Edits:

An edit after discussing in the comments of this answer to give a clear solution:

Scenario 1:

You only need the part before the "."

cat input.txt | cut -d"." -f1 | sort | uniq

will go through the IDs, remove the part after the "." and make the list unique

cat input.txt | cut -d"." -f1 | sort | uniq -c

will additionally show how often the ID was seen.

Scenario 2:

You want to keep the part after the "."

cat input.txt | sort | perl -ne 'print $_ unless $_=~/^$patt\.\d+$/; ($patt)=$_=~/(^\S+)\./'

This will read the list of IDs, sort them and print an ID, if the part before the "." has not been seen before.

You should try all three commands I posted here and maybe make some changes to your test data (removing the ID with ".1", etc) to see how they work and then decide, which command suits you the best.

Original answer:

This should work for you

perl -ne 'print $_ unless $_=~/^$patt\.\d+$/; ($patt)=$_=~/(^\S+)\./'

echo "Traes_1DL_9344DD117.1
Traes_1DL_9344DD117.2
Traes_1DL_9344DD117.3
Traes_1DL_9344DD117.4
Traes_1DL_BDDF1198A.1
Traes_1DL_BDDF1198A.2
Traes_1DL_BDDF1198A.3
Traes_1DL_BDDF1198A.4
Traes_1DL_BDDF1198A.5
Traes_1DL_C91636A55.1
Traes_1DL_C91636A55.2
Traes_1DL_C91636A55.3
Traes_1DL_C91636A55.4
Traes_1DL_C91636A55.5
Traes_1DL_C91636A55.7
Traes_2AL_48B239DD6.1
Traes_2AL_48B239DD6.2
Traes_2AL_48B239DD6.3
Traes_2AL_48B239DD6.4
Traes_2AL_C00552444.1
Traes_2AL_C00552444.2
Traes_2AL_C00552444.3
Traes_2AS_146D16572.1
Traes_2AS_146D16572.2
Traes_2AS_146D16572.3
Traes_2AS_146D16572.4
Traes_2AS_146D16572.5" > input.txt

cat input.txt | perl -ne 'print $_ unless $_=~/^$patt\.\d+$/; ($patt)=$_=~/(^\S+)\./'

Traes_1DL_9344DD117.1
Traes_1DL_BDDF1198A.1
Traes_1DL_C91636A55.1
Traes_2AL_48B239DD6.1
Traes_2AL_C00552444.1
Traes_2AS_146D16572.1

Hi,

I am stuck in same kind of problem, as a newbie in bioinformatics, I am trying to extract the fasta sequences from a file_2 with similar ids from another list file_1

File_1.fasta

>comp148_c0_seq1
>comp169_c0_seq1
>comp258_c0_seq1
>comp285_c0_seq1
>comp350_c0_seq1
>comp424_c0_seq1
>comp783_c0_seq1
>comp1089_c0_seq1

File_2.fasta

>comp6_c1_seq1  -1      22      237
MAILRFMDSWVVGVNVCGKRPRRFVDPINMIRETIIRVHVRPFGVWISIICLIISLTSQCWKEWRRLLIRRF
>comp11_c0_seq1 -2      35      358
MKEDDKVIEDDEKAEGSKGDIQKEEPGADDETEESNKLIGDNQGKDEANADEDDPQNEETIDKSEENKQREEQQQITLLHFIGRSFASLLKNLLKKTCPSAAEGNNYY
>comp42_c0_seq1 +3      114     305
MPSTLKFLLIYESHWYDKNSEKLVNEFLSLLAHCTQLRYMPILLEDYDLLKLIEEKNTRQFDKI
>comp43_c0_seq1 -2      38      298
MSSSNWAFYIGVSNGHVHDNLLVCKAPNCYCFPTRMDHCYIGGTQHHFEWPTDAISRPQWNGIGDTLGCGILLNPKNELAIFFTANG
>comp48_c0_seq1 +3      18      242
MLYKSLINSKSLRGKTPAEVVNMFANDGQRIFDAVTFAPLVLIGPLVLVGGLIYLLRVIGPVSLLAVSVFLIFDF
>comp53_c0_seq1 -1      55      312
MIGNRLRVKRDKVTLKMEISHCLHSQIIGRGGRNTQKIMRDTGCHIHFPDSNKCLTNPVTMPQQAKNDQVSISGCAKDVEKAREML
>comp56_c0_seq1 -2      110     379
MNNARLNAEINELHAAIHANVHYGRPFKPSHISMNKSQATDRSDNNVCGQLATIDNKNENDHDNDNDDNEANDETRERRRFTVADYMPGG
>comp56_c1_seq1 -1      52      408
MWIWSGPIFSTTILFGHISPFLKPGWRRRAYFCPNFPRRLRVYWATTALLSLLIITFLLGRHFFLGVPSQLTTSPEAIFPSTLGLDCGNVTLSFTAAANDEKVPSNQTLAADKVVASFA
>comp72_c0_seq1 +2      14      271
MYALTWNGLMELKLGADTCPDVNVNWEVFGERGLKSISLFAVADKVFIFSTPNELLVYDRGSATISQFPIASPPLKTLLAVSQSSQ
>comp74_c0_seq1 +3      96      305
MVIPFIFLKAQTIQLEAKDESNFCQNRVDLLAHEVEVRVRIGKRQKRALASSAGCCSCGRGPMGERGAPG
>comp79_c0_seq1 -1      31      213
MASAMFCCQVCMLLSSAYHIFGCHSPNRRKRWLRADLFGVSAGLIGLYLSGLYTSFYHFPV

I used awk:

diff <(cat file_1 | grep ">" | sort) <(cat file_2 | grep ">" | sort) | grep "^<" | awk -F\> '{print $2}'

I m just getting ids only, I need sequences to corresponding ID also.

Can anyone suggest awk or perl code for the same?

Thanks
RV