nbisweden/efasta2fasta

Convert extended fasta (efasta) to fasta

efasta2fasta

Convert extended fasta (efasta) to fasta

The one-liner:

perl -0076 -ne 'chomp;($h,@r)=split/\n/;$s=join("",@r);$s=~s/{([\s|\w]*),[^}]*}/$1/g;$s=~s/(.{60})/$1\n/g;print">$h\n$s\n" unless(!$h);' file.efasta

USAGE

./efasta2fasta.pl file.efasta 

DESCRIPTION

Convert efasta to fasta by taking the first item in the list {,,,} for every ambiguity.

efasta - extended fasta format (from Allpath-LG):

"ALLPATHS-LG introduces efasta output format, which extends fasta format to capture ambiguities within the assembly which might otherwise be lost. These ambiguities may arise from biological sources (e.g., SNPs & CNVs) or from uncertainties in the data. In efasta format, ambiguities are represented as a comma-separated list of alternatives within curly braces ("{}"). For example, an A/T SNP would become: ATGTC{A,T}TGTCG. An unresolved homopolymer run where the evidence suggested there should be 6, 7, or 8 Ts would become: GTCACTTTTTT{,T,TT}. Within the braces, alternatives are ordered in terms of decreasing likelihood."

Input:

efasta file(s)

Output:

fasta file named from the input (with added file ending .fas)

AUTHOR

Johan Nylander (JN), [email protected]

COMPANY

BILS/NRM

VERSION

1.0

CREATED

09/22/2015 02:53:00 PM