PTM-Summarizer_Version1.0

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Chinmaya Narayana
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

PTM_ProAdvanced.pl → PTM_summarizer.pl

@@ -1,140 +1,147 @@
-#!/usr/bin/perl
-
-use strict;
-use warnings;
-
-my $ref_fasta="HumanRefSeq_GCF_000001405.39_GRCh38.p13_protein_refseq109_formated.fasta";
-my $infile="SARS_CoV2_Mulit-PTM_PSMs_PTMs.txt";
-
-my %hash=();
-my %hashCount=();
-my %hashLine=();
-my %hash4upset=();
-my %hashUniqPro=();
-my @allM="";
-#my @allM_Pro="";
-
-my $ref_id="";
-my %ref_Seq=();
-open(REF,"$ref_fasta") or die "Could not open the file:$!\n";
-while(<REF>)
-{
-	chomp;
-	$_=~s/\r//g;
-	if(/^>/)
-	{
-		$ref_id = (split /\|/)[1]; ## Header Parse for Master protein accession
-		$ref_id =~s/\>//;
-	}
-	else
-	{
-		$ref_Seq{$ref_id}.="$_";
-	}
-}
-close REF;
-
-open(IN,"$infile") or die "Could not open the file:$!\n";
-while(<IN>)
-{
-	chomp;
-	$_=~s/\r//g;
-	$_=~s/\"//g;
-	unless(/^Annotated/)
-	{
-		my $line=$_;
-		my ($Seq,$mas,$status,$fs,$ptmRS)=(split /\t/)[3,7,15,26,-1];#Sequence, Master Protein, mz, First scan, ptmRS
-		#if(10==10)#if($status eq "Selected")
-		{
-			$mas=~s/\;\s/\;/g;
-			my $annSeq=(split /\./,$Seq)[1];
-			$ptmRS=~s/\s//g;
-			my @allMod=(split /\;/,$ptmRS);
-			foreach my $i (@allMod)
-			{
-				if($i=~/([A-Z])([0-9]*?)\((.*?)\)\:([0-9]*)/)
-				{
-					my ($aa,$pos,$ty,$rs)=($1,$2,$3,$4);
-					if($rs >= 75)
-					{
-						my $k=$annSeq."_".$mas."_".$aa.$pos;
-						unless(($ty eq "Oxidation") || (($ty eq "Deamidated") && (($aa eq "N")||($aa eq "Q"))))
-						{
-							foreach my $m (split /\;/,$mas)
-							{
-								#print "$m\n";	
-								my $Proseq = $ref_Seq{$m};
-								my $ann = $annSeq; $ann=~tr/[a-z]/[A-Z]/;
-								my $index = (index ($Proseq, $ann) + $pos);
-								#print OUT "$annSeq\t$mas\t$m\t$ty\t$aa\t$index\n";
-								my $uniqPro=$m."_".$ty."_".$aa."_".$index;
-								$hashUniqPro{$uniqPro}="$annSeq\t$m\t$ty\t$aa\t$index";
-								#push(@allM_Pro,$ty);
-							}
-							unless(exists $hash{$k}{$ty})
-							{						
-								$hash{$k}{$ty}="";
-								$hashCount{$ty}{$aa}++;
-								$hashLine{$ty}{$aa}.="$_\n";
-								my $mod=$ty."_".$aa;
-								my $ty2=$ty;$ty2=~s/\+HeavyK//g;
-								$hash4upset{$annSeq}{$ty2}.="";
-								push(@allM,$ty2);
-							}							
-						}							
-					}	
-				}
-			}
-		}	
-	}
-}	
-close IN;
-
-open(OUTUNIQPRO,">UniqueProteinSite.txt") or die "Could not create the file:$!\n";
-foreach my $k1 (keys %hashUniqPro)
-{
-	print OUTUNIQPRO "$hashUniqPro{$k1}\n";
-}
-close OUTUNIQPRO;
-
-open(OUT1,">summary.txt") or die "Could not create the file:$!\n";
-foreach my $k1 (keys %hashCount)
-{
-	print OUT1 "$k1\n";
-	foreach my $k2 (keys %{$hashCount{$k1}})
-	{
-		print OUT1 "$k1\t$k2\t$hashCount{$k1}{$k2}\n";
-		my $file=$k1."_".$k2.".txt";
-		open(OUT,">$file") or die "Could not create the file:$!\n";
-		print OUT "$hashLine{$k1}{$k2}\n";
-		close OUT;
-	}
-	#print OUT1 "\n";
-}
-close OUT1;
-
-my @unique = do { my %seen; grep { !$seen{$_}++ } @allM };
-open(OUT2,">ForUpset3.txt") or die "Could not create the file:$!\n";
-print OUT2 "Peptide";
-foreach (@unique)
-{
-	print OUT2 "\t$_";
-}
-print OUT2 "\n";
-foreach my $k1 (keys %hash4upset)
-{
-	print OUT2 "$k1";
-	foreach my $k2 (@unique)
-	{
-		if((exists $hash4upset{$k1}) && (exists $hash4upset{$k1}{$k2}))
-		{
-			print OUT2 "\t1";
-		}
-		else
-		{
-			print OUT2 "\t0";
-		}
-	}
-	print OUT2 "\n";
-}
-close OUT2;
-exit;
+#!/usr/bin/perl
+
+#################### Usage ###########################
+###### perl PTM_summarizer.pl ref.fasta PSM.txt ######
+######################################################
+
+use strict;
+use warnings;
+
+my $ref_fasta=$ARGV[0];
+my $infile=$ARGV[1];
+
+my %hash=();
+my %hashCount=();
+my %hashLine=();
+my %hash4upset=();
+my %hashUniqPro=();
+my @allM="";
+#my @allM_Pro="";
+
+my $ref_id="";
+my %ref_Seq=();
+open(REF,"$ref_fasta") or die "Could not open the file:$!\n";
+while(<REF>)
+{
+	chomp;
+	$_=~s/\r//g;
+	if(/^>/)
+	{
+		$ref_id = (split /\|/)[1]; ## Header Parse for Master protein accession
+		$ref_id =~s/\>//;
+	}
+	else
+	{
+		$ref_Seq{$ref_id}.="$_";
+	}
+}
+close REF;
+
+open(IN,"$infile") or die "Could not open the file:$!\n";
+while(<IN>)
+{
+	chomp;
+	$_=~s/\r//g;
+	$_=~s/\"//g;
+	unless(/^Annotated/)
+	{
+		my $line=$_;
+		my ($Seq,$mas,$status,$fs,$ptmRS)=(split /\t/)[3,7,15,26,-1];#Sequence, Master Protein, mz, First scan, ptmRS
+		#if(10==10)#if($status eq "Selected")
+		{
+			$mas=~s/\;\s/\;/g;
+			my $annSeq=(split /\./,$Seq)[1];
+			$ptmRS=~s/\s//g;
+			my @allMod=(split /\;/,$ptmRS);
+			foreach my $i (@allMod)
+			{
+				if($i=~/([A-Z])([0-9]*?)\((.*?)\)\:([0-9]*)/)
+				{
+					my ($aa,$pos,$ty,$rs)=($1,$2,$3,$4);
+					if($rs >= 75)
+					{
+						my $k=$annSeq."_".$mas."_".$aa.$pos;
+						unless(($ty eq "Oxidation") || (($ty eq "Deamidated") && (($aa eq "N")||($aa eq "Q"))))
+						{
+							foreach my $m (split /\;/,$mas)
+							{
+								#print "$m\n";	
+								my $Proseq = $ref_Seq{$m};
+								my $ann = $annSeq; $ann=~tr/[a-z]/[A-Z]/;
+								my $index = (index ($Proseq, $ann) + $pos);
+								#print OUT "$annSeq\t$mas\t$m\t$ty\t$aa\t$index\n";
+								my $uniqPro=$m."_".$ty."_".$aa."_".$index;
+								my $ty_aa = $ty."_".$aa;
+								$hashUniqPro{$uniqPro}="$annSeq\t$m\t$ty\t$aa\t$ty_aa\t$index";
+								#push(@allM_Pro,$ty);
+							}
+							unless(exists $hash{$k}{$ty})
+							{						
+								$hash{$k}{$ty}="";
+								$hashCount{$ty}{$aa}++;
+								$hashLine{$ty}{$aa}.="$_\n";
+								my $mod=$ty."_".$aa;
+								my $ty2=$ty;$ty2=~s/\+HeavyK//g;
+								$hash4upset{$annSeq}{$ty2}.="";
+								push(@allM,$ty2);
+							}							
+						}							
+					}	
+				}
+			}
+		}	
+	}
+}	
+close IN;
+
+my $outun = $infile; $outun =~s/\.txt$/\_UniqueProteinSite.txt/;
+open(OUTUNIQPRO,">$outun") or die "Could not create the file:$!\n";
+foreach my $k1 (keys %hashUniqPro)
+{
+	print OUTUNIQPRO "$hashUniqPro{$k1}\n";
+}
+close OUTUNIQPRO;
+
+my $out1 = $infile; $out1 =~s/\.txt$/\_summary.txt/;
+open(OUT1,">$out1") or die "Could not create the file:$!\n";
+foreach my $k1 (keys %hashCount)
+{
+	print OUT1 "$k1\n";
+	foreach my $k2 (keys %{$hashCount{$k1}})
+	{
+		print OUT1 "$k1\t$k2\t$hashCount{$k1}{$k2}\n";
+		my $file=$k1."_".$k2.".txt";
+		open(OUT,">$file") or die "Could not create the file:$!\n";
+		print OUT "$hashLine{$k1}{$k2}\n";
+		close OUT;
+	}
+	#print OUT1 "\n";
+}
+close OUT1;
+
+my @unique = do { my %seen; grep { !$seen{$_}++ } @allM };
+open(OUT2,">ForUpset.txt") or die "Could not create the file:$!\n";
+print OUT2 "Peptide";
+foreach (@unique)
+{
+	print OUT2 "\t$_";
+}
+print OUT2 "\n";
+foreach my $k1 (keys %hash4upset)
+{
+	print OUT2 "$k1";
+	foreach my $k2 (@unique)
+	{
+		if((exists $hash4upset{$k1}) && (exists $hash4upset{$k1}{$k2}))
+		{
+			print OUT2 "\t1";
+		}
+		else
+		{
+			print OUT2 "\t0";
+		}
+	}
+	print OUT2 "\n";
+}
+close OUT2;
+exit;