Add spliting of peptides with python. #29
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General best practice would be to put this in a |
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OK, will do! :) |
main.nf
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| @@ -38,6 +38,8 @@ def helpMessage() { | |||
| --max_peptide_length [int] Specifies the maximum peptide length Default: MHC class I: 11 aa, MHC class II: 16 aa | |||
| --min_peptide_length [int] Specifies the minimum peptide length Default: MCH class I: 8 aa, MHC class II: 15 aa | |||
| --tools [str] Specifies a list of tool(s) to use. Available are: 'syfpeithi', 'mhcflurry', 'mhcnuggets-class-1', 'mhcnuggets-class-2'. Can be combined in a list separated by comma. | |||
| --split_peptides_maxchunks [int] Used in combination with '--peptides' or '--proteins': maximum number of peptide chunks that will be created for parallelization. Default: 100 | |||
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How about --peptides_split_maxchunksand --peptides_split_chunksize?
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split_peptides_minsize is just the min. chunk size (apart for one file that contains the rest), it will become bigger if necessary to avoid more than peptides_split_maxchunks chunks .
--peptides_split_minchunksize or would that be too long?
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I'm wondering if we even need both. Wouldn't it be enough to let users define the max number of chunks?
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You mean the actual number of chunks that is created? That would be a third parameter, but yes it might be a good solution to keep it simple. Or do you really not want to change the *-minchunksize parameter, then we could let the user define *-maxchunks, I just understood that you wanted to change that as well ...
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I mean that it might be sufficient to have a maxchunksparameter since that defines the size of the chunks anyway indirectly.
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#28
Ok, I did it in python in the end. With this max. 100 chunks will be created and only files with more than 5000 peptides will be split.That's what I would assume might be useful also for others. Let me know if you think this could be optimised.
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