User: moldach686

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moldach68630
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Posts by moldach686

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Actually before we get _too_ sidetracked... I've removed the `470` sample from the `samples.txt` just to simplify things - the error persists. Besides, the error was, and still is, pointing to `BC1217`. Building DAG of jobs... InputFunctionException in line 32 of /scratch/moldach/MADDOG/SN ...
written 3 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... I've spent some time searching for this but I have no idea how to do such a thing in Python (I use R). [There was this example of how to do the opposite of what you suggested.][1]: The original string : {"Nikhil" : 1, "Akshat" : 2, "Akash" : 3} The converted dictionary : {'Nikhil': 1, 'Aks ...
written 3 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... >>> dict(samples_set) {'BC1217': '/home/moldach/projects/def-mtarailo/common/data/strains_ucalgary/fastq/', '470': '/home/moldach/projects/def-mtarailo/tamaroi/data/', 'MTG109': '/home/moldach/projects/def-mtarailo/tamaroi/data/strains_ucalgary/fastq_MTG/'} ...
written 5 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Okay so you used `sample_dict` here which I suppose is the same as `dict(samples_set)`. I noticed I had the order for the `key` wrong earlier in `samples_set` so I've fixed that now. The following change to the snakemake file: import os import pandas as pd # getting the samples informa ...
written 7 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... I believe one of the errors is that `samples_set` was not defined properly. [Maybe it should look like this instead?][1] import os import pandas as pd # getting the samples information (names, path to r1 & r2) from samples.txt samples_information = pd.read_csv("samples.txt", sep ...
written 12 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... ummm okay, so I'm not really sure how to troubleshoot/test this? Python 3.8.0 (default, Nov 12 2019, 19:43:25) [GCC 5.4.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import os >>> import pandas as pd >>> # g ...
written 13 hours ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Okay so switching to this now produces this error: rule all: input: expand('{sample}_{pair}_fastqc.{ext}', sample=sample_names, pair=['R1', 'R2'], ext=['html', 'zip']), def getHome(sample): return(os.path.join(dict(samples_set)[sample],"{0}_{1}.fastq.gz".forma ...
written 1 day ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Do you mean in the `output` of the rule? output: expand('{QC_DIR}/{QC_TOOL}/before_trim/{sample}_{pair}_fastqc.{ext}', QC_DIR=dirs_dict["QC_DIR"], QC_TOOL=config["QC_TOOL"], sample=sample_names, pair=['R1', 'R2'], ext=['html', 'zip'] If so does this apply to `log:` and `params:` a ...
written 1 day ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... I'm getting the following error: > (snakemake) [moldach@cedar1 DEMO]$ snakemake -n -r Building DAG of jobs... InputFunctionException in line 56 of /scratch/moldach/MADDOG/SNAKEMAKE/DEMO/Snakef AttributeError: 'Wildcards' object has no attribute 'sample' Wildcards: # Directories------------- ...
written 1 day ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Sorry but I'm still confused as to what I need to do. Your suggestion is to use `os.path.join()` instead of `expand()` in wildcards rules, correct? `FASTQ_DIR` hasn't be defined anywhere so I cannot just use that - I assumed you meant you need to set `mydir` instead? Your `def getHome(sample)` f ...
written 3 days ago by moldach68630

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