How to delete a line starting with Specific String but keeping a speific word in that line?

Question

I have gene sequence file and I would like to change the header of each gene. Here is the input:

>lcl|CP000046.1_cds_AAW37389.1_1 [gene=dnaA] [locus_tag=SACOL0001] [protein=chromosomal replication initiator protein DnaA] [protein_id=AAW37389.1] [location=544..1905] [gbkey=CDS]
ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCTGTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCTATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTTAAACCTCACTTTATTACTCTGAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAACAACAAAACCTTCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAACACATTTGACACTTTTGTAATCGGACCCGGTAACCGCTTTCCACATGCAGCGAGTTTAGCTGTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTTATCTATGGAGGTGTTGGTTTA

>lcl|CP000046.1_cds_AAW37390.1_2 [gene=dnaN] [locus_tag=SACOL0002] [protein=DNA polymerase III, beta subunit] [protein_id=AAW37390.1] [location=2183..3316] [gbkey=CDS]
ATGATGGAATTCACTATTAAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCTATTTCACCAAGAACAACATTACCTATATTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTTATATTAACTGGTTCAGACTCTGAAATTTCAATAGAAATCACTATTCCTAAAACTGTAGATGGCGAAGATATTGTCAATATTTCAGAAACAGGCTCAGTAGTACTTCCTGGACGATTCTTTGTTGATATTATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAACAATTCCAGACATTAATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTATTACCTCAAGTTTCTAGAGATG

Expected Output:

>Saureus1|SACOL0001
ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCTGTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCTATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTTAAACCTCACTTTATTACTCTGAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAACAACAAAACCTTCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAACACATTTGACACTTTTGTAATCGGACCCGGTAACCGCTTTCCACATGCAGCGAGTTTAGCTGTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTTATCTATGGAGGTGTTGGTTTA

>Saureus1|SACOL0002
ATGATGGAATTCACTATTAAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCTATTTCACCAAGAACAACATTACCTATATTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTTATATTAACTGGTTCAGACTCTGAAATTTCAATAGAAATCACTATTCCTAAAACTGTAGATGGCGAAGATATTGTCAATATTTCAGAAACAGGCTCAGTAGTACTTCCTGGACGATTCTTTGTTGATATTATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAACAATTCCAGACATTAATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTATTACCTCAAGTTTCTAGAGATG

I know how to delete a line congaing specific word with sed

sed '/^>/ d' inputfile > outputfile

But I am not getting any Idea to get the expected output. Here, in first part I should delete all the text in the gene header except SACOL00 and later preceding that I should keep fasta sysmbol ">" with Strain name.

If this kind of question repeated please excuse me.

Please use code tags for your samples shown rather than quote tags. — RavinderSingh13, Dec 18 '17 at 13:05
Please take a look at [editing-help](http://stackoverflow.com/editing-help). — Cyrus, Dec 18 '17 at 13:06

score 1 · Accepted Answer · answered Dec 18 '17 at 13:13

1

With GNU sed:

sed -E 's/^>.*locus_tag=([^]]*).*/Saureus1|\1/' file

With sed:

sed 's/^>.*locus_tag=\([^]]*\).*/Saureus1|\1/' file

See: The Stack Overflow Regular Expressions FAQ

answered Dec 18 '17 at 13:13

Cyrus

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score 1 · Answer 2 · answered Dec 18 '17 at 13:25

Awk solution:

awk '/^>lcl/{ gsub(/^\[[^=]+=|\]$/,"",$3); printf ">Saureus1|%s\n",$3; next }1' file

The output:

>Saureus1|SACOL0001
ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCTGTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATTAAAGATGGTGAAGCTATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATTATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTTAAACCTCACTTTATTACTCTGAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAACAACAAAACCTTCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAACACATTTGACACTTTTGTAATCGGACCCGGTAACCGCTTTCCACATGCAGCGAGTTTAGCTGTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTTATCTATGGAGGTGTTGGTTTA

>Saureus1|SACOL0002
ATGATGGAATTCACTATTAAAAGAGATTATTTTATTACACAATTAAATGACACATTAAAAGCTATTTCACCAAGAACAACATTACCTATATTAACTGGTATCAAAATCGATGCGAAAGAACATGAAGTTATATTAACTGGTTCAGACTCTGAAATTTCAATAGAAATCACTATTCCTAAAACTGTAGATGGCGAAGATATTGTCAATATTTCAGAAACAGGCTCAGTAGTACTTCCTGGACGATTCTTTGTTGATATTATAAAAAAATTACCTGGTAAAGATGTTAAATTATCTACAAATGAACAATTCCAGACATTAATTACATCAGGTCATTCTGAATTTAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTATTACCTCAAGTTTCTAGAGATG

How to delete a line starting with Specific String but keeping a speific word in that line?

2 Answers2