louisfaure / bulktools-py

python CLI for full bulk RNAseq pipeline, from fastq to anndata count matrix

bulktools-py

Analysis pipeline for bulk data. From fastq to anndata containing count matrix.

Installation

conda create -n bulktools -c bioconda -c defaults star subread python=3.8 -y
conda activate bulktools
pip install git+https://github.com/LouisFaure/bulktools-py.git

Usage

To work by default, the data structure should look like this:

├── fastq/ <-- the first element of the filename before '_' is the sample name
│   ├── sample1_S1_R1_L001.fastq.gz
│   └── sample2_S2_R1_L001.fastq.gz
├── genes.gtf <-- genome annotation
├── star_index/ <-- index folder created using STAR tool
│   ├── ...

Command

bt -s star_index -g genes.gtf

Full usage

usage: bt [-h] [--fq_path FQ_PATH] [--bam_path BAM_PATH] [--star_ref STAR_REF] [--gtf GTF]
          [--n_threads N_THREADS] [--adata_out ADATA_OUT]
          [cleanup]

Full bulk pipeline, from fastq to adata count matrix!
Performs the following: fastq -STAR-> bam -featureCounts-> anndata.h5ad

positional arguments:
  cleanup               remove temporary folders and files.

optional arguments:
  -h, --help            show this help message and exit
  --fq_path FQ_PATH, -f FQ_PATH
                        Path for input fastq files (relative, default: fastq).
  --bam_path BAM_PATH, -b BAM_PATH
                        Path for aligned BAMs (default: aligned).
  --star_ref STAR_REF, -s STAR_REF
                        STAR index path.
  --gtf GTF, -g GTF     GTF file path for featureCounts.
  --n_threads N_THREADS, -n N_THREADS
                        Total number of threads to use for both STAR and featureCounts.
  --adata_out ADATA_OUT, -o ADATA_OUT
                        Path for the adata output (relative, default: adata_bulk_star.h5ad).

bulktools-py's Issues

Different fastq files

Hi

I am really interested in try this package, I always wanted to run DESeq in python, but I have a doubt, If I have several fastq files from different replicates of each condition. Should I run the bulk pipeline for each fastq file and then merge the adata output? Does the pipeline recognize different fastq file in the folder?

Is there any Jupiter notebook available to see an example?

Thanks

Victor

Error installing package

Hi Louis,

I tried to install the package (using conda as you indicated) and I had the following error:

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for bulktools

Running setup.py clean for bulktools
Failed to build bulktools
Installing collected packages: pytz, commonmark, typing-extensions, six, pyparsing, pygments, numpy, natsort, scipy, rich, python-dateutil, packaging, h5py, pandas, anndata, bulktools
Running setup.py install for bulktools ... error
error: subprocess-exited-with-error

กม Running setup.py install for bulktools did not run successfully.
ฉฆ exit code: 1
จtฉค> [20 lines of output]
running install
/home/victor/miniconda3/envs/bulktools/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib
creating build/lib/bulktools
copying bulktools/init.py -> build/lib/bulktools
copying bulktools/pipeline.py -> build/lib/bulktools
running egg_info
writing bulktools.egg-info/PKG-INFO
writing dependency_links to bulktools.egg-info/dependency_links.txt
writing entry points to bulktools.egg-info/entry_points.txt
writing requirements to bulktools.egg-info/requires.txt
writing top-level names to bulktools.egg-info/top_level.txt
reading manifest file 'bulktools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'bulktools.egg-info/SOURCES.txt'
error: [Errno 2] No such file or directory: 'make'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

กม Encountered error while trying to install package.
จtฉค> bulktools

Could you give me any advice, please?

Best

Victor