tb-consensus-aligner 1.0.0__tar.gz

tb_consensus_aligner-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: tb_consensus_aligner
+Version: 1.0.0
+Summary: Building consensus fasta files and variable multi-sequence alignments for mycobacterial genomes.
+Author-email: scg40 <gian.schuepbach@swisstph.ch>
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Requires-Dist: biopython>=1.80
+
+# TBConsensusAligner
+TBConsensusAligner is a tool designed to create a multi-sequence alignment via consensus 
+genomes created from VCF files. 
+It can currently be used in different modes as follows
+- VCF to SNP alignment `-s all`
+    - input = VCFs, output = SNP alignment
+    - runs `consensus_galaxy.py` and `snp_aligner_galaxy.py`
+
+- VCF to consensus FASTA files `-s consensus`
+    - input = VCFs, output = consensus FASTA files
+    - runs only `consensus_galaxy.py`
+
+If the script produces a SNP alignment from VCFs, the user can choose whether to ouptut just the SNP alignment
+or the used consensus FASTA files as well with the `-m` option. 
+
+When running the `consensus_galaxy.py` the user has to provide the VCF files, the reference genome used in their creation and the multisample
+depth file from bamtools depth. Optionally, the user can provide one or several BED files to mask certain regions of the genome.
+
+## Usage
+The script is run via the command line.
+
+***usage***:
+
+```
+Usage:   TBConsensusAligner [options] 
+
+Options: -s STR         ['consensus' or 'all'] Create either consensus files or consensus files and a variable alignment
+
+         -m STR         ['everything' or 'alignment_only'] If -s all is chosen, output either consensus files and the alignment or just the alignment
+
+         -v list[STR]   Path to the input VCF files
+
+         -r STR         Path to the reference genome
+
+         -d STR         Path to the depth file created by samtools depth
+
+         -c STR         Path to the outgroup VCF for the alignment
+
+         -b list[STR]   Path to the BED files to mask certain genomic regions
+
+         -o STR         Path to the output directory
+
+         -g FLOAT       Percentage of undefined states allowed per polymorphic position in the alignment default at 90 percent value=0.9
+
+         -t BOOLEAN     Test Mode to run the script with smaller genomes
+
+```
+
+## Example usages command line
+
+### From 3 VCFs to alignment, output consensus FASTAs and SNP alignment, masked by two bedfiles 
+
+```
+python yourfolder/galaxy_main.py \
+-s all \
+-m everything \
+-v path/to/vcf1/vcf1.vcf -v path/to/vcf2/vcf2.vcf -v path/to/vcf2/vcf2.vcf \
+-r path/to/reference/reference_genome.reference.fasta \
+-d path/to/depthfile/depthfile.tabular \
+-c path/to/outgroupvcf/outgroup.vcf \
+-b path/to/bedfile1/bed1.bed -b path/to/bedfile2/bed2.bed \
+-o output
+-g 0.9
+
+```
+
+## Logic consensus_galaxy.py 
+
+This script produces consensus FASTA files from VCFs. The user provides the VCFs, the reference genome,
+the multisample depth file obtained from `bamtools depth` and optionally BED files to mask certain genomic regions.
+
+***algorithm***
+
+We loop through each position in the reference genome and build the consensus sequence base per base with the following rules:
+
+```
+- SNPs and MNPs with a frequency >90% are encoded with the alternative base from the VCF.
+- SNPs and MNPs with a frequency between 10% and 90% are encoded with the ambiguity base.
+- SNPs and MNPs with a frequency <10% are encoded with the ancestral base from the reference genome.
+
+- Large deletions (coverage 0) are encoded by dashes (-).
+- Small deletions with frequency >90% are encoded by dashes (-).
+- Small deletions with frequency between 10% and 90% are encoded with a 'N'.
+- Small deletions with frequency <10% are encoded with the ancestral base from the reference genome.
+
+- Small insertions (alternative bases longer than reference base) are encoded with the ancestral state from the reference genome.
+
+- Sites to exclude specified in the bed files are encoded with a 'N'.
+- Variants that have a phred score < 20 are encoded with a 'N'.
+- Sites that are not in the VCF and are covered by less than 5 reads (via depth file) are encoded with a 'N'.
+
+- If more than one ALT allele is present, we consider the one with the highest allele frequency.
+```
+Since the VCF for which the script is tailored to does not have the allele frequency `AF` calculated, we calculate it using 
+`RO = REF allele occurance` and `AO = ALT allele occurance` with 
+`AF = AO / ( sum(all AO's) + RO )`.
+
+## Logic snp_aligner_galaxy.py
+
+This script produces a SNP alignment i.e. multi-sequence alignment of polymorphic positions in FASTA format from consensus FASTA files.
+The consensus FASTAs are generated in the previous step by `consensus_galaxy.py` wrapped in `TBConsensusAligner`.
+
+***algorithm***
+
+The script creates a multi-sequence alignment from the consensus FASTAs in form of an 2D array where each row represents a sequence
+and each column a genomic position. Each column is checked for the abundance of a polymorphism. If such a polymorphism is detected,
+the column is appended to the alignment of polymorphic positions. For each polymorphic position, the corresponding nucleotide from 
+outgroup VCF is retrieved to get the outgroup's sequence.
+
+The algorithm to populate the multi-sequence alignment of polymorphic positions is asd follows.
+The user can control the proportion of gaps or undefined states (`-`or`N`) for a polymorphic position
+to be kept in the alignment (argument `-g`). By default, this is set to `0.9`, meaning that if a polymorphic position has 
+more than 90% gaps or undefined states, it will not be in the final alignment.
+
+## Directory structure used for development
+
+* TBConsensusAligner
+    * test_data
+        - snp_alignment.fasta
+        - test_G77777.consensus.fasta
+        - test_G77777.vcf.gz
+        - test_G88888_k1.consensus.fasta
+        - test_G88888_k1.vcf.gz
+        - test_G99999.k2.consensus.fasta
+        - test_G99999.k2.vcf.gz
+        - test_Galaxy_multiple_depths_header.tabular
+        - test_reference_200bp.reference.fasta
+        - test_regions_blindspots_modlin_farhat_and_PE_PPE_PGRS.bed
+        - test.outgroup.all.pos.vcf.gz
+    - consensus_galaxy.py
+    - main_galaxy.py
+    - README.md
+    - snp_aligner_galaxy.py
+    - TBConsensusAligner.xml
+
+
+
+

tb_consensus_aligner-1.0.0/README.md

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+# TBConsensusAligner
+TBConsensusAligner is a tool designed to create a multi-sequence alignment via consensus 
+genomes created from VCF files. 
+It can currently be used in different modes as follows
+- VCF to SNP alignment `-s all`
+    - input = VCFs, output = SNP alignment
+    - runs `consensus_galaxy.py` and `snp_aligner_galaxy.py`
+
+- VCF to consensus FASTA files `-s consensus`
+    - input = VCFs, output = consensus FASTA files
+    - runs only `consensus_galaxy.py`
+
+If the script produces a SNP alignment from VCFs, the user can choose whether to ouptut just the SNP alignment
+or the used consensus FASTA files as well with the `-m` option. 
+
+When running the `consensus_galaxy.py` the user has to provide the VCF files, the reference genome used in their creation and the multisample
+depth file from bamtools depth. Optionally, the user can provide one or several BED files to mask certain regions of the genome.
+
+## Usage
+The script is run via the command line.
+
+***usage***:
+
+```
+Usage:   TBConsensusAligner [options] 
+
+Options: -s STR         ['consensus' or 'all'] Create either consensus files or consensus files and a variable alignment
+
+         -m STR         ['everything' or 'alignment_only'] If -s all is chosen, output either consensus files and the alignment or just the alignment
+
+         -v list[STR]   Path to the input VCF files
+
+         -r STR         Path to the reference genome
+
+         -d STR         Path to the depth file created by samtools depth
+
+         -c STR         Path to the outgroup VCF for the alignment
+
+         -b list[STR]   Path to the BED files to mask certain genomic regions
+
+         -o STR         Path to the output directory
+
+         -g FLOAT       Percentage of undefined states allowed per polymorphic position in the alignment default at 90 percent value=0.9
+
+         -t BOOLEAN     Test Mode to run the script with smaller genomes
+
+```
+
+## Example usages command line
+
+### From 3 VCFs to alignment, output consensus FASTAs and SNP alignment, masked by two bedfiles 
+
+```
+python yourfolder/galaxy_main.py \
+-s all \
+-m everything \
+-v path/to/vcf1/vcf1.vcf -v path/to/vcf2/vcf2.vcf -v path/to/vcf2/vcf2.vcf \
+-r path/to/reference/reference_genome.reference.fasta \
+-d path/to/depthfile/depthfile.tabular \
+-c path/to/outgroupvcf/outgroup.vcf \
+-b path/to/bedfile1/bed1.bed -b path/to/bedfile2/bed2.bed \
+-o output
+-g 0.9
+
+```
+
+## Logic consensus_galaxy.py 
+
+This script produces consensus FASTA files from VCFs. The user provides the VCFs, the reference genome,
+the multisample depth file obtained from `bamtools depth` and optionally BED files to mask certain genomic regions.
+
+***algorithm***
+
+We loop through each position in the reference genome and build the consensus sequence base per base with the following rules:
+
+```
+- SNPs and MNPs with a frequency >90% are encoded with the alternative base from the VCF.
+- SNPs and MNPs with a frequency between 10% and 90% are encoded with the ambiguity base.
+- SNPs and MNPs with a frequency <10% are encoded with the ancestral base from the reference genome.
+
+- Large deletions (coverage 0) are encoded by dashes (-).
+- Small deletions with frequency >90% are encoded by dashes (-).
+- Small deletions with frequency between 10% and 90% are encoded with a 'N'.
+- Small deletions with frequency <10% are encoded with the ancestral base from the reference genome.
+
+- Small insertions (alternative bases longer than reference base) are encoded with the ancestral state from the reference genome.
+
+- Sites to exclude specified in the bed files are encoded with a 'N'.
+- Variants that have a phred score < 20 are encoded with a 'N'.
+- Sites that are not in the VCF and are covered by less than 5 reads (via depth file) are encoded with a 'N'.
+
+- If more than one ALT allele is present, we consider the one with the highest allele frequency.
+```
+Since the VCF for which the script is tailored to does not have the allele frequency `AF` calculated, we calculate it using 
+`RO = REF allele occurance` and `AO = ALT allele occurance` with 
+`AF = AO / ( sum(all AO's) + RO )`.
+
+## Logic snp_aligner_galaxy.py
+
+This script produces a SNP alignment i.e. multi-sequence alignment of polymorphic positions in FASTA format from consensus FASTA files.
+The consensus FASTAs are generated in the previous step by `consensus_galaxy.py` wrapped in `TBConsensusAligner`.
+
+***algorithm***
+
+The script creates a multi-sequence alignment from the consensus FASTAs in form of an 2D array where each row represents a sequence
+and each column a genomic position. Each column is checked for the abundance of a polymorphism. If such a polymorphism is detected,
+the column is appended to the alignment of polymorphic positions. For each polymorphic position, the corresponding nucleotide from 
+outgroup VCF is retrieved to get the outgroup's sequence.
+
+The algorithm to populate the multi-sequence alignment of polymorphic positions is asd follows.
+The user can control the proportion of gaps or undefined states (`-`or`N`) for a polymorphic position
+to be kept in the alignment (argument `-g`). By default, this is set to `0.9`, meaning that if a polymorphic position has 
+more than 90% gaps or undefined states, it will not be in the final alignment.
+
+## Directory structure used for development
+
+* TBConsensusAligner
+    * test_data
+        - snp_alignment.fasta
+        - test_G77777.consensus.fasta
+        - test_G77777.vcf.gz
+        - test_G88888_k1.consensus.fasta
+        - test_G88888_k1.vcf.gz
+        - test_G99999.k2.consensus.fasta
+        - test_G99999.k2.vcf.gz
+        - test_Galaxy_multiple_depths_header.tabular
+        - test_reference_200bp.reference.fasta
+        - test_regions_blindspots_modlin_farhat_and_PE_PPE_PGRS.bed
+        - test.outgroup.all.pos.vcf.gz
+    - consensus_galaxy.py
+    - main_galaxy.py
+    - README.md
+    - snp_aligner_galaxy.py
+    - TBConsensusAligner.xml
+
+
+
+

tb_consensus_aligner-1.0.0/pyproject.toml

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+[build-system]                              # Define the tools needed to build the project
+requires = ["setuptools>=61.0.0", "wheel"]  # Use Version 61.0.0 or newer
+build-backend = "setuptools.build_meta"     # USe setuptools to process metadata configuration
+
+[project]                                   # Human readable description
+name = "tb_consensus_aligner"               # Official name of the package
+version = "1.0.0"                           # Current version
+description = "Building consensus fasta files and variable multi-sequence alignments for mycobacterial genomes."    
+readme = "README.md"                        # Use the README.md file as the official documentation that is being opened
+requires-python = ">=3.8"
+authors = [
+    {name = "scg40", email = "gian.schuepbach@swisstph.ch"}
+]
+classifiers = [                             # Key words used to categorize the tool
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+dependencies = [                            # Automatically checks if Biopython is installed, if not, installs installed
+    "biopython>=1.80"
+]
+
+[project.scripts]                           # Craete command line shortcut
+tb-consensus-aligner = "tb_consensus_aligner.main_galaxy:main"
+
+[tool.setuptools]                           # Dictate to setuptools which folder contains the scripts
+packages = ["tb_consensus_aligner"]

tb_consensus_aligner-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+