drl / acc2fasta

Perl script that takes in a list of accession numbers (TXT, CSV) and fetches the fasta files from genbank

acc2fasta.pl - convert a bunch of accession numbers into a bunch of sequences

SYNOPSIS

acc2fasta.pl [-q] <acc_file> [-l] <list_file> [-d] <num> [-fw]

DESCRIPTION

acc2fasta.pl takes a file of accession numbers, either in CSV (Filemaker export) of TXT (one accession per line), and fetches the respective sequence with a cleaned header. If the input_file is in CSV, the -list option provides a way of filtering. Check the 'test' files, for concrete examples.

OPTIONS

-query

CSV or TXT file of accession numbers.

-list

List of identifiers (e.g. 'seq1A') in TXT format (i.e Windows Text format when exporting from excel) for which ACCs will be fetched.

-desc

Indicates the maximum allowed length of sequence descriptions (headers) in output fasta file (Default is 50).

-full_desc

Forces full sequence descriptions (headers) in the output fasta file (overwrites [-desc]).

-whitespaces

Words in sequence descriptions (headers) in the output fasta file are separated by spaces (Default is underscore '_').

DIAGNOSTICS

AUTHOR

Dominik R. Laetsch, [email protected]