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#!/usr/bin/perl
# ftp ftp://ftp.expasy.org/databases/enzyme/enzyme.dat
# ftp ftp://ftp.expasy.org/databases/enzyme/enzclass.txt
# ./get_ec.pl enzyme.dat enzclass.txt
# /am/ncbiapdata/scripts/misc/txt2inc.sh ecnum_ambiguous.txt
# /am/ncbiapdata/scripts/misc/txt2inc.sh ecnum_deleted.txt
# /am/ncbiapdata/scripts/misc/txt2inc.sh ecnum_replaced.txt
# /am/ncbiapdata/scripts/misc/txt2inc.sh ecnum_specific.txt
$enzfile = shift || die "Must supply enzyme.dat filename\n";
$clsfile = shift || die "Must supply enzclass.txt filename\n";
open (ENZIN, $enzfile) || die "Unable to open $enzfile\n";
open (CLSIN, $clsfile) || die "Unable to open $clsfile\n";
open (OUT_LIVE, ">ecnum_specific.txt") || die "Unable to open ecnum_specific.txt\n";
open (OUT_DEL, ">ecnum_deleted.txt") || die "Unable to open ecnum_deleted.txt\n";
open (OUT_TRANS, ">ecnum_replaced.txt") || die "Unable to open ecnum_replaced.txt\n";
open (OUT_AMB, ">ecnum_ambiguous.txt") || die "Unable to open ecnum_ambiguous.txt\n";
while ($thisline = <ENZIN>) {
$thisline =~ s/\r//;
$thisline =~ s/\n//;
if ($thisline =~ /^CC/) {
#ignore comment lines
} elsif ($thisline =~ /^ID\s+(.*)/) {
$current_id = $1;
#by default, entry type is 1
$entry_type = 1;
$print_id = 1;
$add_space = 0;
} elsif ($thisline =~ /^DE\s+(.*)/) {
$disposition = $1;
if ($disposition =~ /Deleted entry/) {
print OUT_DEL "$current_id";
$entry_type = 2;
} elsif ($disposition =~ /Transferred entry: (.*)/) {
print OUT_TRANS "$current_id";
$entry_type = 3;
$disposition = $1;
}
if ($entry_type == 1) {
if ($print_id == 1) {
print OUT_LIVE "$current_id\t";
$print_id = 0;
}
if ($add_space == 1) {
print OUT_LIVE " ";
}
#use substitution to remove trailing period
$disposition =~ s/\.\s*$//;
print OUT_LIVE "$disposition";
if ($disposition !~ /-\s*$/) {
$add_space = 1;
}
} elsif ($entry_type == 3) {
$next_id = $disposition;
#use substitution to remove and
$next_id =~ s/ and//;
$next_id =~ s/and //;
#use substitution to remove commas (note use of g for global)
$next_id =~ s/,//g;
#use substitution to remove trailing period
$next_id =~ s/\.\s*$//;
#use substitution to replace spaces with tabs (note use of g for global)
$next_id =~ s/\s+/\t/g;
print OUT_TRANS "\t$next_id";
}
} elsif ($thisline =~ /^\/\//) {
if ($entry_type == 1) {
print OUT_LIVE "\n";
} elsif ($entry_type == 2) {
print OUT_DEL "\n";
} elsif ($entry_type == 3) {
print OUT_TRANS "\n";
}
}
}
while ($thisline = <CLSIN>) {
$thisline =~ s/\r//;
$thisline =~ s/\n//;
$thisline =~ s/\.\s+/\./;
if ($thisline =~ /^(.+- )\s+(.*)/) {
$ec_num = $1;
$ec_name = $2;
#use substitution to delete spaces (note use of g for global)
$ec_num =~ s/\s+//g;
#use substitution to remove trailing period
$ec_name =~ s/\.\s*$//;
print OUT_AMB "$ec_num\t$ec_name\n";
$ec_num =~ s/-/n/g;
print OUT_AMB "$ec_num\t$ec_name\n";
}
}
close (ENZIN);
close (CLSIN);
close (OUT_LIVE);
close (OUT_DEL);
close (OUT_TRANS);
close (OUT_AMB);
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