config.py

###
# configuration that should be handled manually and will differ between systems
###

# BASE = '/home/hjp/sleuth_paper_analysis'
# BASE = '/Users/hjp/analysis/sleuth_paper'
# TODO: make this a absolute path before submission
from os.path import expanduser, splitext
from os import getenv

HOME = expanduser('~')
BASE = HOME + '/sleuth_paper_analysis'

N_THREADS = 40

###
# software
###
BIN = BASE + '/software/bin'

KALLISTO = BIN + '/kallisto'

CUFFLINKS = BIN + '/cufflinks'

RSEM_PATH = BASE + '/software/rsem_simulate'
RSEM_SIMULATE = RSEM_PATH + '/rsem-simulate-reads'
RSEM_SIMULATE = BIN + '/rsem-simulate-reads'

# UPDATED_PATH = 'PATH=' + ':'.join([
#     RSEM_PATH,
#     getenv('PATH')
#     ])
UPDATED_PATH = 'PATH=' + BIN + ':$PATH'
HISAT = BIN + '/hisat2'

SAMTOOLS = BIN + '/samtools'

FEATURE_COUNTS = BIN + '/featureCounts'

SEQTK = BIN + '/seqtk'

BOWTIE = BIN + '/bowtie'

BitSeq_parseAlignment = BIN + '/parseAlignment'

# import os

# os.environ['PATH'] = RSEM_PATH + ':' + os.environ['PATH']
# print(RSEM_PATH + ':' + os.environ['PATH'])
# os.environ['PATH'] = RSEM_PATH + ':' + os.environ['PATH']
# print(type(os.environ['PATH']))

###
# annotations
###
TRANSCRIPTOME_NAME = 'Homo_sapiens.GRCh38.cdna.all.rel80'
TRANSCRIPTOME_FA = BASE + '/annotation/' + TRANSCRIPTOME_NAME + '.fa'
TRANSCRIPTOME_GTF = BASE + '/annotation/' + TRANSCRIPTOME_NAME + '.gtf'

# NOTE: bowtie creates files with this prefix
BOWTIE_INDEX = BASE + '/index/' + TRANSCRIPTOME_NAME

KALLISTO_INDEX = BASE + '/index/' + TRANSCRIPTOME_NAME + '.kidx'

GENOME_NAME = 'Homo_sapiens.GRCh38.dna.primary_assembly.rel80'
GENOME_FA = BASE + '/annotation/' + GENOME_NAME + '.fa'

# STAR_DIRECTORY = BASE + '/index/star_' + TRANSCRIPTOME_NAME
# STAR_INDEX = STAR_DIRECTORY + '/Genome'
HISAT_INDEX = BASE + '/index/' + GENOME_NAME



RSEM_ANNOTATION_DIR = '/'.join([
    BASE,
    'annotation',
    TRANSCRIPTOME_NAME + '_rsem'])
RSEM_ANNOTATION = RSEM_ANNOTATION_DIR + '/ref'
RSEM_MODEL = BASE + '/geuvadis/results/rsem/HG00365_7/out.stat/out.model'

MOUSE_NAME = 'Mus_musculus.GRCm38.cdna.all.rel84'
MOUSE_TRANSCRIPTOME_FA = BASE + '/annotation/' + MOUSE_NAME + '.fa'
MOUSE_TRANSCRIPTOME_GTF = BASE + '/annotation/' + MOUSE_NAME + '.gtf'

MOUSE_KALLISTO_INDEX = BASE + '/index/' + MOUSE_NAME + '.kidx'

MOUSE_GENOME_NAME = 'Mus_musculus.GRCm38.dna.primary_assembly.rel84'
MOUSE_GENOME_FA = BASE + '/annotation/' + MOUSE_GENOME_NAME + '.fa'

MOUSE_HISAT_INDEX = BASE + '/index/' + MOUSE_GENOME_NAME

###
# functions
###
def source_r(base, fname):
    return 'OMP_NUM_THREADS=1 Rscript --vanilla --default-packages=methods,stats,utils -e \'setwd("{0}")\' -e \'source("{1}")\''.format(base, fname)

def source_rmd(base, file_name, output_name = None):
    if output_name is None:
        output_name = splitext(file_name)[0]
        output_name += '.html'
    return 'OMP_NUM_THREADS=1 Rscript --vanilla --default-packages=methods,stats,utils,knitr -e \'setwd("{0}")\' -e \'rmarkdown::render("{1}", output_file = "{2}")\''.format(base, file_name, output_name)

def get_sample_ids(fname):
    ret = []
    with open(fname, 'r') as fhandle:
        for line in fhandle:
            ret.append(line.strip("\n"))
    return ret