Enable VGNC xrefs for 15 more species

Created by: mkszuba

Description

xref_config.ini: enable VGNC xrefs for pig (full gene set) and 14 more new species (cytochrome P450 only)

Use case

As requested by VGNC.

Benefits

More species with VGNC xrefs.

Possible Drawbacks

Increased run time of the xref pipeline. Species from commit 3eb69e91 may or may not prove problematic.

Testing

Have you added/modified unit tests to test the changes?

No.

If so, do the tests pass/fail?

N/A

Have you run the entire test suite and no regression was detected?

No, there aren't any xref-pipeline tests in the test suite.

misc-scripts/xref_mapping/xref_config.ini

@@ -547,6 +547,141 @@ priority        = 1
 parser          = VGNCParser
 data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
 
+[source VGNC::sus_scrofa]
+# Used by sus_scrofa
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::aotus_nancymaae]
+# Used by aotus_nancymaae
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::carlito_syrichta]
+# Used by carlito_syrichta
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::cercocebus_atys]
+# Used by cercocebus_atys
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::chlorocebus_sabaeus]
+# Used by chlorocebus_sabaeus
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::macaca_fascicularis]
+# Used by macaca_fascicularis
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::macaca_nemestrina]
+# Used by macaca_nemestrina
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::mandrillus_leucophaeus]
+# Used by mandrillus_leucophaeus
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::nomascus_leucogenys]
+# Used by nomascus_leucogenys
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::otolemur_garnettii]
+# Used by otolemur_garnettii
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::pan_paniscus]
+# Used by pan_paniscus
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::propithecus_coquereli]
+# Used by propithecus_coquereli
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::rhinopithecus_bieti]
+# Used by rhinopithecus_bieti
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::cebus_capucinus]
+# Used by cebus_capucinus
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
+[source VGNC::saimiri_boliviensis_boliviensis]
+# Used by saimiri_boliviensis_boliviensis
+name            = VGNC
+download        = Y
+order           = 29
+priority        = 1
+parser          = VGNCParser
+data_uri        = ftp://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz
+
 [source HGNC::homo_sapiens#01]
 # Used by homo_sapiens
 name            = HGNC
@@ -1956,6 +2091,66 @@ source          = VGNC::microcebus_murinus
 taxonomy_id     = 9555
 source          = VGNC::papio_anubis
 
+[species sus_scrofa]
+taxonomy_id     = 9823
+source          = VGNC::sus_scrofa
+
+[species aotus_nancymaae]
+taxonomy_id     = 37293
+source          = VGNC::aotus_nancymaae
+
+[species carlito_syrichta]
+taxonomy_id     = 1868482
+source          = VGNC::carlito_syrichta
+
+[species cercocebus_atys]
+taxonomy_id     = 9531
+source          = VGNC::cercocebus_atys
+
+[species chlorocebus_sabaeus]
+taxonomy_id     = 60711
+source          = VGNC::chlorocebus_sabaeus
+
+[species macaca_fascicularis]
+taxonomy_id     = 9541
+source          = VGNC::macaca_fascicularis
+
+[species macaca_nemestrina]
+taxonomy_id     = 9545
+source          = VGNC::macaca_nemestrina
+
+[species mandrillus_leucophaeus]
+taxonomy_id     = 9568
+source          = VGNC::mandrillus_leucophaeus
+
+[species nomascus_leucogenys]
+taxonomy_id     = 61853
+source          = VGNC::nomascus_leucogenys
+
+[species otolemur_garnettii]
+taxonomy_id     = 30611
+source          = VGNC::otolemur_garnettii
+
+[species pan_paniscus]
+taxonomy_id     = 9597
+source          = VGNC::pan_paniscus
+
+[species propithecus_coquereli]
+taxonomy_id     = 379532
+source          = VGNC::propithecus_coquereli
+
+[species rhinopithecus_bieti]
+taxonomy_id     = 61621
+source          = VGNC::rhinopithecus_bieti
+
+[species cebus_capucinus]
+taxonomy_id     = 1737458
+source          = VGNC::cebus_capucinus
+
+[species saimiri_boliviensis_boliviensis]
+taxonomy_id     = 39432
+source          = VGNC::saimiri_boliviensis_boliviensis
+
 [species ciona_intestinalis]
 taxonomy_id     = 7719
 source          = cint_aniseed_v1::ciona_intestinalis