{ "metadata": { "name": "", "signature": "sha256:292724af375076d064649042cf460365dbc52ff26fd210bfd69773a36d532f50" }, "nbformat": 3, "nbformat_minor": 0, "worksheets": [ { "cells": [ { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Annotation (Blast)" ] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Trinity Assembly" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \">\" /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "145222\r\n" ] } ], "prompt_number": 6 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail -5 /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">c391854_g1_i1 len=228 path=[1:0-227]\r\n", "GTTTTTTCTTTCTCTATTTTTGGTTACCTTTTAGTTTTTAAAACAAATTGGCAAATTGTT\r\n", "ATTCACCAGGGTATTTAGTTACAATTCAGCATGCATCTTTTGGGGGATACTTGGAAGTAT\r\n", "TGGCCCTTGCAGTATAGTTTCTGTTTTGTTATATTGGACCTAATGAAAGTTGTGTTATAT\r\n", "TGGACCCAGTGCAGGTTATATGTTATAATGGACCCCACAGAACATTTT\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/web/whale/blast/db/uniprot_sprot \\\n", "-out /Volumes/web/cnidarian/seastar_trinity1_uniport_sprot.tab \\\n", "-evalue 1E-20 \\\n", "-max_target_seqs 1 \\\n", "-outfmt 6 \\\n", "-num_threads 6" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/seastar_trinity1_uniport_sprot.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "c120_g1_i1\tsp|O06411|PIT_MYCTU\t69.14\t81\t25\t0\t307\t65\t255\t335\t7e-30\t 114\r\n", "c1231_g1_i1\tsp|Q57IW8|FEOB_SALCH\t48.20\t139\t71\t1\t3\t419\t455\t592\t1e-38\t 143\r\n", "c1262_g1_i1\tsp|Q8CQ17|SAER_STAES\t99.14\t116\t1\t0\t457\t110\t114\t229\t2e-78\t 238\r\n", "c1367_g1_i1\tsp|Q0VGK4|GDPD1_RAT\t45.45\t110\t58\t1\t1\t330\t87\t194\t2e-24\t98.6\r\n", "c1630_g1_i1\tsp|P37965|GLPQ_BACSU\t62.50\t96\t35\t1\t290\t3\t110\t204\t1e-27\t 106\r\n", "c2156_g1_i1\tsp|Q96MW7|TIGD1_HUMAN\t65.62\t64\t22\t0\t5\t196\t290\t353\t7e-22\t92.4\r\n", "c2356_g1_i1\tsp|Q9K9G9|FAPD_BACHD\t73.15\t108\t29\t0\t1\t324\t209\t316\t1e-51\t 173\r\n", "c2398_g1_i1\tsp|O14981|BTAF1_HUMAN\t82.61\t115\t20\t0\t345\t1\t1389\t1503\t3e-62\t 211\r\n", "c2437_g1_i1\tsp|O13066|RAGP1_XENLA\t59.27\t329\t133\t1\t1052\t69\t30\t358\t8e-121\t 367\r\n", "c2471_g1_i1\tsp|P35881|TRA5_LACLA\t100.00\t108\t0\t0\t2\t325\t116\t223\t9e-73\t 227\r\n" ] } ], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [ "blastn \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/nt \\\n", "-out /Volumes/web/cnidarian/seastar_trin_nt_3.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 14 \\\n", "-max_hsps 1 \\\n", "-evalue 1E-20 \\\n", "-max_target_seqs 1 \\\n", "-task blastn\n", "#running on hummingbird - COMPLETE" ], "language": "python", "metadata": {}, "outputs": [ { "ename": "SyntaxError", "evalue": "invalid syntax (, line 1)", "output_type": "pyerr", "traceback": [ "\u001b[0;36m File \u001b[0;32m\"\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m blastn -query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta -db /Volumes/Data/blast_db/nt -out /Volumes/web/cnidarian/seastar_trin_nt_3.tab -outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" -num_threads 14 -max_hsps 1 -evalue 1E-20 -max_target_seqs 1 -task blastn\u001b[0m\n\u001b[0m ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n" ] } ], "prompt_number": 5 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/seastar_trin_nt_3.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "c144_g1_i1\tgi|3850557|gb|AC005947.1|AC005947\t99.19\t248\t5e-120\t 439\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens chromosome 19, cosmid R30373, complete sequence\r\n", "c206_g1_i1\tgi|11544493|emb|AL355984.11|\t96.85\t222\t9e-98\t 365\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHuman DNA sequence from clone RP11-501K3 on chromosome 13, complete sequence\r\n", "c636_g1_i1\tgi|9664668|gb|AF269347.1|AF269347\t100.00\t207\t1e-100\t 374\t1282\tStaphylococcus epidermidis\tStaphylococcus epidermidis\tfirmicutes\tBacteria\tStaphylococcus epidermidis strain SR1 clone step.1002d09 genomic sequence\r\n", "c637_g1_i1\tgi|19697316|gb|AC092958.4|\t100.00\t204\t6e-99\t 369\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens 3 BAC RP11-639B1 (Roswell Park Cancer Institute Human BAC Library) complete sequence\r\n", "c647_g1_i1\tgi|15187234|gb|AC020925.8|\t100.00\t239\t7e-118\t 432\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens chromosome 5 clone CTD-2134K2, complete sequence\r\n", "c712_g1_i1\tgi|11321810|gb|AC007717.8|AC007717\t99.59\t242\t7e-118\t 432\t9606\t" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "Homo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens chromosome 18, clone RP11-315O17, complete sequence\r\n", "c751_g1_i1\tgi|20279379|gb|AC026392.7|\t97.39\t153\t8e-66\t 259\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens chromosome 10 clone RP11-238C10, complete sequence\r\n", "c760_g1_i1\tgi|13157563|emb|AL357149.13|\t98.71\t233\t3e-110\t 407\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHuman DNA sequence from clone RP11-352E13 on chromosome 6, complete sequence\r\n", "c774_g1_i1\tgi|517309970|emb|HF679023.1|\t99.62\t262\t1e-128\t 468\t1279085\tFusarium fujikuroi IMI 58289\tFusarium fujikuroi IMI 58289\tascomycetes\tEukaryota\tFusarium fujikuroi IMI 58289 draft genome, chromosome FFUJ_chr01\r\n", "c861_g1_i1\tgi|14970792|emb|AL139406.14|\t100.00\t203\t2e-98\t 367\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHuman DNA sequence from clone RP11-425M17 on chromosome 10, complete sequence\r\n" ] } ], "prompt_number": 60 }, { "cell_type": "code", "collapsed": false, "input": [ "!wget http://eagle.fish.washington.edu/cnidarian/seastar_trin_nt_3.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "--2014-07-30 07:16:15-- http://eagle.fish.washington.edu/cnidarian/seastar_trin_nt_3.tab\r\n", "Resolving eagle.fish.washington.edu... 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"stream", "stream": "stdout", "text": [ "\r", "98% [=====================================> ] 7,404,287 270K/s eta 5s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "100%[======================================>] 7,532,329 303K/s in 98s \r\n", "\r\n", "2014-07-30 07:17:54 (74.9 KB/s) - `seastar_trin_nt_3.tab' saved [7532329/7532329]\r\n", "\r\n" ] } ], "prompt_number": 63 }, { "cell_type": "code", "collapsed": false, "input": [ "!grep \"virus\" /Volumes/web/cnidarian/seastar_trin_nt_3.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "c5107_g1_i1\tgi|73697523|gb|DQ112131.1|\t98.62\t218\t4e-102\t 379\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens endogenous virus Human endogenous retrovirus K HERV-K7, complete sequence\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c9659_g1_i1\tgi|430768498|dbj|AB618031.1|\t99.50\t201\t1e-95\t 358\t946522\tHerpes simplex virus (type 1 /strain RH2)\tHerpes simplex virus (type 1 /strain RH2)\tviruses\tViruses\tHerpes simplex virus (type 1 /strain RH2) DNA, nearly complete genome\r\n", "c14533_g1_i1\tgi|113715669|gb|DQ453159.1|\t92.38\t223\t9e-85\t 322\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c36532_g1_i1\tgi|294478921|gb|GU568037.1|\t83.33\t306\t1e-84\t 322\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c66484_g1_i1\tgi|375281968|gb|JN700521.1|\t97.54\t203\t2e-91\t 343\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c72379_g1_i1\tgi|375281968|gb|JN700521.1|\t91.29\t241\t4e-90\t 340\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c109304_g1_i1\tgi|400530476|gb|JX142173.1|\t100.00\t223\t3e-109\t 403\t10298\tHuman herpesvirus 1\tHerpes simplex virus type 1\tviruses\tViruses\tHuman herpesvirus 1 strain Mckrae, partial genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c118932_g1_i1\tgi|375281968|gb|JN700521.1|\t97.56\t205\t2e-92\t 347\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c129231_g1_i1\tgi|375281968|gb|JN700521.1|\t83.26\t215\t5e-56\t 226\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c146941_g1_i1\tgi|294478921|gb|GU568037.1|\t79.14\t187\t1e-32\t 149\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c180360_g1_i1\tgi|113715669|gb|DQ453159.1|\t90.82\t196\t4e-70\t 273\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c185354_g1_i1\tgi|430768498|dbj|AB618031.1|\t100.00\t224\t1e-109\t 405\t946522\tHerpes simplex virus (type 1 /strain RH2)\tHerpes simplex virus (type 1 /strain RH2)\tviruses\tViruses\tHerpes simplex virus (type 1 /strain RH2) DNA, nearly complete genome\r\n", "c190527_g1_i1\tgi|375281968|gb|JN700521.1|\t98.41\t377\t0.0\t 654\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c191163_g1_i1\tgi|331028441|ref|NG_028797.1|\t100.00\t224\t1e-109\t 405\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens HERV-FRD provirus ancestral Env polyprotein pseudogene (LOC100533729) on chromosome X\r\n", "c191322_g1_i1\tgi|523707052|gb|KF254382.1|\t99.10\t223\t2e-106\t 394\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens endogenous virus HERV-K clone 11A11.Dm13 nonfunctional envelope protein mRNA, complete sequence\r\n", "c192829_g1_i1\tgi|190410749|gb|DQ840344.2|\t94.94\t257\t1e-109\t 405\t396034\tBacillus virus 1\tBacillus virus 1\tviruses\tViruses\tBacillus virus 1, complete genome\r\n", "c204550_g1_i1\tgi|113715669|gb|DQ453159.1|\t89.17\t240\t6e-81\t 309\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c211254_g1_i1\tgi|340343118|ref|NG_029458.1|\t91.67\t204\t6e-74\t 286\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens coxsackie virus and adenovirus receptor (CXADR), RefSeqGene on chromosome 21\r\n", "c212894_g1_i1\tgi|9836490|dbj|AB047242.1|\t100.00\t212\t3e-103\t 383\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens DNA, 3' flanking region of human endogenous retrovirus HERV-K(III)/K102\r\n", "c222957_g1_i1\tgi|113715669|gb|DQ453159.1|\t85.45\t220\t4e-64\t 253\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c264080_g1_i1\tgi|375281966|gb|JN700519.1|\t81.50\t227\t2e-54\t 221\t1147044\tStaphylococcus phage StB27\tStaphylococcus phage StB27\tviruses\tViruses\tStaphylococcus phage StB27, complete genome\r\n", "c267661_g1_i1\tgi|357197696|gb|JN675087.1|\t99.07\t323\t6e-159\t 569\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_22q11.21 endogenous virus HERV-K, complete sequence\r\n", "c290309_g1_i1\tgi|379979844|gb|JN700520.2|\t91.16\t181\t1e-64\t 255\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c292583_g1_i1\tgi|357197645|gb|JN675036.1|\t97.64\t212\t3e-96\t 360\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_5q33.2 endogenous virus HERV-K, complete sequence\r\n", "c298314_g1_i1\tgi|379979844|gb|JN700520.2|\t76.01\t296\t7e-50\t 206\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c298319_g1_i1\tgi|4959376|gb|AF108842.1|H18HERV2\t97.74\t265\t1e-122\t 448\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens human endogenous retrovirus HERV-H18 pol pseudogene, partial sequence; and env pseudogene and 3' LTR, complete sequence\r\n", "c298749_g1_i1\tgi|407302226|gb|JX262222.1|\t97.12\t208\t6e-93\t 349\t1229791\tPropionibacterium phage P100_1\tPropionibacterium phage P100_1\tviruses\tViruses\tPropionibacterium phage P100_1, complete genome\r\n", "c299795_g1_i1\tgi|113715669|gb|DQ453159.1|\t95.43\t219\t2e-93\t 351\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c300145_g1_i1\tgi|392494166|gb|JN192400.1|\t85.19\t270\t7e-81\t 309\t1197952\tStaphylococcus phage vB_SepiS-phiIPLA5\tStaphylococcus phage vB_SepiS-phiIPLA5\tviruses\tViruses\tStaphylococcus phage vB_SepiS-phiIPLA5, complete genome\r\n", "c300886_g1_i1\tgi|294478921|gb|GU568037.1|\t83.89\t360\t1e-104\t 389\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c300989_g1_i1\tgi|375281968|gb|JN700521.1|\t96.38\t221\t3e-97\t 363\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c302616_g1_i1\tgi|113715669|gb|DQ453159.1|\t82.32\t198\t2e-48\t 201\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c303417_g1_i1\tgi|294478921|gb|GU568037.1|\t87.21\t172\t3e-48\t 201\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c303722_g1_i1\tgi|91982906|gb|DQ431235.1|\t78.45\t478\t3e-103\t 385\t376758\tPropionibacterium phage PA6\tPropionibacterium phage PA6\tviruses\tViruses\tPropionibacterium phage PA6, complete genome\r\n", "c304151_g1_i1\tgi|375281968|gb|JN700521.1|\t87.45\t239\t4e-77\t 297\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c304506_g1_i1\tgi|113715669|gb|DQ453159.1|\t80.95\t252\t1e-59\t 239\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c305123_g1_i1\tgi|375281968|gb|JN700521.1|\t94.34\t265\t3e-111\t 410\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c306132_g1_i1\tgi|113715669|gb|DQ453159.1|\t84.46\t193\t3e-52\t 214\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c306624_g1_i1\tgi|113715669|gb|DQ453159.1|\t71.12\t277\t2e-26\t 129\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c306949_g1_i1\tgi|113715669|gb|DQ453159.1|\t86.75\t166\t2e-48\t 201\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c307243_g1_i1\tgi|113715669|gb|DQ453159.1|\t78.45\t232\t3e-46\t 194\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c307816_g1_i1\tgi|294478921|gb|GU568037.1|\t86.05\t215\t7e-61\t 242\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c309944_g1_i1\tgi|407302132|gb|JX262220.1|\t96.77\t341\t7e-158\t 565\t1229789\tPropionibacterium phage P100D\tPropionibacterium phage P100D\tviruses\tViruses\tPropionibacterium phage P100D, complete genome\r\n", "c311131_g1_i1\tgi|294478921|gb|GU568037.1|\t99.66\t296\t5e-147\t 529\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c312061_g1_i2\tgi|485726856|gb|KC661278.1|\t74.28\t1563\t0.0\t 976\t1327777\tMycobacterium phage SiSi\tMycobacterium phage SiSi\tviruses\tViruses\tMycobacterium phage SiSi, complete genome\r\n", "c313678_g1_i1\tgi|357197622|gb|JN675013.1|\t97.13\t209\t2e-93\t 351\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_1q23.3 endogenous virus HERV-K, complete sequence\r\n", "c313775_g1_i1\tgi|448927458|gb|JX997161.1|\t77.25\t189\t2e-27\t 134\t1278248\tParamecium bursaria Chlorella virus CVG-1\tParamecium bursaria Chlorella virus CVG-1\tviruses\tViruses\tParamecium bursaria Chlorella virus CVG-1, partial genome\r\n", "c314342_g1_i1\tgi|113715669|gb|DQ453159.1|\t90.09\t343\t5e-128\t 466\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c316602_g1_i1\tgi|73697528|gb|DQ112136.1|\t97.64\t212\t3e-96\t 360\t9598\tPan troglodytes\tchimpanzee\tprimates\tEukaryota\tPan troglodytes endogenous virus Chimpanzee endogenous retrovirus K CERV-K60, complete sequence\r\n", "c317379_g1_i1\tgi|113715669|gb|DQ453159.1|\t80.61\t165\t3e-34\t 154\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c319887_g1_i1\tgi|541905708|gb|KF558370.1|\t78.92\t204\t1e-38\t 168\t10372\tHuman herpesvirus 7\tHuman herpesvirus 7\tviruses\tViruses\tHuman herpesvirus 7 isolate UCL-1, partial genome\r\n", "c320673_g1_i1\tgi|407301898|gb|JX262215.1|\t95.77\t213\t3e-91\t 343\t1229782\tPropionibacterium phage P9.1\tPropionibacterium phage P9.1\tviruses\tViruses\tPropionibacterium phage P9.1, complete genome\r\n", "c322195_g1_i1\tgi|379979844|gb|JN700520.2|\t77.78\t162\t3e-27\t 131\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c323549_g1_i1\tgi|538015421|gb|KC342645.2|\t91.83\t416\t2e-167\t 598\t1273712\tStaphylococcus phage JS01\tStaphylococcus phage JS01\tviruses\tViruses\tStaphylococcus phage JS01, complete genome\r\n", "c323549_g2_i1\tgi|238683986|gb|FJ713816.1|\t80.88\t204\t2e-42\t 181\t648017\tStaphylococcus phage phiPVL-CN125\tStaphylococcus phage phiPVL-CN125\tviruses\tViruses\tStaphylococcus phage phiPVL-CN125, complete genome\r\n", "c323684_g2_i1\tgi|375281968|gb|JN700521.1|\t92.96\t284\t5e-115\t 423\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c324362_g1_i1\tgi|375281968|gb|JN700521.1|\t92.93\t198\t1e-76\t 295\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c326834_g1_i1\tgi|113715669|gb|DQ453159.1|\t76.80\t194\t9e-31\t 143\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c326954_g1_i2\tgi|294478921|gb|GU568037.1|\t96.03\t151\t7e-62\t 246\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c327053_g1_i1\tgi|118566996|gb|DQ831957.1|\t93.54\t573\t0.0\t 866\t398839\tStaphylococcus phage CNPH82\tStaphylococcus phage CNPH82\tviruses\tViruses\tStaphylococcus phage CNPH82, complete genome\r\n", "c327250_g1_i1\tgi|357197676|gb|JN675067.1|\t99.57\t233\t6e-113\t 416\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_12q13.2 endogenous virus HERV-K, complete sequence\r\n", "c327918_g1_i2\tgi|113715669|gb|DQ453159.1|\t89.68\t252\t2e-89\t 338\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c328284_g1_i1\tgi|383395315|gb|JQ086376.1|\t99.80\t999\t0.0\t 1793\t1147146\tEnterobacteria phage HK630\tEnterobacteria phage HK630\tviruses\tViruses\tEnterobacteria phage HK630, complete genome\r\n", "c328543_g1_i1\tgi|357197695|gb|JN675086.1|\t97.55\t286\t2e-133\t 484\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_21q21.1 endogenous virus HERV-K, complete sequence\r\n", "c328588_g1_i1\tgi|8272463|gb|AF156961.1|AF156961\t96.26\t214\t2e-92\t 347\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens human endogenous retrovirus W gagC3.37 G gag (gag) gene, complete cds\r\n", "c328620_g1_i1\tgi|113715669|gb|DQ453159.1|\t78.50\t200\t9e-38\t 167\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c329058_g1_i1\tgi|260066562|gb|FJ706172.1|\t83.89\t298\t4e-84\t 320\t504553\tPropionibacterium phage PAS50\tPropionibacterium phage PAS50\tviruses\tViruses\tPropionibacterium phage PAS50, complete genome\r\n", "c330211_g1_i1\tgi|375281968|gb|JN700521.1|\t96.50\t286\t1e-129\t 471\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c330833_g1_i1\tgi|294478921|gb|GU568037.1|\t97.59\t83\t3e-30\t 141\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c331249_g1_i1\tgi|390353591|ref|XM_783136.3|\t72.48\t367\t6e-46\t 194\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus xenotropic and polytropic retrovirus receptor 1 homolog (LOC583216), mRNA\r\n", "c331425_g1_i1\tgi|113715669|gb|DQ453159.1|\t82.89\t263\t2e-69\t 271\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c331947_g1_i1\tgi|294478921|gb|GU568037.1|\t79.33\t179\t2e-33\t 152\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c332127_g1_i1\tgi|294478921|gb|GU568037.1|\t92.49\t213\t4e-82\t 313\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c333085_g1_i1\tgi|342239923|gb|JN256079.1|\t77.29\t753\t5e-161\t 578\t1056830\tMycobacterium phage Charlie\tMycobacterium phage Charlie\tviruses\tViruses\tMycobacterium phage Charlie, complete genome\r\n", "c333200_g1_i2\tgi|73697518|gb|DQ112126.1|\t97.45\t196\t2e-87\t 331\t9598\tPan troglodytes\tchimpanzee\tprimates\tEukaryota\tPan troglodytes endogenous virus Chimpanzee endogenous retrovirus K CERV-KOLD35587, complete sequence\r\n", "c333502_g1_i2\tgi|12831080|gb|AF323672.1|\t99.02\t307\t3e-150\t 540\t151534\tLactococcus phage bIL311\tLactococcus phage bIL311\tviruses\tViruses\tBacteriophage bIL311, complete genome\r\n", "c335392_g1_i1\tgi|375281968|gb|JN700521.1|\t95.35\t86\t2e-29\t 138\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c335969_g1_i4\tgi|113715669|gb|DQ453159.1|\t85.32\t470\t6e-148\t 533\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c336566_g1_i1\tgi|407301992|gb|JX262217.1|\t72.21\t878\t2e-121\t 446\t1229786\tPropionibacterium phage P101A\tPropionibacterium phage P101A\tviruses\tViruses\tPropionibacterium phage P101A, complete genome\r\n", "c336751_g1_i3\tgi|533122128|ref|XM_005376350.1|\t70.04\t277\t2e-23\t 120\t34839\tChinchilla lanigera\tlong-tailed chinchilla\trodents\tEukaryota\tPREDICTED: Chinchilla lanigera BCL2/adenovirus E1B 19kDa interacting protein 1 (Bnip1), transcript variant X2, mRNA\r\n", "c336846_g1_i1\tgi|113715669|gb|DQ453159.1|\t98.79\t247\t8e-118\t 432\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c337779_g1_i1\tgi|379979844|gb|JN700520.2|\t73.15\t216\t3e-23\t 118\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c337960_g1_i1\tgi|357197677|gb|JN675068.1|\t98.99\t296\t2e-144\t 520\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_12q14.1 endogenous virus HERV-K, complete sequence\r\n", "c338683_g1_i2\tgi|294478921|gb|GU568037.1|\t86.56\t186\t2e-53\t 219\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c339068_g1_i1\tgi|113715669|gb|DQ453159.1|\t86.18\t152\t1e-39\t 172\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c339068_g2_i1\tgi|523496554|dbj|AB823818.1|\t76.51\t149\t3e-21\t 111\t1352230\tThermus phage phi OH2\tThermus phage phi OH2\tviruses\tViruses\tPhage phi OH2 DNA, complete genome\r\n", "c339606_g2_i1\tgi|73697539|gb|DQ112147.1|\t99.23\t647\t0.0\t 1144\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens endogenous virus Human endogenous retrovirus K HERV-K50B, complete sequence\r\n", "c339606_g3_i1\tgi|87196989|gb|DQ360576.1|\t99.71\t345\t1e-173\t 618\t45617\tHuman endogenous retrovirus K\tHuman endogenous retrovirus K\tviruses\tViruses\tHuman endogenous retrovirus K clone 5b9 envelope glycoprotein (env) gene, partial cds\r\n", "c340708_g2_i1\tgi|407301992|gb|JX262217.1|\t97.92\t288\t3e-136\t 493\t1229786\tPropionibacterium phage P101A\tPropionibacterium phage P101A\tviruses\tViruses\tPropionibacterium phage P101A, complete genome\r\n", "c341050_g1_i3\tgi|5764573|gb|AF172471.1|\t94.42\t197\t9e-79\t 302\t9593\tGorilla gorilla\twestern gorilla\tprimates\tEukaryota\tGorilla gorilla endogenous virus HERV-K-like retrovirus LTR, sequence\r\n", "c341111_g1_i1\tgi|357197650|gb|JN675041.1|\t95.06\t445\t0.0\t 700\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_6q14.1 endogenous virus HERV-K, complete sequence\r\n", "c341187_g1_i1\tgi|357197642|gb|JN675033.1|\t98.20\t222\t3e-103\t 383\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_4q35.2 endogenous virus HERV-K, complete sequence\r\n", "c342206_g1_i1\tgi|357197623|gb|JN675014.1|\t99.27\t410\t0.0\t 722\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_1q22 endogenous virus HERV-K, complete sequence\r\n", "c342380_g1_i3\tgi|294478921|gb|GU568037.1|\t94.85\t97\t9e-34\t 152\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c343731_g1_i2\tgi|113715669|gb|DQ453159.1|\t86.58\t231\t3e-71\t 277\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c343919_g1_i2\tgi|113715669|gb|DQ453159.1|\t81.77\t373\t4e-98\t 367\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c343919_g2_i2\tgi|294478921|gb|GU568037.1|\t73.92\t464\t4e-75\t 291\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c349356_g3_i3\tgi|148278805|gb|EF580878.1|\t84.36\t211\t2e-55\t 224\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens IntegrationSite702 Human T-lymphotropic virus 1 integration site\r\n", "c349413_g1_i3\tgi|357197692|gb|JN675083.1|\t94.87\t273\t3e-117\t 430\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens isolate HML-2_19q13.41 endogenous virus HERV-K, complete sequence\r\n", "c350951_g1_i5\tgi|82522791|gb|DQ192837.1|\t97.17\t212\t5e-95\t 356\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens 403_1 foamy virus integration site genomic sequence\r\n", "c351626_g1_i1\tgi|390353395|ref|XM_786195.3|\t68.45\t1141\t2e-107\t 401\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus feline leukemia virus subgroup C receptor-related protein 2-like (LOC586411), mRNA\r\n", "c351626_g1_i2\tgi|543350788|ref|XM_005520402.1|\t72.17\t327\t3e-36\t 165\t181119\tPseudopodoces humilis\tTibetan ground-tit\tbirds\tEukaryota\tPREDICTED: Pseudopodoces humilis feline leukemia virus subgroup C cellular receptor family, member 2 (FLVCR2), mRNA\r\n", "c353622_g1_i3\tgi|526120503|gb|KC961304.1|\t69.23\t312\t1e-23\t 123\t1367205\tChoristoneura rosaceana alphabaculovirus\tChoristoneura rosaceana alphabaculovirus\tviruses\tViruses\tChoristoneura rosaceana alphabaculovirus, complete genome\r\n", "c354442_g5_i1\tgi|390356247|ref|XM_786933.3|\t67.97\t434\t6e-32\t 149\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus BCL2/adenovirus E1B 19 kDa protein-interacting protein 3-like (LOC587188), mRNA\r\n", "c354456_g1_i2\tgi|182206|gb|M85205.1|HUMERV\t91.76\t267\t4e-103\t 383\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHuman endogenous retrovirus pHE.1 mRNA sequence\r\n", "c355035_g2_i1\tgi|439709|dbj|D14469.1|CHVK1F1\t81.10\t127\t2e-22\t 118\t10507\tChlorella virus\tChlorella virus\tviruses\tViruses\tChlorella virus CVK1F1 gene, repeat region\r\n", "c356299_g2_i1\tgi|523707000|gb|KF254345.1|\t99.63\t273\t2e-134\t 488\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens endogenous virus HERV-K clone GGL2-03 mRNA sequence\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c356370_g3_i4\tgi|148278809|gb|EF580882.1|\t82.26\t389\t5e-104\t 387\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens IntegrationSite706 Human T-lymphotropic virus 1 integration site\r\n", "c356405_g1_i1\tgi|39546497|gb|AY394587.1|\t80.18\t227\t1e-45\t 192\t9785\tLoxodonta africana\tAfrican savanna elephant\tplacentals\tEukaryota\tLoxodonta africana endogenous virus ERV-L clone LOX8 nonfunctional reverse transcriptase, partial sequence\r\n", "c356530_g1_i1\tgi|407302226|gb|JX262222.1|\t94.52\t16785\t0.0\t26079\t1229791\tPropionibacterium phage P100_1\tPropionibacterium phage P100_1\tviruses\tViruses\tPropionibacterium phage P100_1, complete genome\r\n", "c356530_g1_i5\tgi|407302226|gb|JX262222.1|\t94.62\t16610\t0.0\t25886\t1229791\tPropionibacterium phage P100_1\tPropionibacterium phage P100_1\tviruses\tViruses\tPropionibacterium phage P100_1, complete genome\r\n", "c356530_g1_i6\tgi|260066562|gb|FJ706172.1|\t93.49\t522\t0.0\t 789\t504553\tPropionibacterium phage PAS50\tPropionibacterium phage PAS50\tviruses\tViruses\tPropionibacterium phage PAS50, complete genome\r\n", "c356541_g1_i2\tgi|407302086|gb|JX262219.1|\t93.73\t7006\t0.0\t10632\t1229788\tPropionibacterium phage P105\tPropionibacterium phage P105\tviruses\tViruses\tPropionibacterium phage P105, complete genome\r\n", "c356541_g4_i1\tgi|407301898|gb|JX262215.1|\t91.70\t1783\t0.0\t 2544\t1229782\tPropionibacterium phage P9.1\tPropionibacterium phage P9.1\tviruses\tViruses\tPropionibacterium phage P9.1, complete genome\r\n", "c360790_g1_i1\tgi|402761649|gb|JX274647.1|\t80.46\t174\t2e-35\t 158\t1211286\tStaphylococcus phage SP6\tStaphylococcus phage SP6\tviruses\tViruses\tStaphylococcus phage SP6, complete genome\r\n", "c361160_g1_i1\tgi|379979844|gb|JN700520.2|\t78.60\t215\t2e-42\t 181\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c362310_g1_i1\tgi|375281968|gb|JN700521.1|\t92.05\t264\t1e-102\t 381\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c362793_g1_i1\tgi|2801468|gb|AF033811.1|AF033811\t100.00\t314\t3e-158\t 567\t11801\tMoloney murine leukemia virus\tMoloney murine leukemia virus\tviruses\tViruses\tMoloney murine leukemia virus, complete genome\r\n", "c365378_g1_i1\tgi|343488517|ref|NG_029732.1|\t100.00\t270\t1e-134\t 488\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens v-ets avian erythroblastosis virus E26 oncogene homolog (ERG), RefSeqGene on chromosome 21\r\n", "c367384_g1_i1\tgi|113715669|gb|DQ453159.1|\t92.69\t219\t2e-85\t 324\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c367513_g1_i1\tgi|392494233|gb|JN192401.1|\t88.14\t253\t5e-83\t 316\t1197953\tStaphylococcus phage vB_SepiS-phiIPLA7\tStaphylococcus phage vB_SepiS-phiIPLA7\tviruses\tViruses\tStaphylococcus phage vB_SepiS-phiIPLA7, complete genome\r\n", "c367639_g1_i1\tgi|294478921|gb|GU568037.1|\t76.90\t303\t2e-57\t 232\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c368199_g1_i1\tgi|375281968|gb|JN700521.1|\t92.17\t115\t1e-37\t 165\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n" ] }, { "output_type": "stream", "stream": "stdout", "text": [ "c369387_g1_i1\tgi|392494233|gb|JN192401.1|\t100.00\t216\t2e-105\t 390\t1197953\tStaphylococcus phage vB_SepiS-phiIPLA7\tStaphylococcus phage vB_SepiS-phiIPLA7\tviruses\tViruses\tStaphylococcus phage vB_SepiS-phiIPLA7, complete genome\r\n", "c369407_g1_i1\tgi|82522749|gb|DQ192795.1|\t100.00\t291\t5e-146\t 526\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens 395_17 foamy virus integration site genomic sequence\r\n", "c370122_g1_i1\tgi|375281968|gb|JN700521.1|\t98.12\t426\t0.0\t 733\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c370337_g1_i1\tgi|340343118|ref|NG_029458.1|\t100.00\t211\t1e-102\t 381\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens coxsackie virus and adenovirus receptor (CXADR), RefSeqGene on chromosome 21\r\n", "c371542_g1_i1\tgi|124295486|gb|DQ340064.2|\t91.53\t295\t6e-114\t 419\t365048\tGeobacillus phage GBSV1\tGeobacillus phage GBSV1\tviruses\tViruses\tGeobacillus phage GBSV1, complete genome\r\n", "c372160_g1_i1\tgi|430768498|dbj|AB618031.1|\t100.00\t209\t1e-101\t 378\t946522\tHerpes simplex virus (type 1 /strain RH2)\tHerpes simplex virus (type 1 /strain RH2)\tviruses\tViruses\tHerpes simplex virus (type 1 /strain RH2) DNA, nearly complete genome\r\n", "c372969_g1_i1\tgi|375281968|gb|JN700521.1|\t95.54\t202\t2e-85\t 324\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c375796_g1_i1\tgi|116235513|gb|DQ908929.1|\t79.67\t182\t3e-34\t 154\t405947\tStaphylococcus phage 80\tStaphylococcus phage 80\tviruses\tViruses\tStaphylococcus phage 80, complete genome\r\n", "c376029_g1_i1\tgi|343488517|ref|NG_029732.1|\t99.55\t223\t1e-107\t 398\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens v-ets avian erythroblastosis virus E26 oncogene homolog (ERG), RefSeqGene on chromosome 21\r\n", "c378159_g1_i1\tgi|375281968|gb|JN700521.1|\t96.03\t277\t3e-123\t 450\t1147043\tStaphylococcus phage StB20\tStaphylococcus phage StB20\tviruses\tViruses\tStaphylococcus phage StB20, complete genome\r\n", "c379336_g1_i1\tgi|392494166|gb|JN192400.1|\t96.88\t256\t3e-116\t 426\t1197952\tStaphylococcus phage vB_SepiS-phiIPLA5\tStaphylococcus phage vB_SepiS-phiIPLA5\tviruses\tViruses\tStaphylococcus phage vB_SepiS-phiIPLA5, complete genome\r\n", "c379480_g1_i1\tgi|261278322|ref|NG_013083.1|\t100.00\t247\t3e-122\t 446\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens poliovirus receptor-related 1 (herpesvirus entry mediator C) (PVRL1), RefSeqGene on chromosome 11\r\n", "c380097_g1_i1\tgi|379979844|gb|JN700520.2|\t91.30\t115\t6e-36\t 159\t1147042\tStaphylococcus phage StB12\tStaphylococcus phage StB12\tviruses\tViruses\tStaphylococcus phage StB12, complete genome\r\n", "c381323_g1_i1\tgi|294478921|gb|GU568037.1|\t91.67\t228\t9e-85\t 322\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c381723_g1_i1\tgi|321157037|emb|FR671407.1|\t96.83\t221\t2e-98\t 367\t870471\tStreptococcus phage 34117\tStreptococcus phage 34117\tviruses\tViruses\tStreptococcus phage 34117\r\n", "c382172_g1_i1\tgi|347658928|ref|NG_030026.1|\t100.00\t213\t8e-104\t 385\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens human immunodeficiency virus type I enhancer binding protein 3 (HIVEP3), RefSeqGene on chromosome 1\r\n", "c383223_g1_i1\tgi|113715669|gb|DQ453159.1|\t81.68\t202\t2e-47\t 197\t447909\tGeobacillus virus E2\tGeobacillus virus E2\tviruses\tViruses\tGeobacillus virus E2, complete genome\r\n", "c383788_g1_i1\tgi|294478921|gb|GU568037.1|\t95.95\t148\t3e-60\t 241\t749413\tDeep-sea thermophilic phage D6E\tDeep-sea thermophilic phage D6E\tviruses\tViruses\tDeep-sea thermophilic phage D6E, complete genome\r\n", "c386747_g1_i1\tgi|17646227|gb|AF411058.1|\t100.00\t269\t4e-134\t 486\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens clone BAC_22700 cytotoxic T-lymphocyte-associated protein 4 (CTLA4) and inducible T-cell co-stimulator (ICOS) genes, complete cds; and endogenous virus HERV-H, partial sequence\r\n", "c386864_g1_i1\tgi|302486955|ref|NG_024228.1|\t93.61\t219\t6e-87\t 329\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens BCL2/adenovirus E1B 19kDa interacting protein 3 pseudogene (LOC100421703) on chromosome 19\r\n", "c387552_g1_i1\tgi|260593638|ref|NG_013006.1|\t99.52\t208\t2e-99\t 370\t9606\tHomo sapiens\thuman\tprimates\tEukaryota\tHomo sapiens complement component (3d/Epstein Barr virus) receptor 2 (CR2), RefSeqGene on chromosome 1\r\n", "c388401_g1_i1\tgi|8918415|dbj|AP001553.1|\t76.00\t200\t1e-31\t 145\t106284\tStaphylococcus phage phiETA\tStaphylococcus phage phiETA\tviruses\tViruses\tStaphylococcus phage phiETA DNA, complete genome\r\n", "c388944_g1_i1\tgi|392494166|gb|JN192400.1|\t96.82\t283\t5e-129\t 470\t1197952\tStaphylococcus phage vB_SepiS-phiIPLA5\tStaphylococcus phage vB_SepiS-phiIPLA5\tviruses\tViruses\tStaphylococcus phage vB_SepiS-phiIPLA5, complete genome\r\n", "c391559_g1_i1\tgi|219522368|gb|FJ025921.1|\t100.00\t218\t2e-106\t 394\t585091\tSimian adenovirus 37.1\tSimian adenovirus 37.1\tviruses\tViruses\tSimian adenovirus 37.1, complete genome\r\n" ] } ], "prompt_number": 61 }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/refseq_protein \\\n", "-out /Volumes/web/cnidarian/seastar_trin_reseq_protein_2.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 4 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/nr \\\n", "-out /Volumes/web/cnidarian/seastar_trin_nr_2.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 2 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "blastn \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/est_others \\\n", "-out /Volumes/web/cnidarian/seastar_trin_est_others_2.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 2 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "\n", "#fail\n", "\n", "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/swissprot \\\n", "-out /Volumes/web/cnidarian/seastar_trin_swissprot_2.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 8 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "#fail Segmentation fault: 11\n", "\n", "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar/trinity_assemblies/run1/Trinity.fasta \\\n", "-db /Volumes/Data/blast_db/uniprot_sprot \\\n", "-out /Volumes/web/cnidarian/seastar_trin_uniprot_sprot_2.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 8 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "CLC Assembly" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/SeaStar_transc_v2.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_1\r\n", "CAAATATATGAACGGTTGATTGTCAACGATTAGTACATGTTTTCATTGTTCCCCACGCCC\r\n", "GCCCCCCCCCACTCAAACATTTAAAGTGTGAAATATTATTTATCCACAAATTTCCTTAAA\r\n", "CCTGCAAACTTGTCTGCTGTCTCTTATTGGAAGTTATGAAAAAGAACAACGGGTTTTCTT\r\n", "TAAAGGGTCTGCGTGCGATTTTCAACCTTTTGAGTAATAGCAGTTATTTTGATAACCGAT\r\n", "TTTTTTCAAAGCTCAACAGCTTTTTAAAATAAGGAATCCTATAATGGCCAAACGAATACT\r\n", "ATAAAAATAAGGGTTCTCTTAATTGTATAAAACGTATAATTTTATCAATTTTGGGACCGT\r\n", "GTAATTTTTTAAAGACCACAAGAATGTTACATACAACAAATAGACGAAACTCGTAGCTTT\r\n", "GGAAACTACGTCATGGGCGTTTGGTCAAAAGCTGGAGAGAAAGAGAGGTGGGGTGCCAGA\r\n", "CTTAAGTAGTCACGTGATCTGACCAACGCACATCGGAAGCTCGATCGGATGAAATCTTCT\r\n" ] } ], "prompt_number": 47 }, { "cell_type": "code", "collapsed": false, "input": [ "!sed 's/3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)/Phel_clc/g' /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 48 }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">Phel_clc_contig_1\r\n", "CAAATATATGAACGGTTGATTGTCAACGATTAGTACATGTTTTCATTGTTCCCCACGCCC\r\n", "GCCCCCCCCCACTCAAACATTTAAAGTGTGAAATATTATTTATCCACAAATTTCCTTAAA\r\n", "CCTGCAAACTTGTCTGCTGTCTCTTATTGGAAGTTATGAAAAAGAACAACGGGTTTTCTT\r\n", "TAAAGGGTCTGCGTGCGATTTTCAACCTTTTGAGTAATAGCAGTTATTTTGATAACCGAT\r\n", "TTTTTTCAAAGCTCAACAGCTTTTTAAAATAAGGAATCCTATAATGGCCAAACGAATACT\r\n", "ATAAAAATAAGGGTTCTCTTAATTGTATAAAACGTATAATTTTATCAATTTTGGGACCGT\r\n", "GTAATTTTTTAAAGACCACAAGAATGTTACATACAACAAATAGACGAAACTCGTAGCTTT\r\n", "GGAAACTACGTCATGGGCGTTTGGTCAAAAGCTGGAGAGAAAGAGAGGTGGGGTGCCAGA\r\n", "CTTAAGTAGTCACGTGATCTGACCAACGCACATCGGAAGCTCGATCGGATGAAATCTTCT\r\n" ] } ], "prompt_number": 49 }, { "cell_type": "code", "collapsed": false, "input": [ "cp /Users/sr320/Dropbox/Steven/eimd/data/Phel_transcriptome_clc.fa /Volumes/web/whale/eimd_14/" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 50 }, { "cell_type": "code", "collapsed": false, "input": [ "#for genefish - COMPLETED\n", "blastx \\\n", "-query /Volumes/web/cnidarian/SeaStar_transc_v2.fa \\\n", "-db /Users/Shared/data/blast/db/uniprot_sprot \\\n", "-out /Volumes/web/cnidarian/seastar_clc_uniprot_sprot_1.tab \\\n", "-outfmt 6 \\\n", "-num_threads 8 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!wc -l /Volumes/web/cnidarian/seastar_clc_uniprot_sprot_1.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ " 8913 /Volumes/web/cnidarian/seastar_clc_uniprot_sprot_1.tab\r\n" ] } ], "prompt_number": 3 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/seastar_clc_uniprot_sprot_1.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_4\tsp|P25001|COX1_PISOC\t88.39\t517\t48\t1\t7061\t5547\t1\t517\t0.0\t 749\r\n", "3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_7\tsp|Q33818|CYB_ASTPE\t79.94\t329\t66\t0\t993\t7\t51\t379\t9e-168\t 479\r\n" ] } ], "prompt_number": 4 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "#running hummingbird -- complete \n", "blastn \\\n", "-query /Volumes/web/cnidarian/SeaStar_transc_v2.fa \\\n", "-db /Volumes/Data/blast_db/nt \\\n", "-out /Volumes/web/cnidarian/seastar_clc_nt_1.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 14 \\\n", "-max_hsps 1 \\\n", "-evalue 1E-10 \\\n", "-max_target_seqs 1 \\\n", "-task blastn" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/seastar_clc_nt_1.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "head: /Volumes/web/cnidarian/seastar_clc_nt_1.tab: No such file or directory\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/seastar_clc_nt_1.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_2\tgi|378345425|gb|JN676976.1|\t81.71\t175\t1e-33\t 154\t7602\tAsterias amurensis\tAsterias amurensis\tstarfish\tEukaryota\tAsterias amurensis microsatellite Aamr32 sequence\r\n", "3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)_contig_4\tgi|28881689|emb|X55514.2|\t80.20\t4707\t0.0\t 4239\t7612\tPisaster ochraceus\tochreous starfish\tstarfish\tEukaryota\tPisaster ochraceus mitochondrial DNA for NADH dehydrogenase subunits 1, 2, 3 and 4L, cytochrome oxidase subunits I, II and III, ATPase subunits 6 and 8, and 13 tRNAs\r\n" ] } ], "prompt_number": 11 }, { "cell_type": "code", "collapsed": false, "input": [ "!sed 's/3291_5903_10007_H94MGADXX_V_CF71_ATCACG_R1_(paired)_trimmed_(paired)/Phel_clc/g' /Volumes/web/cnidarian/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 27 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -2 /Volumes/web/cnidarian/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "head: /Volumes/web/cnidarian/seastar_clc_nt_1_c.tab: No such file or directory\r\n" ] } ], "prompt_number": 54 }, { "cell_type": "code", "collapsed": false, "input": [ "pwd" ], "language": "python", "metadata": {}, "outputs": [ { "metadata": {}, "output_type": "pyout", "prompt_number": 23, "text": [ "u'/Users/sr320/Dropbox/Steven/eimd/data'" ] } ], "prompt_number": 23 }, { "cell_type": "code", "collapsed": false, "input": [ "!wget http://eagle.fish.washington.edu/cnidarian/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "--2014-07-25 14:48:16-- http://eagle.fish.washington.edu/cnidarian/seastar_clc_nt_1_c.tab\r\n", "Resolving eagle.fish.washington.edu... 128.95.149.81\r\n", "Connecting to eagle.fish.washington.edu|128.95.149.81|:80... connected.\r\n", "HTTP request sent, awaiting response... " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "200 OK\r\n", "Length: 2456177 (2.3M) [text/plain]\r\n", "Saving to: `seastar_clc_nt_1_c.tab'\r\n", "\r\n", "\r", " 0% [ ] 0 --.-K/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", " 9% [==> ] 226,187 1.06M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "22% [=======> ] 548,359 1.29M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "39% [==============> ] 960,847 1.50M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "56% [====================> ] 1,381,423 1.61M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "73% [===========================> ] 1,796,607 1.68M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "86% [================================> ] 2,130,911 1.66M/s " ] }, { "output_type": "stream", "stream": "stdout", "text": [ "\r", "98% [=====================================> ] 2,427,471 1.62M/s \r", "100%[======================================>] 2,456,177 1.63M/s in 1.4s \r\n", "\r\n", "2014-07-25 14:48:17 (1.63 MB/s) - `seastar_clc_nt_1_c.tab' saved [2456177/2456177]\r\n", "\r\n" ] } ], "prompt_number": 35 }, { "cell_type": "code", "collapsed": false, "input": [ "pwd" ], "language": "python", "metadata": {}, "outputs": [ { "metadata": {}, "output_type": "pyout", "prompt_number": 55, "text": [ "u'/Users/sr320/Dropbox/Steven/eimd/data'" ] } ], "prompt_number": 55 }, { "cell_type": "code", "collapsed": false, "input": [ "!tail ../data/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Phel_clc_contig_30533\tgi|390339526|ref|XM_784428.3|\t68.12\t436\t4e-31\t 145\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus glutamate receptor, ionotropic kainate 2-like (LOC584569), mRNA\r\n", "Phel_clc_contig_30544\tgi|390364561|ref|XM_792971.3|\t71.62\t229\t1e-23\t 120\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus vacuolar protein sorting-associated protein 13D-like (LOC593499), mRNA\r\n", "Phel_clc_contig_30557\tgi|513193816|ref|XM_004942680.1|\t80.18\t227\t2e-49\t 206\t9031\tGallus gallus\tchicken\tbirds\tEukaryota\tPREDICTED: Gallus gallus phosphoinositide kinase, FYVE finger containing (PIKFYVE), transcript variant X13, mRNA\r\n", "Phel_clc_contig_30558\tgi|390359524|ref|XM_795034.3|\t69.96\t263\t7e-23\t 118\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus uncharacterized LOC581299 (LOC581299), mRNA\r\n", "Phel_clc_contig_30560\tgi|390358520|ref|XM_781665.3|\t73.67\t452\t4e-69\t 271\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus neurobeachin-like (LOC581678), mRNA\r\n", "Phel_clc_contig_30562\tgi|390340515|ref|XM_781287.3|\t68.03\t269\t1e-11\t80.6\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial-like (LOC581276), mRNA\r\n", "Phel_clc_contig_30563\tgi|390338081|ref|XM_777767.3|\t71.15\t305\t6e-30\t 141\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus lysine (K)-specific demethylase 1B (KDM1B), mRNA\r\n", "Phel_clc_contig_30565\tgi|390341005|ref|XM_777026.2|\t73.88\t134\t1e-12\t84.2\t7668\tStrongylocentrotus purpuratus\tpurple sea urchin\tsea urchins\tEukaryota\tPREDICTED: Strongylocentrotus purpuratus topoisomerase (DNA) III alpha (top3a), mRNA\r\n", "Phel_clc_contig_30572\tgi|74382121|emb|CR524827.16|\t64.61\t421\t2e-11\t80.6\t7955\tDanio rerio\tzebrafish\tbony fishes\tEukaryota\tZebrafish DNA sequence from clone CH211-167H17 in linkage group 16, complete sequence\r\n", "Phel_clc_contig_30578\tgi|116633454|emb|CT833258.1|\t68.97\t522\t4e-49\t 205\t39946\tOryza sativa Indica Group\tlong-grained rice\tmonocots\tEukaryota\tOryza sativa (indica cultivar-group) cDNA clone:OSIGCRA202E04, full insert sequence\r\n" ] } ], "prompt_number": 7 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"Eukaryota\" ../data/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "8611\r\n" ] } ], "prompt_number": 8 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"Strongylocentrotus\" ../data/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "3912\r\n" ] } ], "prompt_number": 12 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"Bacteria\" ../data/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "2117\r\n" ] } ], "prompt_number": 9 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \"Viruses\" ../data/seastar_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "31\r\n" ] } ], "prompt_number": 10 }, { "cell_type": "heading", "level": 1, "metadata": {}, "source": [ "Hewson" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"greenbird_197DC8B3.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"greenbird_197DC82A.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Hewson_transc_clc.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ ">T1_GGACTCC_L001_R1_001_(paired)_contig_1\r\n", "GCTCGGAGATGTGTATAAGAGACAGGTCCGGGAACGTATTCACCGCGCCATTGCTGATGC\r\n", "GCGATTACTAGCGATTCCAACTTCATGGGGCCGAGTTGCAGGCCCCAATCCGAACTGAGG\r\n", "CACACTTTTTGGGATTGGCTGACCGTTACCGGATCGCAACCCTCTGTATGCACCATTGTA\r\n", "GCACGTGTGTAGCCCTGGGCATAAGGGCCATGATGACTTGACGTCGTCCCCACCTTCCTC\r\n", "TCTGCTTGCGCAGGCAGTCCCGTTAGAGTCCCCAGCTTCACCTGTTGGCAACTAACGGTA\r\n", "GGGGTTGCGCTCGTTGCGGGACTTAACCCAACACCTCACGGCACGAGCTGACGACAGCCA\r\n", "TGCAGCACCTTTGTTTCACGTCCGAAGAACAGGCCATCTCTGGCCTTTGCGATCACATTC\r\n", "AAGCCCAGGTAAGGTTCCTCGCGTACCATCGAATTAAACCACATGCTCCACCGCTTGTGC\r\n", "GGACCCCCGTCAATTCCTTTGAGTTTCACCCTTGCGGGCGTACTCCCCAGGTGGCTCACT\r\n" ] } ], "prompt_number": 51 }, { "cell_type": "code", "collapsed": false, "input": [ "!fgrep -c \">\" /Volumes/web/cnidarian/Hewson_transc_clc.fa" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "22606\r\n" ] } ], "prompt_number": 53 }, { "cell_type": "code", "collapsed": false, "input": [ "#running hummingbird - complete\n", "blastn \\\n", "-query /Volumes/web/cnidarian/Hewson_transc_clc.fa \\\n", "-db /Volumes/Data/blast_db/nt \\\n", "-out /Volumes/web/cnidarian/Hewson_clc_nt_1.tab \\\n", "-outfmt \"6 qseqid sseqid pident length evalue bitscore staxids sscinames scomnames sblastnames sskingdoms stitle\" \\\n", "-num_threads 12 \\\n", "-max_hsps 1 \\\n", "-evalue 1E-10 \\\n", "-max_target_seqs 1 \\\n", "-task blastn" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head -1 /Volumes/web/cnidarian/Hewson_clc_nt_1.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "T1_GGACTCC_L001_R1_001_(paired)_contig_1\tgi|284010065|dbj|AB540004.1|\t88.93\t1147\t0.0\t 1490\t708099\tReichenbachiella sp. YMK\tReichenbachiella sp. YMK\tCFB group bacteria\tBacteria\tReichenbachiella sp. YMK gene for 16S rRNA, partial sequence\r\n" ] } ], "prompt_number": 29 }, { "cell_type": "code", "collapsed": false, "input": [ "!tr '|' \"\\t\" /Volumes/web/cnidarian/Hewson_clc_nt_1_b.tab\n" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 30 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -1 /Volumes/web/cnidarian/Hewson_clc_nt_1_b.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "T1_GGACTCC_L001_R1_001_(paired)_contig_1\tgi\t284010065\tdbj\tAB540004.1\t\t88.93\t1147\t0.0\t 1490\t708099\tReichenbachiella sp. YMK\tReichenbachiella sp. YMK\tCFB group bacteria\tBacteria\tReichenbachiella sp. YMK gene for 16S rRNA, partial sequence\r\n" ] } ], "prompt_number": 31 }, { "cell_type": "code", "collapsed": false, "input": [ "!sed 's/T1_GGACTCC_L001_R1_001_(paired)/Hewson/g' /Volumes/web/cnidarian/Hewson_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 32 }, { "cell_type": "code", "collapsed": false, "input": [ "!head -1 /Volumes/web/cnidarian/Hewson_clc_nt_1_c.tab" ], "language": "python", "metadata": {}, "outputs": [ { "output_type": "stream", "stream": "stdout", "text": [ "Hewson_contig_1\tgi\t284010065\tdbj\tAB540004.1\t\t88.93\t1147\t0.0\t 1490\t708099\tReichenbachiella sp. YMK\tReichenbachiella sp. YMK\tCFB group bacteria\tBacteria\tReichenbachiella sp. YMK gene for 16S rRNA, partial sequence\r\n" ] } ], "prompt_number": 33 }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Galaxy" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "https://usegalaxy.org/u/sroberts320/h/eimd" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Galaxy_198305B5.png\"/" ] }, { "cell_type": "markdown", "metadata": {}, "source": [] }, { "cell_type": "heading", "level": 2, "metadata": {}, "source": [ "Hewson" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\"Screenshot_7_25_14__3_12_PM_19830DD6.png\"/" ] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "blastx \\\n", "-query /Volumes/web/cnidarian/Hewson_transc_clc.fa \\\n", "-db /Users/Shared/data/blast/db/uniprot_sprot \\\n", "-out /Volumes/web/cnidarian/Hewson_clc_uniprot_sprot_1.tab \\\n", "-outfmt 6 \\\n", "-num_threads 4 \\\n", "-max_hsps 1 \\\n", "-max_target_seqs 1 \\\n", "-evalue 1E-20" ], "language": "python", "metadata": {}, "outputs": [] }, { "cell_type": "code", "collapsed": false, "input": [ "!head /Volumes/web/cnidarian/Hewson_clc_uniprot_sprot_1.tab" ], "language": "python", "metadata": {}, "outputs": [], "prompt_number": 2 }, { "cell_type": "code", "collapsed": false, "input": [], "language": "python", "metadata": {}, "outputs": [] } ], "metadata": {} } ] }