Modifying headers


 
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Top Forums UNIX for Dummies Questions & Answers Modifying headers
# 1  
Old 08-15-2011
Modifying headers

I have a FASTA file with thousands of sequences that looks something like this:
Quote:
>LBHCV-1-C1.seq_Contig_1_(1311)
---------TGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGCCTTGATTGTGATGCTGCTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGAGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C10.seq_Contig_1_(1312)
--------TTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGACTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C11.seq_Contig_1_(1314)
------CTTTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
I need to modfy the header in such way that everything after the dot is remove. Thus, I will end up with something like this:
Quote:
>LBHCV-1-C1
---------TGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGCCTTGATTGTGATGCTGCTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGAGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C10
--------TTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGACTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
>LBHCV-1-C11
------CTTTGGATATGATGATGAACTGGTCACCTACAGCAGCCCTGGTGGTGTCGCAGTTACTCCGGATCCCACAAGCCGTCGTGG-ATATGGTGGCGGGGGCCCACTGGGG-AATCCTGGC-GGGCCTTGCCTACTATTCCATGGTGGGGAACTGGGCTAAGGTCTTGATTGTGATGCTACTATTCGCCGGCGTTGACGGGGACACCTACACAACGGGGGGA GCGGCGGGCAAGAACGCGCAGGGCCTCACGAGCCTCTTTGCAGTCGGGGCGTCTCAGAAAATCCAGCTCGTAAACACCAACGGCAGCT-GGC-ACATCAAA---------
Thanks
# 2  
Old 08-15-2011
Try:
Code:
perl -i -pe 's/\..*//' file

 
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