User: moldach686

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moldach68630
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Posts by moldach686

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Extract Reads From A Bam File That Fall Within A Given Region
... **WARNING** THIS WILL CREATE HEADERLESS FILE POSSIBLY LEADING TO DOWNSTREAM ERRORS: _e.g._ ``` $ samtools sort -n HG002_Chr22.bam -o HG002_Chr22_sort.bam [E::sam_parse1] no SQ lines present in the header samtools sort: truncated file. Aborting $ bedtools bamtofastq -i HG002_Chr22.bam -fq HG002_Ch ...
written 6 days ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Your sample solution using dummy-data worked great! Since we ran out of space above, to summarize: Accept data from a `samples.txt` files via: # getting the samples information (names, path to r1 & r2) from samples.txt samples_information = pd.read_csv("samples.txt", sep='\t', index_ ...
written 4 months ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Worked for me. I've made a PR regarding how to include the directories that come before `"{sample}_R1_fastqc.html"`: How do I tell `"{QC_DIR}/{QC_TOOL}/{sample}_R1_fastqc.html"` comes from `QC_DIR=dirs_dict["QC_DIR"], QC_TOOL=config["QC_TOOL"])`? For example, if there was no *dynamically* genera ...
written 5 months ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Yes I had also tried that. >>> def getHome(sample): ... return(list(os.path.join(samples_dict[sample],"{0}_{1}.fastq.gz".format(sample,pair)) for pair in ['R1','R2'])) ... snakemake -n -r Building DAG of jobs... InputFunctionException in line 31 of /SNAKEMAKE/DEM ...
written 5 months ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... A rose by any other name `samples_set = dict(zip(sample_names, sample_locations))` So does the function then need to be changed? >>> samples_set = dict(zip(sample_names, sample_locations)) >>> def getHome(sample): ... return(list(os.path.join(dict(samples_se ...
written 5 months ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... Thanks Jeremy, I think there is some progress snow: >>> import os >>> import pandas as pd >>> samples_information = pd.read_csv("samples.txt", sep='\t', index_col=False) >>> sample_names = list(samples_information['sample']) >>> sam ...
written 5 months ago by moldach68630
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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 /SNAKEMAKE/DEMO/Snakefile: ...
written 5 months 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 5 months ago by moldach68630
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Comment: C: Using wildcards to accept paired-end reads from Snakemake
... >>> dict(samples_set) {'BC1217': '/foo/bar/pow/', '470': '/wam/bam/crash/', 'MTG109': '/penguin/fire/station/'} ...
written 5 months 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 5 months ago by moldach68630

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