starts script for table additions

mutations/import/20210831.Weigand.123.csv

@@ -0,0 +1,5 @@
+Chrom,Gene,Pos,Ref,Mut,Description,Example,Library,Platform,Analysis,Lineage,Submitter,Date
+NC_045512,ORFa,26158,G,A,Some human readable description,NA,NA,NA,NA,NA,YourName - YourAffiliation,YYYYMMDD
+NC_045512,ORFa,cow,G,A,Some human readable description,NA,NA,NA,NA,NA,Roy Kent - AFC Richmond,20210905
+NC_045512,ORF1a,7243,G,A,Some human readable description,NA,NA,NA,NA,NA,Josef Martinez - ATLUTD,20210905
+NC_045512,ORF1a,70243,G,A,Some human readable description,NA,NA,NA,NA,NA,George Bello - ATLUTD,20210905

mutations/src/table-add.pl

@@ -0,0 +1,58 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+use File::Basename;
+use Scalar::Util qw(looks_like_number);
+
+# Adds submitted mutations to existing table
+# M. Weigand - CDC
+# 20210901
+
+&GetOptions(	'indir=s' => \my$indir,
+		'now=s' => \my$now,
+		'latest=s' => \my$latest,
+		'log=s' => \my$log,
+		'out=s' => \my$out);
+
+my@new = glob("$indir/[!mut_template]*csv");
+open(my $fh, '>>', $out) or die "Could not open file '$out' $!";
+open(my $lg, '>>', $log) or die "Could not open file '$log' $!";
+
+foreach my$n (@new){
+	open IN, "$n";
+	while( my$i = <IN> ){
+		unless($i =~ m/^Chrom/){
+			chomp$i;
+			if( &REQ($i) eq "pass"){
+				print $fh "$i\n";
+				print $lg basename($n,'.csv').": $i\n";
+			}else{
+				print "ERROR IN SUBMISSION: \'$i\' \n";
+			}
+		}
+	}
+	close IN;
+
+}
+close $fh;
+close $lg;
+
+
+####
+sub REQ {
+	my@mut = split(",", $_[0]);
+	if(grep { $_ eq 'NA'} @mut[0..5]){
+		return("fail");
+	}elsif($mut[-2] =~ /YourName/){
+		return("fail");
+	}elsif($mut[-1] eq 'YYYYMMDD' ){
+		return("fail");
+	}elsif(!looks_like_number($mut[2])){
+		return("fail");
+	}elsif($mut[2] >= 29903){
+		return("fail");
+	}else{
+		return("pass");
+	}
+}
+