<commit_before>##########################################################
##########################################################
##########################################################
## Geneset annotations
##########################################################
[general]

# location of indexed genome 
genome=hg19

# location of indexed genome 
genome_dir=/ifs/mirror/genomes/plain

# location of indexed genome with faidx
faidx_dir=/ifs/mirror/genomes/faidx

# name of database
database=csvdb

# database options for csv2db script
csv2db_options=--backend=sqlite --retry --map=gene_id:str --map=contig:str --map=transcript_id:str 

# scratchdir for data not to be backed up
scratchdir=/tmp

# a version string
version=

##########################################################
##########################################################
##########################################################
[gaps]
# minimum gap size
min_size=100

##########################################################
##########################################################
##########################################################
[geneset]
# comma separated list of regular expressions for contigs
# to be removed from ensembl_filename_gtf during genome
# sanitization
remove_contigs=

# size of flank for annotating genome by geneset
flank=5000

# size of a promotor
promotor_size=5000

# size of gene territories
territories_radius=100000

##########################################################
##########################################################
##########################################################
[great]

## definitions for great basal regions upstream/downstream from TSS
upstream=5000
downstream=1000

## maximal extent of region
radius=1000000

##########################################################
##########################################################
##########################################################
# size for genestructures
[genestructures]
# extend each gene by 10kb in either direction
flank=10000

# annotate in intervals of 1kb.
increment=1000

##########################################################
##########################################################
##########################################################
# information about ENSEMBL gene set. The ENSEMBL gene set is imported
# from the dumps provided by ENSEMBL.
[ensembl]
  
filename_gtf=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.gtf.gz
filename_pep=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.pep.all.fa.gz
filename_cdna=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.cdna.all.fa.gz

# biomart dataset to use


# Set biomart host.
# 'www.biomart.org' contains the lastest ensembl release.
#
# In order to access archived versions, use hosts such as:
# may2009.archive.ensembl.org
# sep2009.archive.ensembl.org
# may2012.archive.ensembl.org
biomart_host=www.biomart.org

# When accessing an archive server, use
# biomart_mart=ENSEMBL_MART_ENSEMBL
biomart_mart=ensembl

# biomart dataset to use
# to discover the dataset you need, open an R session and enter the commands:
#     library(biomaRt)
#     ensembl <- useMart(ensembl)
#     listDatasets(ensembl)
biomart_dataset=hsapiens_gene_ensembl

# information about UCSC databases
[ucsc]
# UCSC database host
host=genome-mysql.cse.ucsc.edu

# UCSC database user name
user=genome

# UCSC database name
database=hg19

# repeats to collect as ',' separated list
repeattypes=DNA,LINE,SINE,LTR,Transposon

# RNA repeats to collect as ',' separated list
rnatypes=RNA,rRNA,scRNA,snRNA,srpRNA,tRNA

# Mappability track
mappability=mappability.bw

# local mirror directory for UCSC files
dir=/ifs/mirror/ucsc<commit_msg>pipeline.ini for pipeline_annotations<commit_after>##########################################################
##########################################################
##########################################################
## Geneset annotations
##########################################################
[general]

# location of indexed genome 
genome=hg19

# location of indexed genome 
genome_dir=/ifs/mirror/genomes/plain

# location of indexed genome with faidx
faidx_dir=/ifs/mirror/genomes/faidx

# name of database
database=csvdb

# database options for csv2db script
csv2db_options=--backend=sqlite --retry --map=gene_id:str --map=contig:str --map=transcript_id:str 

# scratchdir for data not to be backed up
scratchdir=/tmp

# a version string
version=

##########################################################
##########################################################
##########################################################
[gaps]
# minimum gap size
min_size=100

##########################################################
##########################################################
##########################################################
[geneset]
# comma separated list of regular expressions for contigs
# to be removed from ensembl_filename_gtf during genome
# sanitization
remove_contigs=

# size of flank for annotating genome by geneset
flank=5000

# size of a promotor
promotor_size=5000

# size of gene territories
territories_radius=100000

##########################################################
##########################################################
##########################################################
[great]

## definitions for great basal regions upstream/downstream from TSS
upstream=5000
downstream=1000

## maximal extent of region
radius=1000000

##########################################################
##########################################################
##########################################################
# size for genestructures
[genestructures]
# extend each gene by 10kb in either direction
flank=10000

# annotate in intervals of 1kb.
increment=1000

##########################################################
##########################################################
##########################################################
# information about ENSEMBL gene set. The ENSEMBL gene set is imported
# from the dumps provided by ENSEMBL.
[ensembl]
  
filename_gtf=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.gtf.gz
filename_pep=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.pep.all.fa.gz
filename_cdna=/ifs/mirror/ensembl/hg19/Homo_sapiens.GRCh37.60.cdna.all.fa.gz

# biomart dataset to use


# Set biomart host.
# 'www.biomart.org' contains the lastest ensembl release.
#
# In order to access archived versions, use hosts such as:
# may2009.archive.ensembl.org
# sep2009.archive.ensembl.org
# may2012.archive.ensembl.org
biomart_host=www.biomart.org

# When accessing an archive server, use
# biomart_mart=ENSEMBL_MART_ENSEMBL
biomart_mart=ensembl

# biomart dataset to use
# to discover the dataset you need, open an R session and enter the commands:
#     library(biomaRt)
#     ensembl <- useMart("ensembl")
#     listDatasets(ensembl)
biomart_dataset=hsapiens_gene_ensembl

# information about UCSC databases
[ucsc]
# UCSC database host
host=genome-mysql.cse.ucsc.edu

# UCSC database user name
user=genome

# UCSC database name
database=hg19

# repeats to collect as ',' separated list
repeattypes=DNA,LINE,SINE,LTR,Transposon

# RNA repeats to collect as ',' separated list
rnatypes=RNA,rRNA,scRNA,snRNA,srpRNA,tRNA

# Mappability track
mappability=mappability.bw

# local mirror directory for UCSC files
dir=/ifs/mirror/ucsc
{'fraction_non_alphanumeric': 0.35442525634106853, 'fraction_numerical': 0.021586616297895305, 'mean_word_length': 7.423863636363636, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4815535', 'n_tokens_mistral': 2249, 'n_tokens_neox': 1955, 'n_words': 495}