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I have a large number of input files organized like this: data/ ├── set1/ │ ├── file1_R1.fq.gz │ … Read more Snakemake - Dynamically Derive The Targets From Input Files

I'm working on a script that currently contains multiple lists of DNA sequences (each list has … Read more Algorithm To To Cluster Similar Strings In Python?

I am using the following regex: orfre = '^(?:...)*?((ATG)(...){%d,}?(?=(TAG|TAA|TGA)))' % (… Read more Using Regex To Search Until Desired Pattern

I just wrote a function that will look at a text file and count all of the instances of True and Fa… Read more What Causes Python Error 'bad Escape \c'?

I need to extract Gleason scores from a flat file of prostatectomy final diagnostic write-ups. Thes… Read more Pyparsing: Extract Variable Length, Variable Content, Variable Whitespace Substring

I'm trying to assign flat, single-linkage clusters to sequence IDs separated by an edit distanc… Read more Single Linkage Clustering Of Edit Distance Matrix With Distance Threshold Stopping Criterion