NCBI provides specifications for several Fasta defline identifier formats/conventions at ftp://ftp.ncbi.nih.gov/blast/documents/formatdb.html. This script will automatically detect the convention used sequence-by-sequence, and convert all deflines to the requested format.

fasta-validate.pl

#!/usr/bin/env perl

# Copyright (c) 2012-2013, Daniel S. Standage <daniel.standage@gmail.com>
#
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
# ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
# OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

use strict;
use Getopt::Long;

# Program usage statement
sub print_usage
{
  my $OUT = shift(@_);
  print $OUT "Usage: $0 [options] sequence.fa
  Options:
    -h|--help    print this help message and exit
    --outfile    print sequences with converted deflines to the specified file;
                 default is the terminal (stdout)
    --outfmt     defline format to use when printing validated sequences; valid
                 options include the following: 'idonly', 'General', and
                 'Local'; default is 'idonly'
    --db         the 'General' defline format includes a database name in the
                 second field; specify the value to be used when printing
                 validated sequences in 'General' format
";
}

# NCBI BLAST provides the reference list of valid defline patterns: see "FASTA
# Defline Format" at ftp://ftp.ncbi.nih.gov/blast/documents/formatdb.html.
# We support a subset of these defline patterns.
my $deflines =
{
  'gb\|([^\|]+)\|(\S*)'  => "GenBank",
  'emb\|([^\|]+)\|(\S*)' => "EMBL",
  'dbj\|([^\|]+)\|(\S*)' => "DDBJ",
  'sp\|([^\|]+)\|(\S*)'  => "SWISS-PROT",
  'pdb\|([^\|]+)\|(\S*)' => "PDB",
  'gnl\|[^\|]+\|(\S+)'   => "General",
  'ref\|([^\|]+)\|(\S*)' => "RefSeq",
  'lcl\|(\S+)'           => "Local",
  '([^\|\s]+)'           => "idonly",
};
my $defline_outformats =
{
  "General" => ">gnl|%s|%s\n",
  "Local"   => ">lcl|%s\n",
  "idonly"  => ">%s\n",
};
my $idsfound = {};

# Parse command line options
my $outfmt      = "idonly";
my $db          = "";
my $outfilename = "";
GetOptions
(
  "h|help"    => sub { print_usage(\*STDOUT); exit(0); },
  "outfmt=s"  => \$outfmt,
  "db=s"      => \$db,
  "outfile=s" => \$outfilename,
);

# Create output stream
my $OUT = \*STDOUT;
if($outfilename ne "")
{
  open($OUT, ">", $outfilename);
  unless($OUT)
  {
    printf("error: unable to open output file '%s'\n", $outfilename);
    exit(1);
  }
}

# Verify output format
if(defined $defline_outformats->{$outfmt})
{
  if($outfmt eq "General" and $db eq "")
  {
    printf(STDERR "error: must provide a db value when using output format ".
           "'%s'\n", $outfmt);
    print_usage(\*STDERR);
    exit(1);
  }
  
  if($outfmt ne "General" and $db ne "")
  {
    printf(STDERR "warning: database '%s' ignored when using output format ".
           "'%s'\n", $outfmt);
  }
}
else
{
  printf(STDERR "error: unsupported output format '%s'\n", $outfmt);
  print_usage(\*STDERR);
  exit(1);
}

# Verify input file
my $infile = shift(@ARGV);
unless($infile)
{
  print(STDERR "error: must provide an input sequence file\n");
  print_usage(\*STDERR);
  exit(1);
}
open(my $IN, "<", $infile);
unless($IN)
{
  printf(STDERR "error: could not open input sequence file '%s'\n", $infile);
  exit(1);
}

# Validate deflines, and print if outfile is indicated
my $counts = {};
foreach my $format_name(keys(%$defline_outformats))
{
  $counts->{ $format_name } = 0;
}
while(my $line = <$IN>)
{
  chomp($line);
  if($line =~ m/^>/)
  {
    my $gi;
    my $idacc;
    my $locus;
    foreach my $defline_format(keys(%$deflines))
    {
      my $format_name = $deflines->{$defline_format};
      if($line =~ m/^>$defline_format/)
      {
        $idacc = $1;
        $locus = $2;
        $counts->{ $format_name } += 1;
        if($idsfound->{$idacc})
        {
          printf(STDERR "warning: found duplicated sequence ID '%s'\n", $idacc);
        }
        $idsfound->{$idacc} = 1;
        last;
      }
      elsif($line =~ m/^>gi\|(\d+)\|$defline_format/)
      {
        $gi = $1;
        $idacc = $2;
        $locus = $3;
        $counts->{ $format_name } += 1;
        if($idsfound->{$gi})
        {
          printf(STDERR "warning: found duplicated sequence ID '%s'\n", $gi);
        }
        $idsfound->{$gi} = 1;
        last;
      }
    }
    
    if($idacc)
    {
      my $replace = $idacc;
      $replace .= " locus=$locus" if($locus);
      $replace = "$gi accession=$replace" if($gi);
      $replace = "lcl|$replace" if($outfmt eq "Local");
      $replace = "gnl|$db|$replace" if($outfmt eq "General");
      $line =~ s/>\S+/>$replace/;
    }
    else
    {
      printf(STDERR "warning: could not validate defline format: '%s'\n",$line);
    }
  }
  printf($OUT "%s\n", $line);
}

# Print report about validated deflines
while(my($format, $format_name) = each(%$deflines))
{
  if($counts->{$format_name} > 0)
  {
    printf(STDERR "note: validated %d sequences with '%s' defline format\n",
           $counts->{$format_name}, $format_name);
  }
}