<commit_before><commit_msg>add compara-import.v4.ini<commit_after>[ENSEMBL]
	LOCAL = /exports/software/ensembl/ensembl85/
[DATABASE_COMPARA]
	NAME = lepbase_compara_32_85
	HOST = mysql.lepbase.org
	PORT = 3307
	RW_USER = importer
	RW_PASS = <PASSWORD>
	RO_USER = anonymous
	RO_PASS =
[DATABASE_TEMPLATE]
	NAME = ensembl_compara_metazoa_32_85
	URL = ftp://ftp.ensemblgenomes.org/pub/release-31/metazoa/mysql/
[DATABASE_CORE]
	HOST = mysql.lepbase.org
	PORT = 3307
	RO_USER = anonymous
	RO_PASS =
[SETUP]
	FASTA_DIR = /data/projects/lepbase/analyses/v4/import/compara
	REMOVE = [ ]
	MAFFT = /exports/software/mafft/mafft-7.267-with-extensions/bin/mafft
	NOISY = /exports/software/noisy/Noisy-1.5.12/bin/noisy
	RAXML = /exports/software/raxml/standard-RAxML-8.2.8/raxmlHPC-PTHREADS-SSE3
	NOTUNG = /exports/software/notung/Notung-2.8.1.7/Notung-2.8.1.7.jar
	NOTUNG_SPECIESTREE = /data/projects/lepbase/analyses/v4/import/speciestree.v4.newick
	JAVA = /usr/lib/jvm/java-8-oracle/bin/java
[TAXA]
	HELMEL = heliconius_melpomene_melpomene_hmel2_core_32_85_1
	HELERD = heliconius_erato_demophoon_v1_core_32_85_1
	HELERL = heliconius_erato_lativitta_v3_core_32_85_1
	CALCEC = calycopis_cecrops_v1x1_core_32_85_1
	PHOSEN = phoebis_sennae_v1x1_core_32_85_1
	BICANY = bicyclus_anynana_v1x2_core_32_85_1
	OPEBRU = operophtera_brumata_v1_core_32_85_1
	CHISUP = chilo_suppressalis_csuogs1_core_32_85_1
	DANPLE = danaus_plexippus_v3_core_32_85_1
	LIMLUN = limnephilus_lunatus_v1_core_32_85_1
	MELCIN = melitaea_cinxia_core_32_85_1
	PLUXYD = plutella_xylostella_dbmfjv1x1_core_32_85_1
	PLUXYP = plutella_xylostella_pacbiov1_core_32_85_1
	PLOINT = plodia_interpunctella_v1_core_32_85_1
	MANSEX = manduca_sexta_msex1_core_32_85_1
	LERACC = lerema_accius_v1x1_core_32_85_1
	PAPGLA = papilio_glaucus_v1x1_core_32_85_1
	PAPXUT = papilio_xuthus_pxut1_core_32_85_1
	PAPXUB = papilio_xuthus_papxu1_core_32_85_1
	PAPPOL = papilio_polytes_ppol1_core_32_85_1
	PAPMAC = papilio_machaon_papma1_core_32_85_1
	BOMMOR = bombyx_mori_asm15162v1_core_32_85_1
	AMYTRA = amyelois_transitella_v1_core_32_85_1
[ORTHOGROUP]
        ORTHOGROUPS_FILE = /data/projects/lepbase/analyses/v4/import/compara/Orthogroups_I1.5.txt
        PREFIX = LBGT004
        SUFFIXLENGTH = 7
        PROTEIN = .faa
        PROTEIN_ALIGN = [ .faa.mafft Mafft ]
        PROTEIN_TRIMMED = .faa_out.fas
        FNAFILE = .fna
        BOUNDEDFILE = .fba
        TREE = .RAxML_bipartitionsBranchLabels.rooting.0.reconciled
        HOMOLOG = .RAxML_bipartitionsBranchLabels.rooting.0.reconciled.homologs.txt
[SPECIES_SET]
	LEPIDOPTERA = [ HELMEL HELERD HELERL CALCEC PHOSEN BICANY OPEBRU CHISUP DANPLE LIMLUN MELCIN PLUXYD PLUXYP PLOINT MANSEX LERACC PAPGLA PAPXUT PAPXUB PAPPOL PAPMAC BOMMOR AMYTRA ]
        TREE_FILE = /data/projects/lepbase/analyses/v4/import/speciestree.v4.newick
        TREE_LABEL = Lepidoptera_v4
[METHOD_LINK]
;	Names and classes of methods used with the main table in which results are stored
;	Method class must be one of DNA-DNA_ALIGNMENT, GENOMIC_SYNTENY, PROTEIN_HOMOLOGY, PROTEIN_FAMILY or PROTEIN-NCRNA_TREE
;	KEY = [ METHOD_CLASS DATABASE_TABLE.DATA_TYPE ]
	BLASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]
	TRANSLATED_BLAT = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]
	TRANSLATED_BLAT_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]
	PECAN = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.multiple_alignment ]
	ORTHEUS = [ DNA-DNA_ALIGNMENT GenomicAlignTree.tree_alignment ]
	LASTZ_NET = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]
	ATAC = [ DNA-DNA_ALIGNMENT GenomicAlignBlock.pairwise_alignment ]
	SYNTENY = [ GENOMIC_SYNTENY SyntenyRegion.synteny ]
	ENSEMBL_ORTHOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]
	ENSEMBL_PARALOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]
	ENSEMBL_PROJECTIONS = [ PROTEIN_HOMOLOGY Homology.homology ]
	ENSEMBL_HOMOEOLOGUES = [ PROTEIN_HOMOLOGY Homology.homology ]
	FAMILY = [ PROTEIN_FAMILY Family.family ]
	PROTEIN_TREES = [ PROTEIN-NCRNA_TREE ProteinTree.protein_tree_node ]
	GERP_CONSTRAINED_ELEMENT = [ PROTEIN-NCRNA_TREE GenomicAlignBlock.constrained_element ]
{'fraction_non_alphanumeric': 0.0721724388471785, 'fraction_numerical': 0.04964882538144829, 'mean_word_length': 5.393188854489164, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 2, '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': '2329481', 'n_tokens_mistral': 1964, 'n_tokens_neox': 1841, 'n_words': 221}