add scripts and results

Author: Guanqiao Feng

clean_fasta_0.pl

@@ -0,0 +1,88 @@
+#!/usr/bin/perl
+
+## clean rat fasta ##
+
+%hash = ();
+
+open FH, "<Rattus_norvegicus_UniProt_MoTrPAC_2017-10-20.fasta";
+open OUT, ">Rattus_norvegicus.fasta";
+$n = 0;
+$m = 0;
+
+while (<FH>)
+{
+    $seq = $_;
+    chomp $seq;
+    $m = $m + 1;
+    if (/^>[^\|]+\|[^\|]+\|(\S+)/)
+    {
+	$name = $1;
+	if (!(exists ($hash{$name})))
+	{
+	    if ($seq =~ m/Rattus norvegicus/)
+	    {
+		if ($m == 1)
+		{
+		    print OUT ">$name\n";
+		}
+		else
+		{
+		    print OUT "\n>$name\n";
+		}
+		$n = 1;
+	    }
+	    else
+	    {
+		$n = 0;
+	    }
+	    $hash{$name} = 0;
+	}
+	else
+	{
+	    $n = 0;
+	}
+    }
+    elsif ($n == 1)
+    {
+	print OUT "$seq";
+    }
+}
+print OUT "\n";
+
+close FH;
+close OUT;
+
+## clean mouse fasta ##
+
+open FH, "<M_musculus_Uniprot_SPROT_2017-04-12.fasta";
+open OUT, ">Mus_musculus.fasta";
+
+$m = 0;
+
+while (<FH>)
+{
+    $seq = $_;
+    chomp $seq;
+    print "$seq\n";
+    $m = $m + 1;
+    if (/^(>\S+)/)
+    {
+	$name = $1;
+	if ($m == 1)
+	{
+	    print OUT "$name\n";
+	}
+	else
+	{
+	    print OUT "\n$name\n";
+	}
+    }
+    elsif (/(\S+)/)
+    {
+	$seqs = $1;
+	print OUT "$seqs";
+    }
+}
+print OUT "\n";
+close FH;
+close OUT;