adding a description to a fasta header

[Seth Frietze]

Hello,

I need to edit the headers of a fasta file. Specifically, I need to add a description to the header. For example, to the below fasta file (with ~50,000 sequences) I need to change the header to have: >comp1_c0_seq1 len=262 path=[2229:0-261] to have >comp1_c0_seq1 comp1_c0 

In other words, I need to keep the SEQ_NAME (comp1_c0_seq1) add a space then add that SEQ_NAME but without the _seq1. I can keep the len= and path= or not.

I ran:

read_fasta -i test.fna | split_vals -k SEQ_NAME -d ' ' | rename_keys -k SEQ_NAME_0,SEQ_NAME | write_fasta -o out.fna -x 

which effectively deleted the len= and path= but now i need to add the extra portion. I have the SEQ_NAME and additional descriptions in a separate file. Will biopieces do this and if so which tool?

Thanks for the great tools!

Seth

>comp1_c0_seq1 len=262 path=[2229:0-261]

GAGATCTCTTTTTACTTAACGCTTAAACATTGAGATGTCAGGATAAGAGGAAGAACTGCA

GGCAGATTTTCAAGACGCCTCCTGGCAATCTGTTTGCTGTCAAAGTTAGAAACTATCAGA

ATAGTTAGAAACTATTGCTATTGGTAGTACATTATCACTAAAGGGGGCTTCTTTTTGCAT

ACCCCTTTGTCTTATGAAAAGGCTTGAACCCACCCTTCTTCATTCTTTAATTGGGAGGGG

GGAAAGAAGTGAAGAATTACTG

>comp3_c0_seq1 len=390 path=[37:0-389]

CCGTGCTTTTCCTTTAAGTGCACTACTTCAAAGAAATTTGGCTGAGTGGGCTTGGCTTTT

TTTAGACAATCTGTTATTGTGCTTTCAACTAAAAAGACACTGAATAAATTATAGATGCTG

GGTTCAGAGCTAAAAAGCAAATGAGCTTATTTGGTGGCTTCAT

[Martin Asser Hansen]

There are probably many ways to do this. Here is one:

read_fasta -i test.fna | split_vals -k SEQ_NAME -d ' ' | split_vals -k SEQ_NAME_0 | merge_vals -k SEQ_NAME_0_0,SEQ_NAME_0_1 -d '_' | merge_vals -k SEQ_NAME_0,SEQ_NAME_0_0 -d ' ' | rename_keys -k SEQ_NAME_0,SEQ_NAME | write_fasta -x

>comp1_c0_seq1 comp1_c0

GAGATCTCTTTTTACTTAACGCTTAAACATTGAGATGTCAGGATAAGAGGAAGAACTGCAGGCAGATTTTCAAGACGCCTCCTGGCAATCTGTTTGCTGTCAAAGTTAGAAACTATCAGAATAGTTAGAAACTATTGCTATTGGTAGTACATTATCACTAAAGGGGGCTTCTTTTTGCATACCCCTTTGTCTTATGAAAAGGCTTGAACCCACCCTTCTTCATTCTTTAATTGGGAGGGGGGAAAGAAGTGAAGAATTACTG

>comp3_c0_seq1 comp3_c0

CCGTGCTTTTCCTTTAAGTGCACTACTTCAAAGAAATTTGGCTGAGTGGGCTTGGCTTTTTTTAGACAATCTGTTATTGTGCTTTCAACTAAAAAGACACTGAATAAATTATAGATGCTGGGTTCAGAGCTAAAAAGCAAATGAGCTTATTTGGTGGCTTCAT

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[Seth Frietze]

Thanks Martin, 

the command worked beautifully!

Seth

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