Skip to content
This repository has been archived by the owner on Jan 28, 2023. It is now read-only.

Commit

Permalink
Add files via upload
Browse files Browse the repository at this point in the history
  • Loading branch information
@CTLife
CTLife authored Aug 4, 2022
1 parent 7908b5e commit d14dd1a
Show file tree
Hide file tree
Showing 11 changed files with 3,277 additions and 0 deletions.
176 changes: 176 additions & 0 deletions Call_Mutations/figures/2-getFraction.pl
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,176 @@
#!/usr/bin/env perl
use strict;
use warnings;
use v5.12;
## Perl5 version >= 5.12
## Suffixes of all self-defined global variables must be "_g".
###################################################################################################################################################################################################





###################################################################################################################################################################################################
my $input_g = ''; ## such as "1-finalSites/HEK293.bed", global variable.
my $output_g = ''; ## such as "2-getFraction/HEK293.bed", global variable.
my $file_g = ''; ## such as "A_C_merge.spikeins.fit.txt", global variable.

{
## Help Infromation
my $HELP = '
------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------------------------------------
Usage:
perl 2-getFraction.pl [-version] [-help] [-f file] [-in inputFile] [-out outFile]
For instance:
perl 2-getFraction.pl -f A_C_merge.spikeins.fit.txt -in 1-finalSites/HEK293.bed -out 2-getFraction/HEK293.bed
Optional arguments:
-version Show version number of this program and exit.
-help Show this help message and exit.
Required arguments:
-f file Linear regression results.
-in inputFile "inputFile" is the name of your input file. (no default)
-out outFile "outFile" is the name of output file. (no default)
------------------------------------------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------------------------------------------------------
';

## Version Infromation
my $version = " Version 0.2, 2021-04-01.";

## Keys and Values
if ($#ARGV == -1) { say "\n$HELP\n"; exit 0; } ## when there are no any command argumants.
if ($#ARGV%2 == 0) { @ARGV = (@ARGV, "-help") ; } ## when the number of command argumants is odd.
my %args = @ARGV;

## Initialize Variables
$input_g = '1-finalSites/HEK293.bed'; ## This is only an initialization value or suggesting value, not default value.
$output_g = '2-getFraction/HEK293.bed'; ## This is only an initialization value or suggesting value, not default value.

## Available Arguments
my $available = " -version -help -in -out -f ";
my $boole = 0;
while( my ($key, $value) = each %args ) {
if ( ($key =~ m/^\-/) and ($available !~ m/\s$key\s/) ) {say "\n\tCann't recognize $key"; $boole = 1; }
}
if($boole == 1) {
say "\tThe Command Line Arguments are wrong!";
say "\tPlease see help message by using 'perl 2-getFraction.pl -help' \n";
exit 0;
}

## Get Arguments
if ( exists $args{'-version' } ) { say "\n$version\n"; exit 0; }
if ( exists $args{'-help' } ) { say "\n$HELP\n"; exit 0; }
if ( exists $args{'-f' } ) { $file_g = $args{'-f' }; }else{say "\n -f is required.\n"; say "\n$HELP\n"; exit 0; }
if ( exists $args{'-in' } ) { $input_g = $args{'-in' }; }else{say "\n -in is required.\n"; say "\n$HELP\n"; exit 0; }
if ( exists $args{'-out' } ) { $output_g = $args{'-out' }; }else{say "\n -out is required.\n"; say "\n$HELP\n"; exit 0; }

## Conditions
$input_g =~ m/^\S+$/ || die "\n\n$HELP\n\n";
$output_g =~ m/^\S+$/ || die "\n\n$HELP\n\n";

## Print Command Arguments to Standard Output
say "\n
################ Arguments ###############################
File: $file_g
Input File: $input_g
Output File: $output_g
##########################################################
\n";
}
###################################################################################################################################################################################################





###################################################################################################################################################################################################
say "\n\n\n\n\n\n##################################################################################################";
say "Running ......";

sub myMakeDir {
my $path = $_[0];
if ( !( -e $path) ) { system("mkdir -p $path"); }
if ( !( -e $path) ) { mkdir $path || die; }
}


&myMakeDir($output_g);
system( "rm -rf $output_g" );

my $file_a = $file_g;
open(fileIn, "<", $input_g ) or die;
open(fileAa, "<", $file_a ) or die;
open(fileO1, ">", $output_g) or die;

my @lines1 = <fileIn> ;
my @lines2 = <fileAa> ;
###################################################################################################################################################################################################





###################################################################################################################################################################################################
my @motifs = @lines2;
my @coefficients1 = @lines2;
my @coefficients2 = @lines2;
for(my $i=0; $i<=$#lines2; $i=$i+1) {
my $temp = $lines2[$i];
$temp =~ m/^(\S+)\s+([e\-\.\d]+)\s+([e\-\.\d]+)\n/ or die "##$temp##";
$motifs[$i] = $1;
$coefficients1[$i] = $2;
$coefficients2[$i] = $3;
}


for(my $i=0; $i<=$#lines1; $i=$i+1) {
my $temp = $lines1[$i];
$temp =~ m/^(chr\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+([\.\d]+)\s+([-+])\s/ or die "##$temp##";
my $chrom = $1;
my $start = $2;
my $end = $3;
my $name = $4;
my $mutation = $5;
my $strand = $6;
$mutation = $mutation/100;
next unless $chrom =~ m/^chr[\dXYM]+$/;

$name =~ m/\.{6}([AGCT]{5})/ or die "##$name\n##";
my $fiveMer = $1;

my $bool = 0;
my $fraction = -1;

for(my $j=0; $j<=$#lines2; $j=$j+1) {
if($motifs[$j] eq $fiveMer) {$fraction = ($mutation-$coefficients2[$j])/$coefficients1[$j]; $bool=$bool+1; }
}

($bool == 1) or die "##$bool##$fiveMer##\n";
if($fraction < 0.01) {$fraction = 0.01};
$fraction = $fraction*100;
$mutation = $mutation*100;
if($fraction > 100) {$fraction = 100; }

print fileO1 "$chrom\t$start\t$end\t$name\t$mutation\t$strand\t$fraction\n";
}

###################################################################################################################################################################################################






say "Done ......";






#####
Loading

0 comments on commit d14dd1a

Please sign in to comment.