Remove-Filter specific sequences from fasta files.
Hello, I have a fasta file with some invalid charachters in some sequences. Those invalid characters are either * or X. I would like to create a new fasta file withour those sequences on it. How can i do this in easy way ? In terminal ?
My fasta
>li|LinJ.02.0010:mRNA-p1
MIMKASGAAVLHAVREKMQEATVAALIVPSSDAHNSEYVATHLQARAFISHFHGSAGTAL ITMEKALLWTDGRYWLAAEEEKYPEFDLMKQGKPEVPSLEEWIAVNLGSKAVVGMNPYVA TVAEWERLSKRINLRPVANIVQDMMPPEKNVQRMYVRPVEFCGATCQERRAAILAELEKE
>li|LinJ.01.0850:mRNA-p1
MQNPEQAHAPKFSAHTDKIYPDGAFYNRIKAVHDERSSLAGEDLRLV`*`KYAEGFRRAGAG LGNAAKEKPRQANERPANPKSGFAEGGRTHGGPRCLLWVAPPGLGGLGVVGATRPKKGAR NVCYTEGKRLLTQTGRRSSRASLRGRGGHHNPF`*`ARAQRAGRGDAKDTSATTVEIAQLRL
>li|LinJ.01.0850:mRNA-p1
MQNPEQAHAPKFSAHTDKIYPDGAFYNRIKAVHDERSSLAGEDLRLV**XX**KYAEGFRRAGAG LGNAAKEKPRQANERPANPKSGFAEGGRTHGGPRCLLWVAPPGLGGLGVVGATRPKKGAR NVCYTEGKRLLTQTGRRSSRASLRGRGGHHNPF**X**ARAQRAGRGDAKDTSATTVEIAQLRL
The new fasta should have only
>li|LinJ.02.0010:mRNA-p1
MIMKASGAAVLHAVREKMQEATVAALIVPSSDAHNSEYVATHLQARAFISHFHGSAGTAL ITMEKALLWTDGRYWLAAEEEKYPEFDLMKQGKPEVPSLEEWIAVNLGSKAVVGMNPYVA TVAEWERLSKRINLRPVANIVQDMMPPEKNVQRMYVRPVEFCGATCQERRAAILAELEKE
thank you in advance
Best Dimitris
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dzisis1986 •
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Hello dzisis1986!
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Cheers!
i have seen your similar reply but at this case you are replacing the unwanted charachers with N . I would like a new fasta without those sequences with unwanted characters on it . Is it the same if i keep the masked with N sequnces on the existing fasta ? Cheers Dimitris