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From: Endre Bakken Stovner <notifications@github.com>
To: kyleam/snakemake-mode <snakemake-mode@noreply.github.com>
Subject: Re: yapf for snakefiles (#18)
Date: Fri, 08 Jul 2016 01:03:48 -0700	[thread overview]
Message-ID: <kyleam/snakemake-mode/issues/18/231299696@github.com> (raw)
In-Reply-To: <kyleam/snakemake-mode/issues/18@github.com>

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Perhaps the easiest way to do this would be to 

1) replace all the stuff that is snakemake-specific with syntactically valid placeholders,
2) then run yapf on the modified file
3) then re-insert the snakemake specific stuff...

So that the below 
```
rule get_gene_expression:
    input:
        expression_matrix
    output:
        "data/expression/series.csv"
    run:
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")
```

becomes

```
for i in [1]: # snakemake
    for j in [2]: # snakemake
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")
```

which you then can run yapf on. After yapf is run, the placeholder `for i in [1] #snakemake`  is replaced with `rule get_gene_expression:`, `for i in [2] #snakemake` is replaced with ```    input:
        expression_matrix
    output:
        "data/expression/series.csv"
    run:
```.

Just throwing it out there for criticism. It is very, very hackish, but seems like the minimally intrusive way of using yapf with snakefiles.

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  reply	other threads:[~2016-07-08  8:03 UTC|newest]

Thread overview: 6+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2016-07-08  7:41 Endre Bakken Stovner
2016-07-08  8:03 ` Endre Bakken Stovner [this message]
2020-04-14  2:10   ` Kyle Meyer
2016-07-09 11:18 ` Endre Bakken Stovner
2020-04-14  2:11   ` Kyle Meyer
2016-10-21 21:30 ` Kyle Meyer

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