Sorry, for not answering your question.

Does the set of replacement names overlap with the set of original names?

I think both sets of names do not overlap. You can see the example data I posted and tell me if you think different.

Thanks again.

*Update*

You were right, after a few records, names may overlap e.g.(A_fumigatus_1 overlaps A_fumigatus_10 or A_fumigatus_17).

So I guess that is the main source of error during translation.

Try this:

#! perl -sw
use strict;
use Inline::Files;

my %reps = map{ split "\t", $_, 2 } <REPLACEMENTS>;
chomp %reps;

while( <DATAFILE> ) {
    my @items = split "\t", $_;
    $_ = $reps{ $_ } // $_ for @items;
    print join "\t", @items;
}


__REPLACEMENTS__
Aspergillus_clavatus_1    XP_001276684.1 pectate lyase, putative [Aspe
+rgillus clavatus NRRL 1]
Aspergillus_fumigatus_2    XP_001276694.1 conserved hypothetical prote
+in [Aspergillus fumigatus NRRL 1]
Aspergillus_flavus_3    XP_001276726.1 tyrosinase central domain prote
+in [Aspergillus flavus NRRL 1]
Aspergillus_terreus_4    XP_001276738.1 endoglucanase, putative [Asper
+gillus terreus NRRL 1]
__DATAFILE__
Aspergillus_clavatus_1    Aspergillus_flavus_198  Aspergillus_terreus_
+166 Aspergillus_fumigatus_2
Aspergillus_clavatus_1    Aspergillus_flavus_3    Aspergillus_terreus_
+4   Aspergillus_fumigatus_2
Aspergillus_clavatus_3    Aspergillus_flavus_198  Aspergillus_terreu_1
+66  Aspergillus_fumigatus_16
[download]

Output:

C:\test>1157643
XP_001276684.1 pectate lyase, putative [Aspergillus clavatus NRRL 1]  
+  Aspergillus_flavus_198  Aspergillus_terreus_166 Aspergillus_fumigat
+us_2
XP_001276684.1 pectate lyase, putative [Aspergillus clavatus NRRL 1]  
+  Aspergillus_flavus_3    Aspergillus_terreus_4   Aspergillus_fumigat
+us_2
Aspergillus_clavatus_3  Aspergillus_flavus_198  Aspergillus_terreu_166
+  Aspergillus_fumigatus_16
[download]

Note:the use of Inline::Files is for testing only, you'll need to open your data files in the normal way.

---

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