我可能会这样处理它：

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @header; 
my %all_rows;
my %seen_cols;

#read STDIN or files specified as args. 
while ( <> ) {
   #detect a header row by keyword. 
   #can probably do this after 'open' but this way
   #means we can use <> and an arbitrary file list. 
   if ( m/^Accesion/ ) { 
      @header = split;       
      shift @header; #drop "accession" off the list so it's just S01,02,03 etc. 
      $seen_cols{$_}++ for @header; #keep track of uniques. 
   }
   else {
      #not a header row - split the row on whitespace.
      #can do /\t/ if that's not good enough, but it looks like it should be. 
      my ( $ID, @fields ) = split; 
      #use has slice to populate row.

      my %this_row;
      @this_row{@header} = @fields;

      #debugging
      print Dumper \%this_row; 

      #push each field onto the all rows hash. 
      foreach my $column ( @header ) {
         #append current to field, in case there's duplicates (no overwriting)
         $all_rows{$ID}{$column} .= $this_row{$column}; 
      }
   }
}

#print for debugging
print Dumper \%all_rows;
print Dumper \%seen_cols;

#grab list of column headings we've seen, and order them. 
my @cols_to_print = sort keys %seen_cols;

#print header row. 
print join "\t", "Accesion", @cols_to_print,"\n";
#iteate keys, and splice. 
foreach my $key ( sort keys %all_rows ) { 
    #print one row at a time.
    #map iterates all the columns, and gives the value or an empty string
    #if it's undefined. (prevents errors)
    print join "\t", $key, (map { $all_rows{$key}{$_} // '' } @cols_to_print),"\n"
}

给定您的输入（排除调试），将打印：

Accesion    S01 S02 S03 
AJ863320    1   2   5   
AM930424    1   1       
AY664038    2           
EU236327        1   2   
EU434346        2   2

这里有一个更简单的解决方案，使用eBay的tsv-utils，特别是tsv-join命令，如下所示：

FILES="S01.tsv S02.tsv S03.tsv"

tsv-select -H -f Accesion $FILES | tsv-uniq >out.tsv

for infile in $FILES
do
        tsv-join -H --filter-file $infile --key-fields 1 \
                    --append-fields 2  --write-all '' \
                    out.tsv >tmp.tsv;
        mv tmp.tsv out.tsv
done

只需要非常基本的攻击技巧。

我使用csvtool来完成这个任务和许多csv/tsv任务（请参阅doc）。

COMPARED=1 # Controls which columns are compared 
COPIED=2-3 # Controls which columns are copied into the new file
TSV_FILES=( a.tsv b.tsv c.tsv )

csvtool join $COMPARED $COPIED "${TSV_FILES[@]}" -u TAB -t TAB

COMPARED和COPIED参数可以是单个数字、数字范围或逗号分隔的数字列表。
-u TAB和-t TAB参数分别告诉csvtool使用TAB作为输入和输出的分隔符。