{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Removing predicted Symbiodinium sequences from *Stylophora pistillata* transcriptome" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### This workflow creates a BLAST database from the *Symbiodinium* clade A and B transcriptomes from [Bayer et al (2012)](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035269) and compares the *S. pistillata* transcriptome from [Karako-Lampert et al. (2014)](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088615) against this database. " ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/jd/ncbi-blast-2.2.30+/db\n" ] } ], "source": [ "#Locate your local blast databse\n", "cd /Users/jd/ncbi-blast-2.2.30+/db" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "33496_Ahyacinthus_CoralContigs.fasta Apalm.nsq\r\n", "Ahya.nhr Pdam.fasta\r\n", "Ahya.nin Pdam.nhr\r\n", "Ahya.nsq Pdam.nin\r\n", "\u001b[31mAmil_Moya.fasta\u001b[m\u001b[m* Pdam.nsq\r\n", "Amil_Moya.nhr \u001b[31mSpist.fasta\u001b[m\u001b[m*\r\n", "Amil_Moya.nin Spist.nhr\r\n", "Amil_Moya.nsq Spist.nin\r\n", "Apalm.fasta Spist.nsq\r\n", "Apalm.nhr SymbiodiniumAB_Bayer.fasta\r\n", "Apalm.nin\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "\n", "Building a new DB, current time: 06/08/2015 17:28:18\n", "New DB name: SymbiodiniumAB\n", "New DB title: SymbiodiniumAB_Bayer.fasta\n", "Sequence type: Nucleotide\n", "Keep Linkouts: T\n", "Keep MBits: T\n", "Maximum file size: 1000000000B\n", "Adding sequences from FASTA; added 148436 sequences in 6.22721 seconds.\n" ] } ], "source": [ "#Make blast database out of Symbiodinium transcriptomes\n", "!makeblastdb -in SymbiodiniumAB_Bayer.fasta -dbtype nucl -out SymbiodiniumAB" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ ">Spi_contig00032 gene=isogroup00001 length=1566\r", "\r\n", "GgATCCATCGAAAGAAAAaGTCGTAGTTGACAGTGATTGCATGACTTCTGTACAACGTCCGATTAGTTTTtGCGTTTTATTGTCTtCTTTTGTACTGgAAATTCGACTCTAGCAAGTTGATTTCGTTTAGTTATGTCTGGCATTGCTTTGGGCAGATTATCAGAAGAGAGAAAAGCTTGGCGTAAAGACcATCCTTTCGGATTTGTGGCCAAACCGGTTAAAAATCCTGATGGTACTCTAAATCTGATGAACTGGGAATGTGCGATCCCaGGAAAGAAAGCGACCCCATGGGAAGGAGGCTCTTTCAAATTGAAGATGATATTTAAAGACGACTATCCATCCTCTCCGCCAAAATGTAAATTTGATCCTCCAATTTTCCATCCTAATGTATACCCATCTGGCACAGTGTGTCTGTCTCTTCTAGATGAAGAGAAAGACTGGAGACCTGCCGTCACTATAAAACAGATTTTATTGGGAATTCAAGACTTACTGAaTGATCCAAaCaTAaGaGATCCAGCTCAAGCAGAAGCATACaCCATTTACTGCCAAAACAGATCAGAATATGAGAAACGAGTCAGAAGTCAAGCTGCAAaGTTCTCAAGTTCATAGTGAATAAAGAAAAATATAAAATACTTCGCTAGCAGACGTGTAGGTTAACaGTGACTGGCAGAAATTGGATTTATTTTTtCTCcGTTtGTAAacAaCAaTGTGGAGTGGAGCAaGAATTCATCCgTAACTGCGTTAATACCACAGCTGTTGTTGTGAATTGGAaGGACAATCATGTCTGTTATTTtAGGAAGTTTCACAATGTACAGTTCAACTAACTTATACTAAAAAaCAGCTAAAGTtCACCTTAGTCTATGTtAGTTTtGTTAAAGCTTCTCTGTAgAAGGTTTGGGAGGgTtGTAATGGCTGTAACTATTCAGGgAGATCTGTCAAAGTACACTCTCTAATCCCATTGTTTCTTAAGGAATGAGTCATTATTTATTGTCTGGTGGGACGGaGGaTTTTAATCGTGTCACAATAAAATTTACCTGATCTTCCCatAagACCTGTAGTAATCTAaTGGTCCCTGTCATTGGCAGTCAaTTTTCTATAGTTTCCTGTTAACCTCTGTTAGCTACAACTGATGCCCCcTCTGTACCCCCCTAAAATTGTGTTCCCCCAAAgAAaTCCTTCCACCCACCCCATaCCTCCAGGTGATAACTAATGActGGTCCTTAATTCATTCTCTTTTTTTtGTTCTTGATTATTTGACTAAACCAAAGGCGatAAGTAAGATATACCCcAAtACGATTTGACGAACAATCTCTAGATTTTTTATTtAATCTTTAGTTGTAGATGTAATCAGAGGTGCAAAGCTTTACTGTTTtGAGTGTAAAGTGCCTGTTTCTAGGGATCCAGTGAAACCAGTAGTGTTGGGATTGTAAAGAGaTCAAAGAaTACCTCAAAGCACCAATCATAATGCTCTAATGTTGACAACTGCTAATGATTGGTtCAGCCTaTGGCTTTCATTAAAAaCGTCAAAAAaTAACGCTTCACTTCATTGCAAGTGATTCAGGTGGa\r", "\r\n", ">Spi_contig00035 gene=isogroup00001 length=1876\r", "\r\n", "AGCAGAGATCTATCAGACGACTATGTTACGACATGAAAaCCTTTTAGGCTTtGTAGCTGCTGACAaCAAaGATAATGGTGCCTGGACACAGCTTTGGCTGGTTACAGATTATTTagAAAGGGgCTCATTGTATGACTATCTTCAACTTGTTACCCTGAATGTTGAATCCATGCTGAAGTTAGCAGTGTCAATAGCCAGTGGACTTGCTCATCTCCACATtGAGATtGTAGGCACCCAAGgAAAGCCAGCTATTGCACATCGTGACTTAAAAaGTAAAAaCATTCTGGTTAAAAGAAATGGGACATGTTGCATAGGTGATTTGGGTCTTGCTGTTCGTCATAGTTCCATTACTGACACAGTTGATGTTCCTCCTGGGAACAGAgTTGGTACAAAGCGCTACATGCCACCTGAATTTTtAGATGACAATATACAGGTGCGGCACTTTGATGCATACAAGCGAGGTGATATGTATGCATTTGGTCTAGTGTTATGGGAAaTTGCAAGGACgTGTGTTTGTGGTGGATTGTGTGATGAATATCAGCTGCCCTACTATGACAGAGTTCCCTGTGATCCCAGCATTGAAGAtATGAGAAAGGTGGTCTGTGTGGAGAGGTATCGCCCTGCCTTTCCAAATAGGTGGATACAAGATCAGACACTACAGTCTATGTCCAAGTTGATGAAAGAATGTTGGTATGCCAATAGTGCTGCAAGACTTACAGCTCTCCGTGTTAAGAAGACTCTTACAACAcTGTGTCAGTTACATGATGTTGATATTATGGTTTAGAGGGaTCCATCAaGAAAACTCATGTAAAACAAGTgCAAGATGGGTGTATCACCAGGACTTATATAACAGGAGGAACCTCCTGATAATCCTTGCAGGCAATTTGTAGGTCCTGTAATGTGATACAGTACATGTCTACCATCATGCTATTGgTTTGCAGTTCAAACaGCAATGCTGTCTTTtATTTTTtGATAAAGCCATGAAGAATAAACGCGACAGAGAAAaTTTATGACTTCCTAGTTAACAAGAAGCATTCtCATTTTTTTTTTTTtttGCCTGCATAATTcTTGtATTTATATCCACAGCAACTGTCACTGACTCAAAGTgTtGgtAaTCatCAGCAACAAAGAACCCAACTTGgTTTTATGAAAGCACGTACATtCAAATGAGCAATTTAAATTGAAAACCTAAAAGGACATATCCATGTGCAACAACTGTAGAACTATGTATGAGCAGTGTCCACTATTCTCCTCCTTAGTTTATTTTAGATGTTTCGAATGAGAATACAGAATAGAGCTTCATCCTTTTGACATTGAAAGCATTTCATACTCAAGTATtGAAGGGTATGATTCTTTGTTGTGAGGAACGACACTCACCAAGTAATCCTCAAAATATTTAAGAGCATACATGGATTTTACCAAAAGATGTGGGTTGGTCATATCTACATTAAGAATTTGTTACAATAGTAAGGTAGTTGCAGTGCTGTAGCTAGCTCTTAGATGAAGCGTGTTTATTGCATTCAAATTGAAATGTTATTGTTTAAAGTGATTCTCAAATTAAAAGACATTGTATTTTTAGACAACTTTTTATCTTCGAAAACCCAGTGGTGTAAGGTAATTACATTATTTTATGTTCATAACAAATACATTTTAACTGTATTCCACCAAACAATGTGAAAGGGGCAGTTTAAGAATTAATGAAATCTTTCTTGATACCCGTTCTtcAGAACGCTTTATAGTATCTTCTTTATAGTTGTAAATAAaCCGAaTACTTTGCGTGTGAGGGGCATTGAaGAAACTGAAGGGTTTTGTTTGACTCTGTTCTAACAGAAtCAAACATAATGTAATTACTCGGAACTTCATTAAACTGGTGGCC\r", "\r\n", ">Spi_contig00040 gene=isogroup00001 length=2118\r", "\r\n", "CGGAGCCGAAAACGAAGAGCTACCGGCGGCGTTTGCACCTTTAGCCAACCCAGTGAGTACCGGAGTtcGAGAAACCGAGGGAGATTTGGGTTATTCAGATGAGGTTTGGGATGCATTAAATGGATTTGTATTTCAATACTCTACAGAAGATCAAGAAGACGAATTAGTAGAGATGCTAATTGGGTGAGCAAACAGTGTAACGGCCGGAGAGTCAAACGAGGATATAGTAGATGTGCTAGGGGAGTGGGCAGAGGGTAACATCCCcGAAGATTCAGGCGACGAATCAGAGGAGAACGCGTCTGAAGATTCAAACGACGAATaGGCGGAGGCCCCcATTTATTCAATATGTAAGAGATCGGGGGGGGgTTGTGGGACCTCGCCCCGGGTATTTGAACGATATGGTCTCTAATTATTGAATTCGATGGGGGTTTTCAACCAACCATAAAGATATTGGTAGTTTGTATTTAATTTTtGGTGGAGGTGCTGGTTTAATTGGAACGGCGTTTAGTATGCTTATACGACTAGAGCTTTCTGCGCCCGGAGCAATGTTAGGAGATGATCATCTTTATAATGTAATTGTTACAGCGCATGCTTTTATTATGATTTTTTTTtGGTtATGCCGGTTATGATTGGGGGgTTTGGTAATTGATTGGTCCCATTATATATTGGGGCGCCGGATATGGCGTTTCCCCGACTAAACAATATTAGTTTTTGACTTTTGCCCCCTGCGCTTTTTTtATTATTAGGCTCTGCTTTTGTTGAACAAGGGGCGGGGACGGGGTGAACAGTTTATCCTCCTCTTGCTAGTATTCAAGCACACTCCGGATGTTCGGTTGATATGGTTATTTTTAGTCTTCATTTAGCTGGGGTTTCTTCTATTTTAGGTGCTATAAACTTTATTACTACAATTTTTAATATGCGAGCCCCGGGTGTGTCTTTTAATAAACTACCTTTATTTGTTTGATCTATTTTAATAACAGCTTTTTTATTACTTTTATCTTTACCTGTTTTAGCTGGTGCTATTACTATGTTGTTAACAGATAGAAACTTTAATACGACTTTTTTCGATCCAGCGGGTGGCGGGGACCCAATATTATTTCAGCATCTATTTTGATTCTTTGGGCATCCAGAAGTTTATATTTTAATTTTGCCTGGTTTTGGTATGATTTCTCAAATAATCCCGACTTTTGTTGCTAAAAAACAAGTTTTCGGGTACTTAGGAATGGTTTATGCCATGCTTTCTATTGGGCTTCTGGGATTTATTGTTTGAGCTCATCATATGTTTACTGTTGGGATGGATGTAGATACAAGAGCATATTTTACTGCTGCTACTATGATTATTGCTGTGCCAACTGGGATTAAAGTTTTTAGTTGGTTGGCAACTATTTATGGAGGTGTTCTTAGGTTAGAGACTCCAATGCTTTGAGCTATGGGGTTTGTTTTTTtATTTACAGTTGGTGGTTTAACTGGGGTTGTATTAGCAAATAGTTCTCTTGATATTGTTCTACATGATACATATTATGTAGTTGCGCATTTTCATTATGTTCTTTCTATGGGGGCTGTTTTTGCTATCTTTGGGGGATTTTACTATTGAATTGGAAAAATAAGTGGTTATTGTTATAATGAATTTTTTGGGAAAGTTCATTTTTGATTAATGTTTATCGGGGTTAATTTAACTTTTTtCCCTCAACATTTTTtAGGTTTAGCAGGATTTCCAAGACGATACTCGGATTATGCAGATGCTTTTTTGGGTTGAAATTTAATAAGTTCTTTAGGGTCTATTATTTCTATTTTGAGTGTTGTTTGGTTTTTATATATTGTTTTTGATCTTTTTGTTACAGAAGAAAAATTTTTGGGTTGAAAAGAAGGATTTTCTTTAGAATGAATTCATTCTTCTCCCCCCTTATTTCATACTTATGAGGAGTTGCCTTTTGTACAAAAATAAATAATTTTTAGAATAGTGCCGGGTTTATATACCGGTTTTGTAAGAAGACAAAGGGTTAGTCTTTGGGTTCATGCCCCAAATAAGTGAGTTCGAATCTCTCTCTTACACAAAATAAAAaTTATAAAAAAAaaGAGGATAACTAAGATAAACTAAAATTAGACGATTTTTTtCGA\r", "\r\n", ">Spi_contig00044 gene=isogroup00001 length=1596\r", "\r\n", "GTTTATTAGTGCGTGTACTACTtGATCAACActACACCCTTGTTTATTCGTaGATATTAATTtATCAACAtACTTCtCcACcATAAaTTACCTTTAATATCTAGTGTTCATGTCTACATCAGGTAAGGGTCTCCAGACACTTCAaCCAAAAGCCGAAATTGACAATCGCTAAACACGATCGTACGTTTTACTGAAACGGGCATCTCGTTtCTTCATGAAAATGGTGCAATATTTGACAACTCATTGATAAAAaCCCaGATTAAAATGCTCagCAcAGACTCGcgAAAAAATGCCAATGCCTTaCGCTTAAtttgtCTAATCTAATATAATTTTTttGATTTtGCACTAACCACGCATTACAACTACATTTACTAAGGTTCTTGATAgTAATGAATTTATTTTtATTTATTTAAAAGTTCATATTTCATAGGAGATGTAAAAaTATTGACGGGCCCCTGTCTtGATAAtAAGAAaCTAGAATTTCCTCTTCTTGTTTTCAGGTAACAGACTTtGAAaTATAaTTTAAGTTTGGCCCTTTGctACGGAACATAAATATCACCTCACTCTTCTCCCAAATTGTTTtCAAATACGCAATACACAAACCCTTTCGCCAAGCCTTGTtcTTCCTTGGTTTTTAAGAGCCATTTTGGTATTTTCACACCGTAATATATTATTCATTCATTAGCCATTAATTAAATACGGCAAACTAGAACATTTtCTCTTTGGGATCGTTTAGATTAATACGAAGCCACAGAAaTACTTGTGTtgGTTCTTCCACACAaTATTAAAATCATTTTTCTCCTGACAAAACAAAgAGAAACTTGAcGgAGGTGAAAACCGTAGATCTTAAAGGGACATGATGTTGGTGATGACGATACTGACAAACTTGAACCCAACCgTTTGAAAATCaTTCCCTACACTTCACAAGTAAAGTTACAaCGATTGtAAGAAATTGAGgAAATTGTTTTGGTACTAATCAGAACAAAAaTCGAAaGAGAATTTCATTCATTTCTTTCAGCTTGAAAATCTTAATCATTATTGAatCATTCTTAAAAATTaTATCAAAATTCATTCATGTTtGGGtCtGTGCTCTGCATGACTAATAGCACTATCGCTTCCTTTATCGTGATTGACCCGGAAGCCGCCGATAATCGAAGGCCAAAATTGCCATACCGTCCACGCAGTCCAAGAGCCGAAGAAAAGAATCCAGAATGCTGTCACGTGAGCAGGAAAGGGTATGCTGATGGTTTCCCAACCGAATTTAACGCAGATTAGCACTTCTGTTGAGACAATGGCGGCGACAACCCAGGCCTGTTGTCCAAACCGCTTGCAGGTAGGGTCGTCCATGTATCTAAATGTTTCATTCAGTgCcACAGCTCCCATCCCAAGGTaCAGCGCCATACgAACTTGCATGATGAAATGAGGTGGAGGAATCCACAAAATAAACTTCATGTAAAACAGGTTTAACtcGGCCAGGAGGAACATAGCAGCAATTCCACAGACTGCCAGCCATCTAGTTAGACTTGTGGTCGCTTTCCAGTCATAAGACGTCCACGAATAAGGAGTGAATTGAGCAGCAACTCTTTTGAACTTGCc\r", "\r\n", ">Spi_contig00046 gene=isogroup00001 length=720\r", "\r\n", "cagactcagcagttctctgacgatggtaaccaacacttatttctggagtagcacatacagtgacagttcttctgattatgctgtgtgtcttggtttatgttggagcttttgaaaaaactaaggaaaacagTGAatgCAATACAAagAGGggACTtGTAGCcTGCATtGCAGtATTTTTGTTGTTTGGGGgTCACTCAGATAAGAGATGGTCCGTTCAAaCGACCTCACCCAGCTTTCTGGCGTATCATtCTTTGCCTAAGTGTTGTTTATGAaTTGGCTCTAATTTTtCTTTTATTCCAGACAACTCATGATGCCAGGCAGTTGCTAAaGTATCTTGATGAAGATTTAGGGAAaCCATTGCCAgaGCAATCTTATGGAGAGGACTGTAGGTTATACACACCAGGACACCCCAaGGGaTCaTTCCaTaCCTTtCTTGaGAAATGTGATGTCTTTATACCAGCTCATTTTTTCGGATGGTGGGCAAAGgcACTCATCCTTCGTGACTACTGGCTATTGACTGTCACTAGTGTTCTTTTTGAAGTCTTGGAATATTCCTTAGAGCATCAGTtaCCAAACTTCAGTGAATGCtGGtGGGATCATTGGATCATGGATGTTCTCATTTGTAATGGTTTTGGGGCATATCTTGGCATGAAGACTTGTGATTATCTTGGAAATAAGCCATATCACTGGAGAGGTTTATGGAACATTCCCACCTACAGT\r", "\r\n" ] } ], "source": [ "!head ../../data/Spist/Spist.fasta" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# BLAST query" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": true }, "outputs": [], "source": [ "!blastn \\\n", "-query /Users/jd/Documents/Projects/Coral-CpG-ratio-MS/data/Spist/Spist.fasta \\\n", "-db /Users/jd/ncbi-blast-2.2.30\\+/db/SymbiodiniumAB \\\n", "-outfmt 6 \\\n", "-evalue 1E-05 \\\n", "-out ../Spist/Spist_zoox_matches" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/Users/jd/Documents/Projects/Coral-CpG-ratio-MS/analyses/Spist\n" ] } ], "source": [ "cd ../../analyses/Spist" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_isotig00175\tkb8_rep_c43333\t97.54\t407\t3\t7\t248\t649\t548\t144\t0.0\t 689\r\n", "Spi_isotig00175\tmf105_rep_c14211\t97.54\t406\t3\t7\t248\t648\t145\t548\t0.0\t 688\r\n", "Spi_isotig00175\tkb8_rep_c24871\t97.05\t407\t5\t7\t248\t649\t408\t4\t0.0\t 678\r\n", "Spi_isotig00175\tmf105_rep_c7972\t96.57\t408\t5\t9\t248\t649\t241\t645\t0.0\t 667\r\n", "Spi_isotig00175\tkb8_rep_c52958\t91.97\t411\t26\t7\t248\t655\t802\t1208\t2e-161\t 569\r\n", "Spi_isotig00175\tkb8_rep_c47844\t91.95\t410\t27\t6\t248\t655\t410\t5\t2e-161\t 569\r\n", "Spi_isotig00175\tkb8_rep_c51649\t90.98\t410\t29\t8\t248\t653\t414\t9\t9e-155\t 547\r\n", "Spi_isotig00175\tkb8_rep_c53044\t91.00\t411\t28\t8\t248\t655\t405\t1\t3e-154\t 545\r\n", "Spi_isotig00175\tmf105_rep_c18178\t91.13\t406\t26\t9\t248\t650\t113\t511\t4e-153\t 542\r\n", "Spi_isotig00175\tkb8_rep_c53549\t90.52\t401\t27\t10\t248\t644\t411\t18\t2e-146\t 520\r\n" ] } ], "source": [ "!head Spist_zoox_matches" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " 3320 39840 234784 Spist_zoox_matches\r\n" ] } ], "source": [ "!wc Spist_zoox_matches" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "ID_CpG Spist_cpg_GOslim.tab Spist_zoox_matches\r\n" ] } ], "source": [ "ls" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", "Spi_isotig00175 \t\n", " 3320 3320 59760 Spist_zoox_matches_IDs\n" ] } ], "source": [ "#Printing only the contig ID from the output file\n", "!awk '{print $1, \"\\t\"}' Spist_zoox_matches > Spist_zoox_matches_IDs\n", "!head Spist_zoox_matches_IDs\n", "!wc Spist_zoox_matches_IDs" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_isotig00175 \t\n", "Spi_isotig00457 \t\n", "Spi_isotig00458 \t\n", "Spi_isotig00459 \t\n", "Spi_isotig00460 \t\n", "Spi_isotig00461 \t\n", "Spi_isotig00462 \t\n", "Spi_isotig00492 \t\n", "Spi_isotig00493 \t\n", "Spi_isotig00494 \t\n", " 138 138 2484 Spist_zoox_matches_IDs_uniq\n" ] } ], "source": [ "#Obtaining only unique seq IDs\n", "!uniq Spist_zoox_matches_IDs > Spist_zoox_matches_IDs_uniq\n", "!head Spist_zoox_matches_IDs_uniq\n", "!wc Spist_zoox_matches_IDs_uniq" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_isotig00175 \t\r\n", "Spi_isotig00457 \t\r\n", "Spi_isotig00458 \t\r\n", "Spi_isotig00459 \t\r\n", "Spi_isotig00460 \t\r\n", "Spi_isotig00461 \t\r\n", "Spi_isotig00462 \t\r\n", "Spi_isotig00492 \t\r\n", "Spi_isotig00493 \t\r\n", "Spi_isotig00494 \t\r\n" ] } ], "source": [ "#Sorting file in order to join\n", "!sort Spist_zoox_matches_IDs_uniq > Spist_zoox_matches_IDs.sorted\n", "!head Spist_zoox_matches_IDs.sorted" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_contig00032 \t 0.484363\n", "Spi_contig00035 \t 0.335179\n", "Spi_contig00040 \t 0.854266\n", "Spi_contig00044 \t 0.867137\n", "Spi_contig00046 \t 0.196592\n", "Spi_contig00075 \t 0.871739\n", "Spi_contig00091 \t 0.937628\n", "Spi_contig00094 \t 0.131292\n", "Spi_contig00095 \t 0.684932\n", "Spi_contig00098 \t 0.584255\n", " 15052 30104 402540 ID_CpG.sorted\n" ] } ], "source": [ "#Now using CpG ratio file obtained from workflow in Pdam_CpG_ratio.ipynb\n", "!head ID_CpG.sorted\n", "!wc ID_CpG.sorted" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Spi_contig00032 0.484363\n", "Spi_contig00035 0.335179\n", "Spi_contig00040 0.854266\n", "Spi_contig00044 0.867137\n", "Spi_contig00046 0.196592\n", "Spi_contig00075 0.871739\n", "Spi_contig00091 0.937628\n", "Spi_contig00094 0.131292\n", "Spi_contig00095 0.684932\n", "Spi_contig00098 0.584255\n", " 14914 29828 369006 ID_CpG.sorted2\n" ] } ], "source": [ "!join -v 1 ID_CpG.sorted Spist_zoox_matches_IDs.sorted > ID_CpG.sorted2\n", "!head ID_CpG.sorted2\n", "!wc ID_CpG.sorted2" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "#Process removed 138 sequences with close matches to Symbiodinium transcriptome" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 2", "language": "python", "name": "python2" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }