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Top Forums Shell Programming and Scripting Paste columns based on common column: multiple files Post 303009519 by genome on Friday 15th of December 2017 09:27:31 AM
Old 12-15-2017
Code:
for i in {1..22}
do
    #--iterate over chromosomes
    saveTemp=""
    files_info="$(find $input_dir -name "*_CHR$i.info"  | sort )"
    files_list=""
    
    #---split by new lines and make it array---
    SAVEIFS=$IFS
    IFS=$'\n'
    files_info=($files_info)
    IFS=$SAVEIFS 
    
    join -j 2 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12  ${files_info[0]}  ${files_info[1]}  > $output_dir/"tempCHR_"$i".info" 

    SAVEtemp=$output_dir/"tempCHR_"$i".info"
    printf "$i joined for first two files\n"

    for (( x=2;x<${#files_info[@]};x++ ))
    do
	join -j 2 -o 1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,2.10,2.11,2.12 $SAVEtemp  ${files_info[$x]}  > $output_dir/"tempchr"$i"_"$x".info" 

	SAVEtemp=$output_dir/"tempchr"$i"_"$x".info"
    done
    mv $SAVEtemp $output_dir/"joined_CHR""$i"".info"
    SAVEtemp=$output_dir/"joined_CHR""$i"".info"
    printf "CHR $i is done for joining\n"
    
    for w in ` awk '{print $2}' $SAVEtemp | grep -v "rs_id" `
    do
	st="" #start null string to concatenate
	
	for (( x=0;x<${#files_info[@]};x++ ))
	do
	    #--loop through files to grep the string
	    
	    temp_st=$(grep -w $w ${files_info[$x]}) 
	    st=$st" "$temp_st

	done
	echo "$st" >> $output_dir/"cols_joined_CHR"$i".info" 
    done

    printf "Proceseed files for $i chromosome!\n"
done

I left it running last evening and script has not finished working with chromosome 1. Smilie Terrible.
 

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Explode(3pm)						User Contributed Perl Documentation					      Explode(3pm)

NAME
MIME::Explode - Perl extension for explode MIME messages SYNOPSIS
use MIME::Explode; my $explode = MIME::Explode->new( output_dir => "tmp", mkdir => 0755, decode_subject => 1, check_content_type => 1, content_types => ["image/gif", "image/jpeg", "image/bmp"], types_action => "exclude" ); print "Number of messages: ", $explode->nmsgs, " "; open(MAIL, "<file.mbox") or die("Couldn't open file.mbox for reading: $! "); open(OUTPUT, ">file.tmp") or die("Couldn't open file.tmp for writing: $! "); my $headers = $explode->parse(*MAIL, *OUTPUT); close(OUTPUT); close(MAIL); for my $part (sort{ $a cmp $b } keys(%{$headers})) { for my $k (keys(%{$headers->{$part}})) { if(ref($headers->{$part}->{$k}) eq "ARRAY") { for my $i (0 .. $#{$headers->{$part}->{$k}}) { print "$part => $k => $i => ", $headers->{$part}->{$k}->[$i], " "; } } elsif(ref($headers->{$part}->{$k}) eq "HASH") { for my $ks (keys(%{$headers->{$part}->{$k}})) { if(ref($headers->{$part}->{$k}->{$ks}) eq "ARRAY") { print "$part => $k => $ks => ", join(($ks eq "charset") ? " " : "", @{$headers->{$part}->{$k}->{$ks}}), " "; } else { print "$part => $k => $ks => ", $headers->{$part}->{$k}->{$ks}, " "; } print "$part => $k => $ks => ", $headers->{$part}->{$k}->{$ks}, " "; } } else { print "$part => $k => ", $headers->{$part}->{$k}, " "; } } } if(my $e = $explode->clean_all()) { print "Error: $e "; } DESCRIPTION
MIME::Explode is perl module for parsing and decoding single or multipart MIME messages, and outputting its decoded components to a given directory ie, this module is designed to allows users to extract the attached files out of a MIME encoded email messages or mailboxes. METHODS
new([, OPTION ...]) This method create a new MIME::Explode object. The following keys are available: output_dir Directory where the decoded files are placed mkdir => octal_number If the value is set to octal number then make the output_dir directory (example: mkdir => 0755). check_content_type => 0 or 1 If the value is set to 1 the content-type of file is checked decode_subject => 0 or 1 If the value is set to 1 then the subject is decoded into a list. $header->{'0.0'}->{subject}->{value} = [ARRAYREF]; $header->{'0.0'}->{subject}->{charset} = [ARRAYREF]; $subject = join("", @{$header->{'0.0'}->{subject}->{value}}); exclude_types => [ARRAYREF] Not save files with specified content types (deprecated in next versions) content_types => [ARRAYREF] Array reference with content types for "include" or "exclude" types_action => "include" or "exclude" If the action is a "include", all attached files with specified content types are saved but if the action is a "exclude", no files are saved except if its in the array of content types. If no array is specified, but the action is a "include", all attached files are saved, otherwise all files are removed if action is a "exclude". The default action is "include". parse(FILEHANDLE, FILEHANDLE) This method parse the stream and splits it into its component entities. This method return a hash reference with all parts. The FILEHANDLE should be a reference to a GLOB. The second argument is optional. nmsgs Returns the number of parsed messages. clean_all Cleans all files from the "output_dir" directory and then removes the directory. If an error happens returns it. AUTHOR
Henrique Dias <henrique.ribeiro.dias@gmail.com> CREDITS
Thanks to Rui Castro for the revision. SEE ALSO
MIME::Tools, perl(1). perl v5.14.2 2011-06-26 Explode(3pm)
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