From mboxrd@z Thu Jan  1 00:00:00 1970
Date: Fri, 08 Jul 2016 01:03:48 -0700
From: Endre Bakken Stovner <notifications@github.com>
Reply-To: kyleam/snakemake-mode <reply+0013cd7c3974a9f08f43748664edced11353b143675f7aa392cf000000011397206492a169ce09cdb427@reply.github.com>
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In-Reply-To: <kyleam/snakemake-mode/issues/18@github.com>
References: <kyleam/snakemake-mode/issues/18@github.com>
Subject: Re: yapf for snakefiles (#18)
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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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<p>Perhaps the easiest way to do this would be to </p>

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

<p>So that the below </p>

<pre><code>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=" ")
</code></pre>

<p>becomes</p>

<pre><code>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=" ")
</code></pre>

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

<pre lang=""><code>
Just throwing it out there for criticism. It is very, very hackish, but seems like the minimally intrusive way of using yapf with snakefiles.
</code></pre>

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