/utilities

random useful scripts for my projects

Primary LanguagePython

Utilities

Setup

To use this it is probably best to load the anaconda enviorment on the cluster

#!/usr/bin/env bash
unset PYTHONPATH
module purge
. /etc/profile.d/modules.sh
module load modules modules-init modules-gs/prod modules-eichler
module load anaconda/201710

or just

source conda.cfg

SeqLengths.py

This seems to need miniconda/4.5.12

SeqLengths.py --help
usage: SeqLengths.py [-h] [-f FOFN] [-o OUT] [-p PLOT] [--plotwith PLOTWITH]
                     [-t THREADS]
                     [infiles [infiles ...]]

Get the lengths of reads from fasta/fastq/(.gz) files.

positional arguments:
  infiles               input fasta/fastq file

optional arguments:
  -h, --help            show this help message and exit
  -f FOFN, --fofn FOFN  input FOFN of fasta/fastq files, replaces infiles
                        argument
  -o OUT, --out OUT     output lengths file. Has the form: readname, length
  -p PLOT, --plot PLOT  Specify a place to plot a hsitogram of read lengths
  --plotwith PLOTWITH   If you have already calcualted readlength before you
                        can specify plotwith to avoid rereading the fasta
                        files
  -t THREADS, --threads THREADS
                        number of threads to use, only used in reading in
                        fasta/fastq files

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