌跡 id、簇的開始和結束以及簇類型的字元。
cat sca_*.gbk > Necha2_SMclusters.gbk
grep "DEFINITION\|Orig\|product=" Necha2_SMclusters.gbk > Necha2_SMclusters_filtered.txt
這給了我一個像這樣的文件
DEFINITION sca_32_chr11_3_0.
Orig. start :: 381231
Orig. end :: 428233
/product="T1PKS"
/product="T1PKS"
/product="T1PKS"
/product="T1PKS"
DEFINITION sca_32_chr11_3_0.
Orig. start :: 464307
Orig. end :: 486217
/product="terpene"
/product="terpene"
/product="terpene"
/product="terpene"
DEFINITION sca_33_chr6_1_0.
Orig. start :: 140267
Orig. end :: 227928
/product="NRPS-like"
/product="T1PKS"
/product="NRPS-like"
/product="T1PKS"
/product="NRPS-like"
/product="NRPS-like"
/product="NRPS-like"
/product="T1PKS"
/product="T1PKS"
/product="T1PKS"
DEFINITION sca_39_chr11_5_0.
Orig. start :: 270154
Orig. end :: 324310
/product="NRPS"
/product="NRPS"
/product="NRPS"
/product="NRPS"
我想從這個文件中獲取一個如下所示的文件。
Locus name start end ClusterType
sca_9_chr7_10_0. 369577 421460 T1PKS,NRPS
sca_33_chr6_1_0. 140267 227928 NRPS-like, T1PKS
sca_32_chr11_3_0 381231 428233 T1PKS
現在,這就是我需要一個包含所有預測叢集的檔案。
太感謝了!
答案1
給定此範例輸入:
$ cat file1.gbk
DEFINITION sca_32_chr11_3_0.
foo
Orig. start :: 381231
Orig. end :: 428233
/product="T1PKS"
/product="T1PKS"
bar
/product="T1PKS"
/product="T1PKS"
//
stuff
DEFINITION sca_32_chr11_3_0.
Orig. start :: 464307
Orig. end :: 486217
/product="terpene"
nonsense
/product="terpene"
/product="terpene"
/product="terpene"
//
DEFINITION sca_33_chr6_1_0.
Orig. start :: 140267
Orig. end :: 227928
/product="NRPS-like"
/product="T1PKS"
whatever
/product="NRPS-like"
/product="T1PKS"
/product="NRPS-like"
/product="NRPS-like"
/product="NRPS-like"
/product="T1PKS"
/product="T1PKS"
/product="T1PKS"
$ cat file2.gbk
here we go
DEFINITION sca_39_chr11_5_0.
Orig. start :: 270154
more irrelevant text
Orig. end :: 324310
/product="NRPS"
/product="NRPS"
/product="NRPS"
/product="NRPS"
這個腳本:
$ cat tst.awk
BEGIN { OFS="\t" }
$1 == "DEFINITION" {
if ( ++cnt == 1 ) {
print "Locus name", "start", "end", "ClusterType"
}
prt()
locus = $2
}
/Orig\. start/ { start = $NF }
/Orig\. end/ { end = $NF }
sub(".*/product=","") { gsub(/"/,""); types[$NF] }
END { prt() }
function prt( ct, type) {
if ( locus != "" ) {
for (type in types) {
ct = (ct=="" ? "" : ct ",") type
}
print locus, start, end, ct
}
delete types
locus = ""
}
將產生以下輸出:
$ awk -f tst.awk *.gbk
Locus name start end ClusterType
sca_32_chr11_3_0. 381231 428233 T1PKS
sca_32_chr11_3_0. 464307 486217 terpene
sca_33_chr6_1_0. 140267 227928 T1PKS,NRPS-like
sca_39_chr11_5_0. 270154 324310 NRPS