Rename fasta headers

Hi all, I'm looking for a simple solution for renaming fasta headers.

I have this fasta header

>trpE___AA_HMM___6fa05435949258489b608db9e58e5ba38821f2f26fffe5755daff43abin_id:MALBOS1|source:AA_HMM|e_value:5.2e99|contig:MALBOS1_000000117228|gene_callers_id:113772|start:215745|stop:217260|length:1515

And I would like to rename it only like this

>MALBOS1_000000117228

That means, remove everything before the pattern "contig:" and after "|gene_callers_id"

Any ideas?

thanks

fasta regex

• 2,622 views • link

updated 3.6 years ago by 炎峰 •

• written 3.7 years ago by diecasfranco •

2 answers

perl -pe 's/>.+contig:(.+?)\|.+/>$1/' < FASTA_IN > FASTA_OUT

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written 3.7 years ago by JC

Thanks JC, it is great solution.

Now I have a different issue here, because I need the gene name at the beginning of the fasta header.

>trpE___AA_HMM___6fa05435949258489b608db9e58e5ba38821f2f26fffe5755daff43abin_id:MALBOS1|source:AA_HMM|e_value:5.2e99|contig:MALBOS1_000000117228|gene_callers_id:113772|start:215745|stop:217260|length:1515

And the output should be

>trpE_MALBOS1_000000117228

Any ideas?

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updated 3.7 years ago by GenoMax

• written 3.7 years ago by diecasfranco •

if the headers are correctly formatted (with >GENENAME__) you can:

perl -pe 's/>(.+?_)_.+contig:(.+?)\|.+/>$1$2/' < FASTA_IN > FASTA_OUT

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written 3.7 years ago by JC

I have a different issue here, because I need the Chromsome name at the beginning of the fasta header.

Chr01:10181894..10189044_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ale:Ty1-RT ID=Chr01:10181894..10189044_INT#LTR/Copia|Class_I/LTR/Ty1_copia/Ale:Ty1-RT;gene=RT;clade=Ale;evalue=2.7e-66;coverage=26.1;probability=0.98

Chr01_Ale_Ty1-RT

Any ideas?

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written 3.6 years ago by 炎峰 •

Here's a solution using cut:

cut -d '|' -f 4 start.fasta | sed 's/contig:/>/' > end.fasta

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written 3.7 years ago by Jeremy •