takes a list of protein accession numbers with SNP information from STDIN, trims the SNPs, and generates a .fasta containing amino acid sequences for each accession

fasta.maker.pl

#!/usr/bin/perl
use strict;
use warnings;
use LWP::Simple;

# pipe STDIN to a loop that
# a) removes the strings after each accession number
# b) puts the remaining accession numbers from each line into an array

# $IN = \*STDIN;

my $line;
my @list;

foreach $line (<STDIN>){
    chomp($line);
    $line =~ s/[ \t]+.*$//;
    @list = split("\n", $line);
}

#append [accn] field to each accession
for (my $index=0; $index < @list; $index++) {
   $list[$index] .= "[accn]";
}

#join the accessions with OR
my $query = join('+OR+',@list);

#assemble the esearch URL
my $base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
my $url = $base . "esearch.fcgi?db=nucleotide&term=$query&usehistory=y";

#post the esearch URL
my $output = get($url);

#parse WebEnv and QueryKey
my $web = $1 if ($output =~ /<WebEnv>(\S+)<\/WebEnv>/);
my $key = $1 if ($output =~ /<QueryKey>(\d+)<\/QueryKey>/);

#assemble the efetch URL
$url = $base . "efetch.fcgi?db=protein&query_key=$key&WebEnv=$web";
$url .= "&rettype=fasta&retmode=text";

#post the efetch URL
my $fasta = get($url);
print "$fasta";