Add clustal output format as an option #50
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I decided to add a flag for sequence type, partially because I just want to move on, but also because ambiguous IUPAC codes can make the automatic determination of sequence type more difficult and not entirely reliable. |
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Hello @uzbit! |
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This is a preliminary pull request to add clustal output format. Now you can add the flag -output_format <fasta|clustal> and the appropriate output will be given, with default fasta as before.
This is work on closing issue #42 .
One thing that needs to be discussed, is that the output format for clustal is different between DNA/Amino, and so there should be some way of determining this from the input or as another flag maybe? Currently it just assumes AA, which will give misleading output for DNA.