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cfriedline/cegma_blast.ipynb

Created January 24, 2014 16:21
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cegma_blast.ipynb
{
"metadata": {
"name": "cegma_blast"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
"input": "blast_xml = \"blast_out.xml\"",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
},
{
"cell_type": "code",
"collapsed": false,
"input": "from Bio.Blast import NCBIXML",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
},
{
"cell_type": "code",
"collapsed": false,
"input": "blast_records = list(NCBIXML.parse(open(blast_xml)))",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 6
},
{
"cell_type": "code",
"collapsed": false,
"input": "gis = set()\nfor b in blast_records:\n for a in b.alignments:\n gis.add(a.hit_id.split(\"|\")[1])\nprint len(gis)",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "2403\n"
}
],
"prompt_number": 315
},
{
"cell_type": "code",
"collapsed": false,
"input": "from Bio import Entrez, SeqIO\nimport treelib",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 141
},
{
"cell_type": "code",
"collapsed": false,
"input": "Entrez.email = \"cfriedline@vcu.edu\"",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 387
},
{
"cell_type": "code",
"collapsed": false,
"input": "search_res = Entrez.read(Entrez.epost(db=\"protein\", id=\",\".join(gis)))\nprint search_res\nwebenv = search_res['WebEnv']\nquery_key = search_res['QueryKey']",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "{u'QueryKey': '1', u'WebEnv': 'NCID_1_136898261_130.14.22.215_9001_1390579252_743986195'}\n"
}
],
"prompt_number": 379
},
{
"cell_type": "code",
"collapsed": false,
"input": "taxa_ids = set()\nreq_gb = Entrez.efetch(db=\"protein\", rettype=\"gb\", webenv=webenv, query_key=query_key)\nfor count, rec in enumerate(SeqIO.parse(req_gb, \"genbank\")):\n for f in rec.features:\n if f.type == 'source':\n db_xref = f.qualifiers['db_xref']\n taxon = None\n for x in db_xref:\n if 'taxon' in x:\n taxon = x\n break\n assert taxon\n taxa_ids.add(taxon.split(\":\")[1]) ",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 403
},
{
"cell_type": "code",
"collapsed": false,
"input": "class CountNode(treelib.Node):\n def __init__(self, tag, ident):\n self.count = 1\n super(CountNode, self).__init__(tag, ident)\n \n @property\n def tag(self):\n return \"%s (%d)\" % (self._tag, self.count)",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 276
},
{
"cell_type": "code",
"collapsed": false,
"input": "def create_tree_node(tree, name, parent):\n if not tree.get_node(name):\n n = CountNode(name, name)\n tree.add_node(n, parent)\n else:\n n = tree.get_node(name)\n n.count += 1",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 277
},
{
"cell_type": "code",
"collapsed": false,
"input": "taxa_res = Entrez.read(Entrez.epost(db=\"taxonomy\", id=\",\".join(list(taxa_ids))))\ntaxa_webenv = taxa_res['WebEnv']\ntaxa_query_key = taxa_res['QueryKey']\ntree = treelib.Tree()\ntree.create_node(\"Root\", \"root\")\nfor taxonomy in Entrez.parse(Entrez.efetch(db=\"taxonomy\", webenv=taxa_webenv, query_key=taxa_query_key)):\n prev = None\n for t in taxonomy['LineageEx']:\n if t['Rank'] != 'no rank':\n name = t['ScientificName']\n if not prev:\n create_tree_node(tree, name, \"root\")\n prev = name\n else:\n create_tree_node(tree, name, prev)\n prev = name",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 399
},
{
"cell_type": "code",
"collapsed": false,
"input": "tree.show()",
"language": "python",
"metadata": {},
"outputs": [
{
"output_type": "stream",
"stream": "stdout",
"text": "Root\n|___ Eukaryota (184)\n| |___ Apicomplexa (2)\n| |___ Aconoidasida (1)\n| |___ Babesiidae (1)\n| |___ Babesia (1)\n| |___ Coccidia (1)\n| |___ Eucoccidiorida (1)\n| |___ Eimeriorina (1)\n| |___ Cryptosporidiidae (1)\n| |___ Cryptosporidium (1)\n| |___ Cryptosporidium muris (1)\n| |___ Fungi (1)\n| |___ Dikarya (1)\n| |___ Ascomycota (1)\n| |___ Saccharomycotina (1)\n| |___ Saccharomycetes (1)\n| |___ Saccharomycetales (1)\n| |___ Debaryomycetaceae (1)\n| |___ Millerozyma (1)\n| |___ Millerozyma farinosa (1)\n| |___ Metazoa (181)\n| |___ Annelida (2)\n| |___ Hirudinida (1)\n| |___ Hirudinea (1)\n| |___ Rhynchobdellida (1)\n| |___ Glossiphoniidae (1)\n| |___ Helobdella (1)\n| |___ Polychaeta (1)\n| |___ Scolecida (1)\n| |___ Capitellida (1)\n| |___ Capitellidae (1)\n| |___ Capitella (1)\n| |___ Arthropoda (135)\n| |___ Chelicerata (4)\n| |___ Arachnida (4)\n| |___ Acari (4)\n| |___ Acariformes (1)\n| |___ Astigmata (1)\n| |___ Analgoidea (1)\n| |___ Pyroglyphidae (1)\n| |___ Dermatophagoidinae (1)\n| |___ Dermatophagoides (1)\n| |___ Parasitiformes (3)\n| |___ Ixodida (2)\n| |___ Ixodoidea (2)\n| |___ Argasidae (1)\n| |___ Ornithodoros (1)\n| |___ Ixodidae (1)\n| |___ Ixodinae (1)\n| |___ Ixodes (1)\n| |___ Mesostigmata (1)\n| |___ Dermanyssina (1)\n| |___ Phytoseioidea (1)\n| |___ Phytoseiidae (1)\n| |___ Typhlodrominae (1)\n| |___ Metaseiulus (1)\n| |___ Crustacea (6)\n| |___ Branchiopoda (2)\n| |___ Phyllopoda (1)\n| |___ Diplostraca (1)\n| |___ Cladocera (1)\n| |___ Anomopoda (1)\n| |___ Daphniidae (1)\n| |___ Daphnia (1)\n| |___ Sarsostraca (1)\n| |___ Anostraca (1)\n| |___ Artemiidae (1)\n| |___ Artemia (1)\n| |___ Malacostraca (2)\n| |___ Eumalacostraca (2)\n| |___ Eucarida (2)\n| |___ Decapoda (2)\n| |___ Dendrobranchiata (2)\n| |___ Penaeoidea (2)\n| |___ Penaeidae (2)\n| |___ Marsupenaeus (1)\n| |___ Penaeus (1)\n| |___ Maxillopoda (2)\n| |___ Copepoda (2)\n| |___ Neocopepoda (2)\n| |___ Podoplea (2)\n| |___ Siphonostomatoida (2)\n| |___ Caligidae (2)\n| |___ Caligus (1)\n| |___ Lepeophtheirus (1)\n| |___ Hexapoda (125)\n| |___ Insecta (125)\n| |___ Neoptera (125)\n| |___ Endopterygota (109)\n| |___ Amphiesmenoptera (48)\n| |___ Lepidoptera (48)\n| |___ Glossata (48)\n| |___ Neolepidoptera (48)\n| |___ Heteroneura (48)\n| |___ Bombycoidea (7)\n| |___ Bombycidae (2)\n| |___ Bombycinae (2)\n| |___ Bombyx (2)\n| |___ Saturniidae (4)\n| |___ Hemileucinae (1)\n| |___ Lonomia (1)\n| |___ Saturniinae (3)\n| |___ Attacini (1)\n| |___ Samia (1)\n| |___ Saturniini (2)\n| |___ Antheraea (2)\n| |___ Sphingidae (1)\n| |___ Sphinginae (1)\n| |___ Sphingini (1)\n| |___ Manduca (1)\n| |___ Gelechioidea (1)\n| |___ Elachistidae (1)\n| |___ Depressariinae (1)\n| |___ Depressaria (1)\n| |___ Geometroidea (1)\n| |___ Geometridae (1)\n| |___ Ennominae (1)\n| |___ Biston (1)\n| |___ Noctuoidea (12)\n| |___ Arctiidae (1)\n| |___ Arctiinae (1)\n| |___ Hyphantria (1)\n| |___ Noctuidae (11)\n| |___ Amphipyrinae (4)\n| |___ Spodoptera (4)\n| |___ Hadeninae (2)\n| |___ Mamestra (1)\n| |___ Mythimna (1)\n| |___ Heliothinae (3)\n| |___ Helicoverpa (2)\n| |___ Heliothis (1)\n| |___ Noctuinae (1)\n| |___ Agrotis (1)\n| |___ Plusiinae (1)\n| |___ Trichoplusia (1)\n| |___ Papilionoidea (18)\n| |___ Nymphalidae (14)\n| |___ Danainae (1)\n| |___ Danaini (1)\n| |___ Danaina (1)\n| |___ Danaus (2)\n| |___ Heliconiinae (10)\n| |___ Heliconiini (10)\n| |___ Heliconius (10)\n| |___ Heliconius cydno (1)\n| |___ Heliconius melpomene (2)\n| |___ Heliconius numata (3)\n| |___ Nymphalinae (2)\n| |___ Melitaeini (2)\n| |___ Euphydryina (1)\n| |___ Euphydryas (1)\n| |___ Melitaeina (1)\n| |___ Melitaea (1)\n| |___ Satyrinae (1)\n| |___ Satyrini (1)\n| |___ Maniolina (1)\n| |___ Aphantopus (1)\n| |___ Papilionidae (3)\n| |___ Papilioninae (3)\n| |___ Papilionini (3)\n| |___ Papilio (3)\n| |___ Pieridae (1)\n| |___ Pierinae (1)\n| |___ Pierini (1)\n| |___ Pieris (1)\n| |___ Pyraloidea (5)\n| |___ Crambidae (4)\n| |___ Crambinae (1)\n| |___ Chilo (1)\n| |___ Pyraustinae (2)\n| |___ Loxostege (1)\n| |___ Ostrinia (1)\n| |___ Spilomelinae (1)\n| |___ Omphisa (1)\n| |___ Pyralidae (1)\n| |___ Galleriinae (1)\n| |___ Galleria (1)\n| |___ Tortricoidea (3)\n| |___ Tortricidae (3)\n| |___ Olethreutinae (1)\n| |___ Grapholitini (1)\n| |___ Cydia (1)\n| |___ Tortricinae (2)\n| |___ Archipini (2)\n| |___ Choristoneura (2)\n| |___ Yponomeutoidea (1)\n| |___ Plutellidae (1)\n| |___ Plutella (1)\n| |___ Coleoptera (19)\n| |___ Adephaga (2)\n| |___ Caraboidea (2)\n| |___ Carabidae (2)\n| |___ Carabini (1)\n| |___ Carabina (1)\n| |___ Carabus (1)\n| |___ Orinocarabus (1)\n| |___ Cicindelinae (1)\n| |___ Cicindelini (1)\n| |___ Cicindela (2)\n| |___ Archostemata (1)\n| |___ Micromalthidae (1)\n| |___ Micromalthus (1)\n| |___ Myxophaga (1)\n| |___ Sphaeriusidae (1)\n| |___ Sphaerius (1)\n| |___ Polyphaga (15)\n| |___ Cucujiformia (8)\n| |___ Chrysomeloidea (2)\n| |___ Chrysomelidae (2)\n| |___ Chrysomelinae (2)\n| |___ Chrysomelini (1)\n| |___ Chrysomela (1)\n| |___ Timarchini (1)\n| |___ Timarcha (1)\n| |___ Cucujoidea (1)\n| |___ Biphyllidae (1)\n| |___ Biphyllus (1)\n| |___ Curculionoidea (3)\n| |___ Curculionidae (3)\n| |___ Curculioninae (1)\n| |___ Curculionini (1)\n| |___ Curculio (1)\n| |___ Scolytinae (2)\n| |___ Dendroctonus (1)\n| |___ Ips (1)\n| |___ Tenebrionoidea (2)\n| |___ Tenebrionidae (2)\n| |___ Tenebrioninae (1)\n| |___ Tenebrio (1)\n| |___ Tribolium (1)\n| |___ Elateriformia (4)\n| |___ Buprestoidea (1)\n| |___ Buprestidae (1)\n| |___ Julodinae (1)\n| |___ Julodis (1)\n| |___ Dascilloidea (1)\n| |___ Dascillidae (1)\n| |___ Dascillus (1)\n| |___ Elateroidea (1)\n| |___ Elateridae (1)\n| |___ Elaterinae (1)\n| |___ Agriotes (1)\n| |___ Scirtoidea (1)\n| |___ Eucinetidae (1)\n| |___ Eucinetus (1)\n| |___ Scarabaeiformia (1)\n| |___ Scarabaeoidea (1)\n| |___ Scarabaeidae (1)\n| |___ Scarabaeinae (1)\n| |___ Scarabaeini (1)\n| |___ Scarabaeus (1)\n| |___ Ateuchetus (1)\n| |___ Staphyliniformia (2)\n| |___ Histeroidea (1)\n| |___ Histeridae (1)\n| |___ Histerinae (1)\n| |___ Histerini (1)\n| |___ Hister (1)\n| |___ Hydrophiloidea (1)\n| |___ Georissidae (1)\n| |___ Georissus (1)\n| |___ Diptera (28)\n| |___ Brachycera (18)\n| |___ Muscomorpha (18)\n| |___ Ephydroidea (12)\n| |___ Drosophilidae (12)\n| |___ Drosophilinae (12)\n| |___ Drosophilini (12)\n| |___ Drosophilina (12)\n| |___ Drosophila (14)\n| |___ Sophophora (9)\n| |___ melanogaster group (6)\n| |___ ananassae subgroup (1)\n| |___ melanogaster subgroup (5)\n| |___ obscura group (2)\n| |___ pseudoobscura subgroup (2)\n| |___ Drosophila pseudoobscura (1)\n| |___ willistoni group (1)\n| |___ willistoni subgroup (1)\n| |___ grimshawi group (1)\n| |___ grimshawi subgroup (1)\n| |___ repleta group (1)\n| |___ mulleri subgroup (1)\n| |___ virilis group (1)\n| |___ Hippoboscoidea (1)\n| |___ Glossinidae (1)\n| |___ Glossina (2)\n| |___ Glossina morsitans (1)\n| |___ Muscoidea (2)\n| |___ Anthomyiidae (1)\n| |___ Delia (1)\n| |___ Muscidae (1)\n| |___ Muscinae (1)\n| |___ Muscini (1)\n| |___ Musca (2)\n| |___ Oestroidea (2)\n| |___ Calliphoridae (1)\n| |___ Luciliinae (1)\n| |___ Lucilia (1)\n| |___ Sarcophagidae (1)\n| |___ Sarcophaginae (1)\n| |___ Sarcophaga (1)\n| |___ Boettcherisca (1)\n| |___ Tephritoidea (1)\n| |___ Tephritidae (1)\n| |___ Dacinae (1)\n| |___ Ceratitidini (1)\n| |___ Ceratitis (2)\n| |___ Nematocera (10)\n| |___ Bibionomorpha (1)\n| |___ Sciaroidea (1)\n| |___ Cecidomyiidae (1)\n| |___ Cecidomyiinae (1)\n| |___ Oligotrophini (1)\n| |___ Mayetiola (1)\n| |___ Culicomorpha (8)\n| |___ Culicoidea (8)\n| |___ Culicidae (8)\n| |___ Anophelinae (4)\n| |___ Anopheles (4)\n| |___ Cellia (3)\n| |___ Anopheles gambiae (2)\n| |___ Nyssorhynchus (1)\n| |___ darlingi group (1)\n| |___ Culicinae (4)\n| |___ Aedini (3)\n| |___ Aedes (2)\n| |___ Stegomyia (2)\n| |___ Ochlerotatus (1)\n| |___ Protomacleaya (1)\n| |___ Culicini (1)\n| |___ Culex (2)\n| |___ Psychodomorpha (1)\n| |___ Psychodoidea (1)\n| |___ Psychodidae (1)\n| |___ Phlebotominae (1)\n| |___ Phlebotomus (2)\n| |___ Hymenoptera (12)\n| |___ Aculeata (9)\n| |___ Apoidea (5)\n| |___ Apidae (4)\n| |___ Apinae (2)\n| |___ Apini (2)\n| |___ Apis (2)\n| |___ Bombinae (2)\n| |___ Bombini (2)\n| |___ Bombus (3)\n| |___ Pyrobombus (1)\n| |___ Megachilidae (1)\n| |___ Megachilinae (1)\n| |___ Megachilini (1)\n| |___ Megachile (1)\n| |___ Vespoidea (4)\n| |___ Formicidae (4)\n| |___ Formicinae (1)\n| |___ Camponotini (1)\n| |___ Camponotus (1)\n| |___ Myrmicinae (2)\n| |___ Attini (1)\n| |___ Acromyrmex (1)\n| |___ Solenopsidini (1)\n| |___ Solenopsis (1)\n| |___ Ponerinae (1)\n| |___ Ponerini (1)\n| |___ Harpegnathos (1)\n| |___ Chalcidoidea (2)\n| |___ Pteromalidae (2)\n| |___ Pteromalinae (2)\n| |___ Hobbya (1)\n| |___ Nasonia (1)\n| |___ Ichneumonoidea (1)\n| |___ Braconidae (1)\n| |___ Aphidiinae (1)\n| |___ Lysiphlebus (1)\n| |___ Siphonaptera (2)\n| |___ Pulicomorpha (2)\n| |___ Pulicoidea (2)\n| |___ Pulicidae (2)\n| |___ Archaeopsyllinae (1)\n| |___ Ctenocephalides (1)\n| |___ Xenopsyllinae (1)\n| |___ Xenopsylla (1)\n| |___ Orthopteroidea (7)\n| |___ Dictyoptera (4)\n| |___ Blattodea (2)\n| |___ Blaberoidea (1)\n| |___ Ectobiidae (1)\n| |___ Blattellinae (1)\n| |___ Blattella (1)\n| |___ Blattoidea (1)\n| |___ Blattidae (1)\n| |___ Blattinae (1)\n| |___ Periplaneta (1)\n| |___ Isoptera (2)\n| |___ Rhinotermitidae (2)\n| |___ Coptotermitinae (1)\n| |___ Coptotermes (1)\n| |___ Heterotermitinae (1)\n| |___ Reticulitermes (2)\n| |___ Orthoptera (3)\n| |___ Caelifera (2)\n| |___ Acridoidea (2)\n| |___ Acrididae (2)\n| |___ Cyrtacanthacridinae (1)\n| |___ Schistocerca (1)\n| |___ Oedipodinae (1)\n| |___ Locusta (1)\n| |___ Ensifera (1)\n| |___ Grylloidea (1)\n| |___ Gryllidae (1)\n| |___ Gryllinae (1)\n| |___ Gryllus (1)\n| |___ Paraneoptera (9)\n| |___ Hemiptera (8)\n| |___ Aleyrodoidea (1)\n| |___ Aleyrodidae (1)\n| |___ Aleyrodinae (1)\n| |___ Bemisia (1)\n| |___ Aphidoidea (1)\n| |___ Aphididae (1)\n| |___ Aphidinae (1)\n| |___ Macrosiphini (1)\n| |___ Acyrthosiphon (1)\n| |___ Coccoidea (1)\n| |___ Pseudococcidae (1)\n| |___ Maconellicoccus (1)\n| |___ Coreoidea (1)\n| |___ Alydidae (1)\n| |___ Riptortus (1)\n| |___ Membracoidea (2)\n| |___ Cicadellidae (2)\n| |___ Cicadellinae (2)\n| |___ Cicadellini (1)\n| |___ Graphocephala (1)\n| |___ Homalodisca (1)\n| |___ Psylloidea (1)\n| |___ Psyllidae (1)\n| |___ Diaphorina (1)\n| |___ Reduvioidea (1)\n| |___ Reduviidae (1)\n| |___ Triatominae (1)\n| |___ Triatoma (1)\n| |___ Phthiraptera (1)\n| |___ Anoplura (1)\n| |___ Pediculidae (1)\n| |___ Pediculus (1)\n| |___ Pediculus humanus (1)\n| |___ Chordata (34)\n| |___ Cephalochordata (1)\n| |___ Branchiostomidae (1)\n| |___ Branchiostoma (1)\n| |___ Craniata (32)\n| |___ Gnathostomata (32)\n| |___ Actinopterygii (8)\n| |___ Acanthopterygii (6)\n| |___ Beloniformes (1)\n| |___ Adrianichthyoidei (1)\n| |___ Adrianichthyidae (1)\n| |___ Oryziinae (1)\n| |___ Oryzias (1)\n| |___ Cyprinodontiformes (1)\n| |___ Cyprinodontoidei (1)\n| |___ Poeciliidae (1)\n| |___ Poeciliinae (1)\n| |___ Xiphophorus (1)\n| |___ Perciformes (2)\n| |___ Labroidei (2)\n| |___ Cichlidae (2)\n| |___ Pseudocrenilabrinae (2)\n| |___ Haplochromini (1)\n| |___ Pundamilia (1)\n| |___ Oreochromini (1)\n| |___ Oreochromis (1)\n| |___ Tetraodontiformes (2)\n| |___ Tetraodontoidei (2)\n| |___ Tetradontoidea (2)\n| |___ Tetraodontidae (2)\n| |___ Takifugu (1)\n| |___ Tetraodon (1)\n| |___ Cypriniformes (1)\n| |___ Cyprinoidea (1)\n| |___ Cyprinidae (1)\n| |___ Danio (1)\n| |___ Salmoniformes (1)\n| |___ Salmonoidei (1)\n| |___ Salmonidae (1)\n| |___ Salmoninae (1)\n| |___ Salmo (1)\n| |___ Amphibia (2)\n| |___ Batrachia (2)\n| |___ Anura (2)\n| |___ Pipoidea (2)\n| |___ Pipidae (2)\n| |___ Xenopodinae (2)\n| |___ Xenopus (3)\n| |___ Silurana (1)\n| |___ Aves (4)\n| |___ Neognathae (4)\n| |___ Anseriformes (1)\n| |___ Anatidae (1)\n| |___ Anas (1)\n| |___ Galliformes (1)\n| |___ Phasianidae (1)\n| |___ Phasianinae (1)\n| |___ Gallus (1)\n| |___ Passeriformes (2)\n| |___ Muscicapidae (1)\n| |___ Ficedula (1)\n| |___ Passeroidea (1)\n| |___ Fringillidae (1)\n| |___ Emberizinae (1)\n| |___ Thraupini (1)\n| |___ Geospiza (1)\n| |___ Lepidosauria (2)\n| |___ Squamata (2)\n| |___ Iguania (1)\n| |___ Iguanidae (1)\n| |___ Polychrotinae (1)\n| |___ Anolis (1)\n| |___ Serpentes (1)\n| |___ Colubroidea (1)\n| |___ Elapidae (1)\n| |___ Elapinae (1)\n| |___ Ophiophagus (1)\n| |___ Mammalia (16)\n| |___ Didelphimorphia (1)\n| |___ Didelphidae (1)\n| |___ Didelphinae (1)\n| |___ Monodelphis (1)\n| |___ Euarchontoglires (10)\n| |___ Primates (4)\n| |___ Haplorrhini (4)\n| |___ Simiiformes (4)\n| |___ Catarrhini (3)\n| |___ Cercopithecoidea (1)\n| |___ Cercopithecidae (1)\n| |___ Cercopithecinae (1)\n| |___ Papio (1)\n| |___ Hominoidea (2)\n| |___ Hominidae (2)\n| |___ Homininae (2)\n| |___ Homo (1)\n| |___ Pan (1)\n| |___ Platyrrhini (1)\n| |___ Cebidae (1)\n| |___ Callitrichinae (1)\n| |___ Callithrix (1)\n| |___ Rodentia (6)\n| |___ Hystricognathi (3)\n| |___ Caviidae (1)\n| |___ Cavia (1)\n| |___ Chinchillidae (1)\n| |___ Chinchilla (1)\n| |___ Octodontidae (1)\n| |___ Octodon (1)\n| |___ Sciurognathi (3)\n| |___ Muridae (2)\n| |___ Murinae (2)\n| |___ Mus (2)\n| |___ Rattus (1)\n| |___ Sciuridae (1)\n| |___ Xerinae (1)\n| |___ Marmotini (1)\n| |___ Ictidomys (1)\n| |___ Laurasiatheria (4)\n| |___ Carnivora (1)\n| |___ Caniformia (1)\n| |___ Canidae (1)\n| |___ Canis (1)\n| |___ Canis lupus (1)\n| |___ Cetacea (1)\n| |___ Odontoceti (1)\n| |___ Delphinidae (1)\n| |___ Orcinus (1)\n| |___ Chiroptera (1)\n| |___ Microchiroptera (1)\n| |___ Vespertilionidae (1)\n| |___ Myotis (1)\n| |___ Tylopoda (1)\n| |___ Camelidae (1)\n| |___ Vicugna (1)\n| |___ Monotremata (1)\n| |___ Ornithorhynchidae (1)\n| |___ Ornithorhynchus (1)\n| |___ Tunicata (1)\n| |___ Appendicularia (1)\n| |___ Oikopleuridae (1)\n| |___ Oikopleura (1)\n| |___ Echinodermata (1)\n| |___ Echinozoa (1)\n| |___ Echinoidea (1)\n| |___ Euechinoidea (1)\n| |___ Echinacea (1)\n| |___ Echinoida (1)\n| |___ Strongylocentrotidae (1)\n| |___ Strongylocentrotus (1)\n| |___ Hemichordata (1)\n| |___ Enteropneusta (1)\n| |___ Harrimaniidae (1)\n| |___ Saccoglossus (1)\n| |___ Mollusca (4)\n| |___ Bivalvia (2)\n| |___ Pteriomorphia (2)\n| |___ Ostreoida (1)\n| |___ Ostreoidea (1)\n| |___ Ostreidae (1)\n| |___ Crassostrea (1)\n| |___ Pectinoida (1)\n| |___ Pectinoidea (1)\n| |___ Pectinidae (1)\n| |___ Argopecten (1)\n| |___ Gastropoda (2)\n| |___ Aplysioidea (1)\n| |___ Aplysiidae (1)\n| |___ Aplysia (1)\n| |___ Lottioidea (1)\n| |___ Lottiidae (1)\n| |___ Lottia (1)\n| |___ Nematoda (2)\n| |___ Chromadorea (2)\n| |___ Ascaridida (1)\n| |___ Ascaridoidea (1)\n| |___ Ascarididae (1)\n| |___ Ascaris (1)\n| |___ Rhabditida (1)\n| |___ Strongylida (1)\n| |___ Trichostrongyloidea (1)\n| |___ Haemonchidae (1)\n| |___ Haemonchinae (1)\n| |___ Haemonchus (1)\n| |___ Placozoa (1)\n| |___ Trichoplax (1)\n| |___ Porifera (1)\n| |___ Demospongiae (1)\n| |___ Ceractinomorpha (1)\n| |___ Haplosclerida (1)\n| |___ Niphatidae (1)\n| |___ Amphimedon (1)\n"
}
],
"prompt_number": 400
},
{
"cell_type": "code",
"collapsed": false,
"input": "tree.save2file(\"tree.txt\")",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 402
}
],
"metadata": {}
}
]
}
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