Merge branch 'dev' into 'master'

dev into master

See merge request tron/easyquant!16

.gitignore

@@ -10,3 +10,8 @@ example_out*
 *.pyc
 
 *.Rproj
+
+.idea/
+dist
+easy_quant.egg-info
+build

.gitlab-ci.yml

@@ -0,0 +1,19 @@
+stages:
+  - test
+  - deploy
+
+test_pipeline:
+  image: condaforge/mambaforge:23.3.1-0
+  stage: test
+  script:
+    - mamba env create -f environment.yml --prefix conda_env/
+    - source /opt/conda/bin/activate conda_env/
+    - pip install .
+    - bash run_test.sh
+
+deploy-job:      # This job runs in the deploy stage.
+  stage: deploy  # It only runs when *both* jobs in the test stage complete successfully.
+  environment: production
+  script:
+    - echo "Deploying application..."
+    - echo "Application successfully deployed."

MANIFEST.in

@@ -0,0 +1 @@
+include requirements.txt

README.md

@@ -1,4 +1,4 @@
-# easyquant
+# bp-quant
 
 *Quantification of reads at defined positions to verify custom input sequences.*
 
@@ -13,67 +13,83 @@ breakpoint (spanning pairs).
 - Input:
     - Table with target sequences and breakpoints position (CSV/TSV format)
     - fastq files / BAM file (BAM input only works in combination with STAR as aligner)
+- Convert target sequences to FASTA format (`bp_quant csv2fasta`)
 - Map reads against sequences using STAR/Bowtie2/BWA
-    - Generate Index of sequences as reference
-    - Map reads
-- Count reads using `requantify.py`
+    - Generate Index of sequences as reference (`bp_quant index`)
+    - Map reads (`bp_quant align`)
+- Count reads using `bp_quant count`
 - Output: 
     - Table with read counts per input sequence
 
 ## Dependencies
 
- - Python 3
-   - pysam (>= 0.16.0.1)
- - STAR (>= 2.7.8a)
- - samtools (>= 1.9)
- - bowtie2 (>= 2.4.4)
- - bwa (>= 0.7.17)
+Look at this [environment.yml](https://github.com/TRON-Bioinformatics/easyquant/blob/master/environment.yml) for the individual dependencies (Hint: File can also be used to build conda environment).
+
 
 ## Installation
 
+```
+# Create conda environment from above or add the dependencies to your path
+pip install bp-quant
+```
+
+Alternatively, bp-quant can be installed from [github repository](https://github.com/TRON-Bioinformatics/easyquant.git):
+
 ```
 git clone https://github.com/TRON-Bioinformatics/easyquant.git
 
-mv config.ini.sample config.ini
+cd easyquant
 
 # If you have conda installed you can simply install the environment like this
-conda env create -f environment.yml
+conda env create -f environment.yml --prefix conda_env/
+conda activate conda_env/
 
-# Otherwise you have to adjust the path to the different tools in your config.ini
+pip install .
 ```
 
-
 ## Usage
 
-
 ```
-usage: easy_quant.py [-h] [-1 FQ1] [-2 FQ2] [-b BAM] -s SEQ_TAB -o OUTPUT_FOLDER [-d BP_DISTANCE] [--allow_mismatches]
-                     [--interval_mode] [-m {star,bowtie2,bwa}] [-t NUM_THREADS] [--star_cmd_params STAR_CMD_PARAMS]
+usage: bp_quant pipeline [-h] [-1 FQ1] [-2 FQ2] [-b BAM] -s SEQ_TAB -o
+                           OUTPUT_FOLDER [-d BP_DISTANCE] [--allow_mismatches]
+                           [--interval_mode] [-m {star,bowtie2,bwa}]
+                           [-t NUM_THREADS]
+                           [--star_cmd_params STAR_CMD_PARAMS]
+                           [--keep_bam | --keep_all]
 
-Processing of demultiplexed FASTQs
+Runs the complete EasyQuant pipeline
 
 optional arguments:
   -h, --help            show this help message and exit
   -1 FQ1, --fq1 FQ1     Specify path to Read 1 (R1) FASTQ file
   -2 FQ2, --fq2 FQ2     Specify path to Read 2 (R2) FASTQ file
   -b BAM, --bam_file BAM
-                        Specify path to input BAM file as alternative to FASTQ input
+                        Specify path to input BAM file as alternative to FASTQ
+                        input
   -s SEQ_TAB, --sequence_tab SEQ_TAB
-                        Specify the reference sequences as table with colums name, sequence, and position
-  -o OUTPUT_FOLDER, --output-folder OUTPUT_FOLDER
+                        Specify the reference sequences as table with colums
+                        name, sequence, and position
+  -o OUTPUT_FOLDER, --output_folder OUTPUT_FOLDER
                         Specify the folder to save the results into.
   -d BP_DISTANCE, --bp_distance BP_DISTANCE
-                        Threshold in base pairs for the required overlap size of reads on both sides of the breakpoint for
+                        Threshold in base pairs for the required overlap size
+                        of reads on both sides of the breakpoint for
                         junction/spanning read counting
-  --allow_mismatches    Allow mismatches within the region around the breakpoint determined by the bp_distance parameter
+  --allow_mismatches    Allow mismatches within the region around the
+                        breakpoint determined by the bp_distance parameter
   --interval_mode       Specify if interval mode shall be used
   -m {star,bowtie2,bwa}, --method {star,bowtie2,bwa}
                         Specify alignment software to generate the index
   -t NUM_THREADS, --threads NUM_THREADS
                         Specify number of threads to use for the alignment
   --star_cmd_params STAR_CMD_PARAMS
-                        Specify STAR commandline parameters to use for the alignment
+                        Specify STAR commandline parameters to use for the
+                        alignment
+  --keep_bam            Do not delete alignment in BAM format during clean up
+                        step
+  --keep_all            Do not perform clean up step after re-quantification
 
+Copyright (c) 2023 TRON gGmbH (See LICENSE for licensing details)
 ```
 
 ### Use case with example data
@@ -84,28 +100,28 @@ with input sequences and positions, as well as two fastq files / one BAM file.
 Fastqs as input:
 
 ```
-python easy_quant.py \
+bp_quant pipeline \
   -1 example_data/example_rna-seq_R1_001.fastq.gz \
   -2 example_data/example_rna-seq_R1_001.fastq.gz \
   -s example_data/CLDN18_Context_seq.csv \
   -d 10 \
   -o example_out \
   -m star \
   -t 6
-  [--interval-mode]
+  [--interval_mode]
 ```
 
 BAM as input:
 
 ```
-python easy_quant.py \
+bp_quant pipeline \
   -b example_data/example_rna-seq.bam \
   -s example_data/CLDN18_Context_seq.csv \
   -d 10 \
   -o example_out \
   -m star \
   -t 6
-  [--interval-mode]
+  [--interval_mode]
 ```