Marcel Martin marcelm
marcelm
/ snakemake-pure-python.py
Last active
November 29, 2023 00:45
pure Python module that uses snakemake to construct and run a workflow
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| #!/usr/bin/env python3 | |
| """ | |
| Running this script is (intended to be) equivalent to running the following Snakefile: | |
| include: "pipeline.conf" # Should be an empty file | |
| shell.prefix("set -euo pipefail;") | |
| rule all: | |
| input: |
marcelm
/ info-file-with-qualities.patch
Created
April 16, 2015 14:58
hack to print out qualities in cutadapt’s info file (will crash when trimming FASTA files)
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| diff --git i/cutadapt/scripts/cutadapt.py w/cutadapt/scripts/cutadapt.py | |
| index 855721d..2eaf435 100755 | |
| --- i/cutadapt/scripts/cutadapt.py | |
| +++ w/cutadapt/scripts/cutadapt.py | |
| @@ -155,6 +155,7 @@ class AdapterCutter(object): | |
| # TODO write only one line, even for multiple matches | |
| for match in matches: | |
| seq = match.read.sequence | |
| + qualities = match.read.qualities | |
| if match is None: |
marcelm
/ star-segfault.fasta
Created
September 23, 2014 16:54
trying to map this to Danio rerio Zv9 with STAR leads to a segfault
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| >segfault | |
| AACTGGAGCAGGTCCTGGTATTCTAACATTAATGTCTCCAGATGAACGCCCATAAACTTGGCTTTCACCTCAAACACTCC | |
| CACAGTCTCTGATGGCGAGATCTCGAAAATTGCATTCTTATACTGATTTGTCTGCAGATCATCGATGTCAATAAGCACTC | |
| CCTTCTCATGCAGACGGGCTGCTGTGTACTTCTGTGATACCTGCTTGCTCTTCTTTGCCTGTTTATCTCCAGGTTTCTTA | |
| GAAACTTTTCCCTTGCTCCCTAAATTGTCCATGCAGGTCTTGATGTACTGATTGTAGTAGTCAATCTGCTCGTTGTAGAA | |
| GGTTGCGGATGTCCTTGGCGATGTCATTGATTAGGTCCTGGTATTTCTTCTCAGGGTGTACTTTGCCCAACTCTCCCAGT | |
| CTTTGCAGGTTGCTCTTGATCTTGTCCTTCTTGCCTTGCAAAGTAAGACTGTCATCTACAACTGGTTTGGCTTGCTTCAT | |
| CTTCTCTGGGGTCTTTGCATCGCGAATGGCTCGCCGCTGCATAGCTCGCTGGTACTCTGCTTCCTGCTCAGGTGAAGCTA | |
| CAGTCTCCAGAATCTCAGTAAGTGTGTCTCCTGGCTGAAATCTGATCACATCTACTATGAGCCTCTTGGTGTTAAGGAGA | |
| AGAGTTTTGGCATCCATTTCAGCATTGGCCTCATCGGGAACATCAAATTTGTTGGTGAGGGTGAGGGAGACTTCTGTCTT |
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