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4

$f in your command is not pointing anywhere since your for loop was defined as for file in *.vcf;. You should use $file instead of $f. EDIT AS THE OP HAS EDITED THE QUESTION: First of all, please copy and paste the error messages you are getting when seeking answers from the community, most of the time the error messages are clear enough to point to the ...


2

You can use ifelse(): anno_maf$COSMIC <- ifelse(anno_maf$Hugo_Symbol %in% your_gene_list, yes = "yes", no = "no")


2

You are using the argument values incorrectly. Argument values are sample attributes, not full character paths. Hence, "IU" is a sample attribute, "gencode_mouse_m13" is a sample attribute, so why would you think "/scratch..." would be treated any differently? The pipeline interface maps sample attributes to command-line arguments. It is modulated by sample ...


2

As explained in the pep docs, the sample_name column should be considered a unique identifier for a sample. The PEP requires that One row corresponds to one sample You have multiple rows with the same name; this is not allowed. You simply need to recast your annotation sheet such that it has file1 and file2 columns, but only 2 rows.


1

The basic outline for loops is for sample in *; do mycommand "$sample" ; done You might need some way of incorporating the name of $sample into the output file name, so you don't keep overwriting the same output file over and over again (or do mkdir with each sample name and write everything for each sample in its own folder).


1

Assuming the names of all the files from one group are in file named list. cat pre_post.list | awk '{print $2}' | sed 's@.*/@@' > post_list.txt cat pre_post.list | awk '{print $1}' | sed 's@.*/@@' > pre_list.txt Now you have two number list for item in $(cat pre_list.txt | grep -Eo '[0-9]{1,4}'); do if grep -q $item clin_name.txt ; ...


1

I believe that uniqsampleID = 1:length(unique(mutations$sampleID)) names(uniqsampleID) = unique(mutations$sampleID) mutations$sampleID = uniqsampleID[mutations$sampleID] should work, assuming mutations is a data frame. Explanation: 1:N creates a vector of length N, containing 1, 2, ..., N. So using 1:length(X) will do this for each item in X, so 1:...


1

Looper does not generate any of these per-sample outputs. Looper does not have any control over where your pipeline puts its outputs. The problem is in your pipeline, not in looper. Assuming you're using a pypiper pipeline, I suggest reading the docs; for example, the "your first pipeline" tutorial: http://pypiper.readthedocs.io/en/latest/tutorials-first....


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