rename fasta headers in FastaAlternateReferenceMaker output

Question

[mosquitoes]

Hi,

I would like to create a new fasta file from the original genome fasta and a vcf file. The fasta file will only have full gene sequences included.

I can use the gatk FastaAlternateReferenceMaker to accomplish this:

java -jar -Xmx16g ~/bin/GenomeAnalysisTK-3.6/GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker -R ref_genome.fasta -o sample_SNV.fasta -V sample_SNV_selected.vcf -L ref_gene.bed

But I would like the output fasta to have the gene names as the header. For instance the current fasta output from gatk is:

 >1 chr01:2350
AGAAAGGACAGAAAAAAAGATGGTGAAGTAGAAAGAGGGCGAAATGAAAAAAGGGAAAGC
AAAAGAGATGATGAAAGTCATAGAGAGAGAGATGAAAAAAGGGAAAGCAAAAGAGATGAT

I would like the output to 1) not have a sequential numerical output and 2) to contain the gene name from column 4 of the .bed file.

Is there a way to either modify 1) the input bed file or 2) the output fasta file by giving 'some tool' the fasta and the bed file?

Thanks!

[GenoMax]

There are many threads related to renaming fasta file headers on biostars. Here are a couple but search for others
renaming all fasta headers in a file
replace fasta headers with another name in a text file

Answer 1

[mosquitoes]

Thanks!

I used this python script and it worked great:

fasta= open('file.fasta')
newnames= open('list.txt')
newfasta= open('file_annot.fasta', 'w')

for line in fasta:
    if line.startswith('>'):
        newname= newnames.readline()
        newfasta.write(newname)
    else:
        newfasta.write(line)

fasta.close()
newnames.close()
newfasta.close()