from collections import namedtuple
import os
CampareeConstants = namedtuple('Constants',
['CAMPAREE_ROOT_DIR',
'CAMPAREE_OUTPUT_DIR_NAME',
'DEFAULT_STAR_OUTPUT_PREFIX',
'DEFAULT_STAR_BAM_FILENAME',
'INTRON_OUTPUT_FILENAME',
'INTRON_OUTPUT_ANTISENSE_FILENAME',
'INTERGENIC_OUTPUT_FILENAME',
'VARIANTS_FINDER_OUTPUT_FILENAME',
'VARIANTS_FINDER_LOG_FILENAME',
'VARIANTS_COMPILATION_OUTPUT_FILENAME',
'VARIANTS_COMPILATION_LOG_FILENAME',
'BEAGLE_OUTPUT_PREFIX',
'BEAGLE_OUTPUT_FILENAME',
'BEAGLE_LOG_FILENAME',
'GENOMEBUILDER_SEQUENCE_FILENAME_PATTERN',
'GENOMEBUILDER_INDEL_FILENAME_PATTERN',
'GENOMEBUILDER_MAPPER_FILENAME_PATTERN',
'GENOMEBUILDER_LOG_FILENAME',
'UPDATEANNOT_OUTPUT_FILENAME_PATTERN',
'UPDATEANNOT_LOG_FILENAME_PATTERN',
'TRANSCRIPTOME_FASTA_OUTPUT_FILENAME_PATTERN',
'TRANSCRIPTOME_FASTA_LOG_FILENAME_PATTERN',
'KALLISTO_INDEX_DIR_PATTERN',
'KALLISTO_INDEX_FILENAME_PATTERN',
'KALLISTO_INDEX_LOG_FILENAME_PATTERN',
'KALLISTO_QUANT_DIR_PATTERN',
'KALLISTO_ABUNDANCE_FILENAME',
'KALLISTO_QUANT_LOG_FILENAME_PATTERN',
'TXQUANT_OUTPUT_TX_FILENAME',
'TXQUANT_OUTPUT_GENE_FILENAME',
'TXQUANT_OUTPUT_PSI_FILENAME',
'TXQUANT_LOG_FILENAME',
'BOWTIE2_INDEX_DIR_PATTERN',
'BOWTIE2_INDEX_PREFIX_PATTERN',
'BOWTIE2_INDEX_LOG_FILENAME_PATTERN',
'BOWTIE2_ALIGN_FILENAME_PATTERN',
'BOWTIE2_ALIGN_LOG_FILENAME_PATTERN',
'ALLELIC_IMBALANCE_OUTPUT_FILENAME',
'ALLELIC_IMBALANCE_LOG_FILENAME',
'MOLECULE_MAKER_OUTPUT_OPTIONS_W_EXTENSIONS',
'MOLECULE_MAKER_OUTPUT_FILENAME_PATTERN',
'MOLECULE_MAKER_DEFAULT_NUM_MOLECULES_PER_PACKET',
'MOLECULE_MAKER_LOG_FILENAME'])
CampareeConstants.__doc__ = """
Provides a list of constants specific to the CAMPAREE pipeline.
These include input/output/logging filenames used by various
steps in the pipeline.
"""
_CAMPAREE_ROOT_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
# The following variables are used to add prefixes to string patterns defined
# in the namedtuple below.
_DEFAULT_STAR_OUTPUT_PREFIX="genome_alignment."
# Prefix for names of all (non-log) files generated by GenomeBuilderStep
_DEFAULT_GENOMEBUILDER_OUTPUT_PREFIX="custom_genome"
CAMPAREE_CONSTANTS = \
CampareeConstants(CAMPAREE_ROOT_DIR=_CAMPAREE_ROOT_DIR,
# Name of sub-directory containing CAMPAREE results in output directory.
CAMPAREE_OUTPUT_DIR_NAME="CAMPAREE",
# Prefix this pipeline assigns to the STAR output files (excluding path),
# if the user does not provide pre-aligned BAM files. This is part of what
# is passed STAR as a command line parameter.
DEFAULT_STAR_OUTPUT_PREFIX=_DEFAULT_STAR_OUTPUT_PREFIX,
# Full name (exlcuding path) of STAR-created BAM file generated by this
# pipeline. The same filename is used across all samples.
DEFAULT_STAR_BAM_FILENAME=_DEFAULT_STAR_OUTPUT_PREFIX + "Aligned.sortedByCoord.out.bam",
INTRON_OUTPUT_FILENAME="intron_quantifications.txt",
INTRON_OUTPUT_ANTISENSE_FILENAME="intron_antisense_quantifications.txt",
INTERGENIC_OUTPUT_FILENAME="intergenic_quantifications.txt",
# Name of file where VariantsFinderStep output is stored.
VARIANTS_FINDER_OUTPUT_FILENAME="variants.txt",
# Name of file where VariantsFinderStep logging is stored.
VARIANTS_FINDER_LOG_FILENAME="VariantsFinderStep.log",
# Name of file where VariantsCompilationStep output is stored.
VARIANTS_COMPILATION_OUTPUT_FILENAME="all_variants.vcf",
# Name of file where VariantsCompilationStep logging is stored.
VARIANTS_COMPILATION_LOG_FILENAME="VariantsCompilationStep.log",
# Prefix assigned to all beagle output files. This is part of what is passed
# to beagle as a command line parameter.
BEAGLE_OUTPUT_PREFIX="beagle",
# Name of output file generated by the beagle program.
BEAGLE_OUTPUT_FILENAME="beagle.vcf.gz",
# Name of file where BeagleStep logging is stored.
BEAGLE_LOG_FILENAME="BeagleStep.log",
# String pattern to construct sequence FASTA filename generated by GenomeBuilderStep
GENOMEBUILDER_SEQUENCE_FILENAME_PATTERN=_DEFAULT_GENOMEBUILDER_OUTPUT_PREFIX + '_{genome_name}.fa',
# String pattern to construct indel filename generated by GenomeBuilderStep
GENOMEBUILDER_INDEL_FILENAME_PATTERN=_DEFAULT_GENOMEBUILDER_OUTPUT_PREFIX + '_indels_{genome_name}.txt',
# String pattern to construct reference mapping filename generated by GenomeBuilderStep
GENOMEBUILDER_MAPPER_FILENAME_PATTERN=_DEFAULT_GENOMEBUILDER_OUTPUT_PREFIX + '_to_parental_coordinate_mapping_{genome_name}.txt',
# Name of file where GenomeBuilderStep logging is stored
GENOMEBUILDER_LOG_FILENAME="GenomeBuilderStep.log",
# Name of updated annotation file generated by UpdateAnnotationForGenomeStep
UPDATEANNOT_OUTPUT_FILENAME_PATTERN='updated_annotation_{genome_name}.txt',
# Name of file where UpdateAnnotationForGenomeStep logging is stored
UPDATEANNOT_LOG_FILENAME_PATTERN='UpdateAnnotationForGenomeStep_{genome_name}.log',
# Name of transcriptome FASTA file generated by TranscriptomeFastaPreparationStep
TRANSCRIPTOME_FASTA_OUTPUT_FILENAME_PATTERN='transcriptome_{genome_name}.fa',
# Name of file where TranscriptomeFastaPreparationStep logging is stored
TRANSCRIPTOME_FASTA_LOG_FILENAME_PATTERN='TranscriptomeFastaPreparationStep_{genome_name}.log',
# Name of directory to store kallisto index files
KALLISTO_INDEX_DIR_PATTERN='transcriptome_{genome_name}_index',
# String pattern to construct path to kallisto index file
KALLISTO_INDEX_FILENAME_PATTERN='transcriptome_{genome_name}.kallisto.index',
# Name of file where KallistoIndexStep logging is stored
KALLISTO_INDEX_LOG_FILENAME_PATTERN='KallistoIndexStep_{genome_name}.log',
# Name of directory to store kallisto quantification results
KALLISTO_QUANT_DIR_PATTERN='transcriptome_{genome_name}_kallisto_quant',
# Name of transcript quantification output file created by kallisto.
KALLISTO_ABUNDANCE_FILENAME='abundance.tsv',
# Name of file where KallistoQuantStep logging is stored
KALLISTO_QUANT_LOG_FILENAME_PATTERN='KallistoQuantStep_{genome_name}.log',
# Name of transcript-level counts file generated by TranscriptGeneQuantificationStep
TXQUANT_OUTPUT_TX_FILENAME="transcript_quantifications.txt",
# Name of gene-level counts file generated by TranscriptGeneQuantificationStep
TXQUANT_OUTPUT_GENE_FILENAME="gene_quantifications.txt",
# Name of PSI values file generated by TranscriptGeneQuantificationStep
TXQUANT_OUTPUT_PSI_FILENAME="isoform_psi_value_quantifications.txt",
# Name of file where TranscriptGeneQuantificationStep logging is stored
TXQUANT_LOG_FILENAME="TranscriptGeneQuantificationStep.log",
# Name of directory to store Bowtie2 index files. Note, right now this
# is the same as kallisto index directory. Maintaining both of these as
# separate variables, so Bowtie2 and kallisto indexes can be stored in
# different directories.
BOWTIE2_INDEX_DIR_PATTERN='transcriptome_{genome_name}_index',
# Prefix used by Bowtie2 when naming/creating all index files
BOWTIE2_INDEX_PREFIX_PATTERN='transcriptome_{genome_name}',
# Name of file where Bowtie2IndexStep logging is stored
BOWTIE2_INDEX_LOG_FILENAME_PATTERN='Bowtie2IndexStep_{genome_name}.log',
# Name of file where Bowtie2 alignment results are stored
BOWTIE2_ALIGN_FILENAME_PATTERN='Bowtie2_transcriptome_alignment_{genome_name}.sam',
# Name of file where Bowtie2AlignStep logging is stored
BOWTIE2_ALIGN_LOG_FILENAME_PATTERN='Bowtie2AlignStep_{genome_name}.log',
# Name of file where allelic imbalance distribution stored
ALLELIC_IMBALANCE_OUTPUT_FILENAME="allelic_imbalance_quantifications.txt",
# Name of file where AllelicImbalanceQuantificationStep logging is stored
ALLELIC_IMBALANCE_LOG_FILENAME="AllelicImbalanceQuantificationStep.log",
# Dictionary mapping the options for molecule output type, to the
# extension of the output file. Note: the keys are used to validate
# the output type entered in the config file.
MOLECULE_MAKER_OUTPUT_OPTIONS_W_EXTENSIONS={"file": "txt", "packet": "pickle"},
# Name of files where molecule representations are stored.
MOLECULE_MAKER_OUTPUT_FILENAME_PATTERN='molecule_{output_type}{packet_num}.{extension}',
# Default number of molecules to store per molecule packet, if the
# output type is set to packet.
MOLECULE_MAKER_DEFAULT_NUM_MOLECULES_PER_PACKET=10_000,
# Name of file where MoleculeMakerStep logging is stored
MOLECULE_MAKER_LOG_FILENAME="MoleculeMakerStep.log"
)
CAMPAREE_VERSION="0.2.0"