<commit_before>###############################################################################
#
#   Name:           Sus_scrofa.ini
#
#   Description:    Configuration file for Pig ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

UCSC_GOLDEN_PATH        = susScr3
UCSC_ASSEMBLIES         = [susScr3 Sscrofa10.2] 

SPECIES_RELEASE_VERSION = 111

# Search config
ENSEMBL_SEARCH_IDXS = [ Gene Sequence GenomicAlignment Marker ]

EXPORTABLE_MISC_SETS = [ BAC ]

ASSEMBLY_CONVERTER_FILES = [Sscrofa10.2_to_Sscrofa9 Sscrofa9_to_Sscrofa10.2]

####################
# Species-specific colours
####################
[ENSEMBL_STYLE]

[ENSEMBL_COLOURS]
# Accept defaults


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults

[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults

####################
# Configure External Genome Browsers
####################

[EXTERNAL_GENOME_BROWSERS]
# None

[ENSEMBL_EXTERNAL_URLS]

####################
# Configure blast data sources.
# Used in blastview to generate database dropdown
####################

[ENSEMBL_BLAST_METHODS]

####################
# Configure blast data sources.
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search
# Accept defaults

[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults

[BLASTN_DATASOURCES]
# Sequence databases to use with search method (BLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ALL     = %_
CDNA_ABINITIO   = %_

[TBLASTX_DATASOURCES]
# Sequence databases to use with search method (TBLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ABINITIO   = %_

[TBLASTN_DATASOURCES]
# Sequence databases to use with search method (TBLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ABINITIO   = %_

[BLASTP_DATASOURCES]
# Sequence databases to use with search method (BLASTP)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
PEP_ABINITIO    = %_

[BLASTX_DATASOURCES]
# Sequence databases to use with search method (BLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
PEP_ABINITIO    = %_

[SAMPLE_DATA]
LOCATION_PARAM    = 7:60063921-60303532
LOCATION_TEXT     = 7:60063921-60303532

GENE_PARAM        = ENSSSCG00000004244
GENE_TEXT         = ENSSSCG00000004244

TRANSCRIPT_PARAM  = ENSSSCT00000011885
TRANSCRIPT_TEXT   = ENSSSCT00000011885

VARIATION_PARAM   = rs327222593
VARIATION_TEXT    = rs327222593

STRUCTURAL_PARAM  = nsv443042
STRUCTURAL_TEXT   = nsv443042

SEARCH_TEXT       = apoptosis

PHENOTYPE_PARAM   = 105
PHENOTYPE_TEXT    = Body weight

ENSEMBL_SOUND     = oink!
VEP_HGVS          = ENSSSCT00000024788.1:c.4G>A\nENSSSCT00000014030.2:c.224+16G>A\nENSSSCT00000002922.2:c.*2176delT
VEP_ID            = rs337595702\nrs329122265\nrs80905614
VEP_VCF           = 1 281897 . G A . . .\n2 39510 . G A . . .\n6 179893 . GA G . . .
VEP_ENSEMBL       = 1 281897 281897 G/A 1\n2 39510 39510 G/A 1\n6 179894 179894 A/- 1
VEP_PILEUP        = 1 281897 G A\n2 39510 G A\n6 179893 * -A
<commit_msg>Merging postreleasefix/92 to master<commit_after>###############################################################################
#
#   Name:           Sus_scrofa.ini
#
#   Description:    Configuration file for Pig ensembl
#
###############################################################################

#################
# GENERAL CONFIG
#################
[general]

UCSC_GOLDEN_PATH        = susScr11
UCSC_ASSEMBLIES         = [susScr3 Sscrofa10.2 susScr11 Sscrofa11.1] 

SPECIES_RELEASE_VERSION = 111

# Search config
ENSEMBL_SEARCH_IDXS = [ Gene Sequence GenomicAlignment Marker ]

EXPORTABLE_MISC_SETS = [ BAC ]

ASSEMBLY_CONVERTER_FILES = [Sscrofa10.2_to_Sscrofa9 Sscrofa9_to_Sscrofa10.2]

####################
# Species-specific colours
####################
[ENSEMBL_STYLE]

[ENSEMBL_COLOURS]
# Accept defaults


####################
# External Database ad Indexer Config
####################

[ENSEMBL_EXTERNAL_DATABASES]
# Accept defaults

[ENSEMBL_EXTERNAL_INDEXERS]
# Accept defaults

####################
# Configure External Genome Browsers
####################

[EXTERNAL_GENOME_BROWSERS]
# None

[ENSEMBL_EXTERNAL_URLS]

####################
# Configure blast data sources.
# Used in blastview to generate database dropdown
####################

[ENSEMBL_BLAST_METHODS]

####################
# Configure blast data sources.
# Used in blastview to generate database dropdown
####################
[ENSEMBL_BLAST_METHODS]
# Registers blast methods. Key values are the
# Bio::Tools::Run::Search classes used to run the search
# Accept defaults

[BLAST_DATASOURCES]
# Registers blast datasources. Key values are used as labels.
# Keys should be registered against methods in species.ini files
# Accept defaults

[BLASTN_DATASOURCES]
# Sequence databases to use with search method (BLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ALL     = %_
CDNA_ABINITIO   = %_

[TBLASTX_DATASOURCES]
# Sequence databases to use with search method (TBLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ABINITIO   = %_

[TBLASTN_DATASOURCES]
# Sequence databases to use with search method (TBLASTN)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
LATESTGP        = %_
LATESTGP_MASKED = %_
CDNA_ABINITIO   = %_

[BLASTP_DATASOURCES]
# Sequence databases to use with search method (BLASTP)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = peptide
PEP_ABINITIO    = %_

[BLASTX_DATASOURCES]
# Sequence databases to use with search method (BLASTX)
# Filesystem location set by DEFAULTS:ENSEMBL_BLAST_DATA_PATH
# Data available from ftp://ftp.ensembl.org/pub/current_mouse/data/fasta/
DATASOURCE_TYPE = dna
PEP_ABINITIO    = %_

[SAMPLE_DATA]
LOCATION_PARAM    = 7:60063921-60303532
LOCATION_TEXT     = 7:60063921-60303532

GENE_PARAM        = ENSSSCG00000004244
GENE_TEXT         = ENSSSCG00000004244

TRANSCRIPT_PARAM  = ENSSSCT00000011885
TRANSCRIPT_TEXT   = ENSSSCT00000011885

VARIATION_PARAM   = rs327222593
VARIATION_TEXT    = rs327222593

STRUCTURAL_PARAM  = nsv443042
STRUCTURAL_TEXT   = nsv443042

SEARCH_TEXT       = apoptosis

PHENOTYPE_PARAM   = 105
PHENOTYPE_TEXT    = Body weight

ENSEMBL_SOUND     = oink!
VEP_HGVS          = ENSSSCT00000024788.1:c.4G>A\nENSSSCT00000014030.2:c.224+16G>A\nENSSSCT00000002922.2:c.*2176delT
VEP_ID            = rs337595702\nrs329122265\nrs80905614
VEP_VCF           = 1 281897 . G A . . .\n2 39510 . G A . . .\n6 179893 . GA G . . .
VEP_ENSEMBL       = 1 281897 281897 G/A 1\n2 39510 39510 G/A 1\n6 179894 179894 A/- 1
VEP_PILEUP        = 1 281897 G A\n2 39510 G A\n6 179893 * -A

{'fraction_non_alphanumeric': 0.16307844592922544, 'fraction_numerical': 0.07003217025488741, 'mean_word_length': 4.708333333333333, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 6, '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': '3613722', 'n_tokens_mistral': 3356, 'n_tokens_neox': 2852, 'n_words': 603}