Mercurial > repos > johnheap > vapper
changeset 19:fe79425b1fa4 draft
Uploaded
| author | johnheap |
|---|---|
| date | Mon, 03 Jun 2019 16:01:16 -0400 |
| parents | e7da2274c9f6 |
| children | 26ec953069b3 |
| files | Tryp_V_T.py |
| diffstat | 1 files changed, 425 insertions(+), 2611 deletions(-) [+] |
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--- a/Tryp_V_T.py Mon Jun 03 16:00:24 2019 -0400 +++ b/Tryp_V_T.py Mon Jun 03 16:01:16 2019 -0400 @@ -1,2611 +1,425 @@ - - - - - - -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - <link rel="dns-prefetch" href="https://github.githubassets.com"> - <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> - <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> - <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> - - - - <link crossorigin="anonymous" media="all" integrity="sha512-3+HOqCwtQal5hOJQ+mdxiq5zmGOTjF6RhjDsPLxbKDYgGlLFeCwzoIanb7j5IiCuXKUqyC2q8FdkC4nmx2P2rA==" rel="stylesheet" href="https://github.githubassets.com/assets/frameworks-a2fba223d5af91496cac70d4ec3624df.css" /> - <link 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class="pl-s">* Galaxy Version</span></td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code blob-code-inner js-file-line"><span class="pl-s"></span></td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Copyright 2019 University of Liverpool</span></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Author John Heap, Computational Biology Facility, UoL</span></td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL</span></td> - </tr> - <tr> - <td id="L7" 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class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Unless required by applicable law or agreed to in writing, software</span></td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an "AS IS" BASIS,</span></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * See the License for the specific language governing permissions and</span></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">"""</span></span></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> subprocess</td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> pandas <span class="pl-k">as</span> pd</td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> re</td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> shutil</td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> import matplotlib as mpl</span></td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> mpl.use('Agg')</span></td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> matplotlib.pyplot <span class="pl-k">as</span> plt</td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> numpy <span class="pl-k">as</span> np</td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> copies the user provided Fasta file to data/reference/file/file.fasta</span></td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">uploadUserReferenceFastq</span>(<span class="pl-smi">refFastq</span>):</td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-c"><span class="pl-c">#</span>propose putting file in '/data/reference/ref/</span></td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-k">not</span> os.path.isdir(refDir): <span class="pl-c"><span class="pl-c">#</span> if directory data/Reference/ref doesn't exist</span></td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code blob-code-inner js-file-line"> os.mkdir(refDir)</td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> refDir<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code blob-code-inner js-file-line"> shutil.copy(refFastq, refPath <span class="pl-k">+</span> refBase) <span class="pl-c"><span class="pl-c">#</span>copy reference file into the directory</span></td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2-build <span class="pl-pds">"</span></span> <span class="pl-k">+</span> refPath <span class="pl-k">+</span> refBase<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> <span class="pl-pds">"</span></span><span class="pl-k">+</span>refPath<span class="pl-k">+</span>ref</td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>Building the bowtie2 reference files.<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptMapping</span>(<span class="pl-smi">inputname</span>, <span class="pl-smi">refFastq</span>, <span class="pl-smi">forwardFN</span>, <span class="pl-smi">reverseFN</span>):</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> where is our Reference data?</span></td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>]</td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>))</td> - </tr> - <tr> - <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> - <td id="LC57" class="blob-code blob-code-inner js-file-line"> refDir <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> - <td id="LC58" class="blob-code blob-code-inner js-file-line"> refName <span class="pl-k">=</span> refDir <span class="pl-k">+</span> ref</td> - </tr> - <tr> - <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> - <td id="LC59" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> now have reference file so we can proceed with the transcript mapping via bowtie2</span></td> - </tr> - <tr> - <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> - <td id="LC60" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>bowtie2 -x <span class="pl-pds">"</span></span><span class="pl-k">+</span>refName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -1 <span class="pl-pds">"</span></span><span class="pl-k">+</span>forwardFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -2 <span class="pl-pds">"</span></span><span class="pl-k">+</span>reverseFN<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -S <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> - <td id="LC61" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>) <span class="pl-c"><span class="pl-c">#</span>outputs a name.sam file</span></td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> - <td id="LC65" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> - <td id="LC66" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> - <td id="LC67" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">processSamFiles</span>(<span class="pl-smi">inputname</span>):</td> - </tr> - <tr> - <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> - <td id="LC68" class="blob-code blob-code-inner js-file-line"> cur_path <span class="pl-k">=</span> os.getcwd()</td> - </tr> - <tr> - <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> - <td id="LC69" class="blob-code blob-code-inner js-file-line"> samName <span class="pl-k">=</span> cur_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname</td> - </tr> - <tr> - <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> - <td id="LC70" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools view -bS <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sam > <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> - <td id="LC71" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools sort <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> - <td id="LC75" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span><span class="pl-k">+</span>argString)</td> - </tr> - <tr> - <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> - <td id="LC76" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> - <td id="LC77" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> - <td id="LC78" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>samtools index <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted <span class="pl-pds">"</span></span><span class="pl-k">+</span>samName<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> - <td id="LC79" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span>argstring = <span class="pl-pds">"</span></span> <span class="pl-k">+</span> argString)</td> - </tr> - <tr> - <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> - <td id="LC80" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> - <td id="LC81" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c"><span class="pl-c">#</span>we have saved out the relevent name.bam, name.sorted and name.sorted.bai files</span></td> - </tr> - <tr> - <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> - <td id="LC82" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> - <td id="LC83" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> we will not have the .gtf file so call cufflinks without -G option</span></td> - </tr> - <tr> - <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> - <td id="LC84" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptAbundance</span>(<span class="pl-smi">inputname</span>):</td> - </tr> - <tr> - <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> - <td id="LC85" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>cufflinks -o <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.cuff -u -p 8 <span class="pl-pds">"</span></span><span class="pl-k">+</span>inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> - <td id="LC86" class="blob-code blob-code-inner js-file-line"> subprocess.call(argString, <span class="pl-v">shell</span> <span class="pl-k">=</span> <span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> - <td id="LC87" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted<span class="pl-pds">"</span></span>) <span class="pl-c"><span class="pl-c">#</span>remove name.sorted</span></td> - </tr> - <tr> - <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> - <td id="LC88" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.sorted.bai<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> - <td id="LC89" class="blob-code blob-code-inner js-file-line"> os.remove(inputname<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>.bam<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> - <td id="LC90" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span></td> - </tr> - <tr> - <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> - <td id="LC91" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> - <td id="LC92" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptsForBlast</span>(<span class="pl-smi">name</span>, <span class="pl-smi">refFastq</span>):</td> - </tr> - <tr> - <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> - <td id="LC93" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> quick and dirty just to see.</span></td> - </tr> - <tr> - <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> - <td id="LC94" class="blob-code blob-code-inner js-file-line"> refBase <span class="pl-k">=</span> os.path.basename(refFastq)</td> - </tr> - <tr> - <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> - <td id="LC95" class="blob-code blob-code-inner js-file-line"> ref <span class="pl-k">=</span> os.path.splitext(refBase)[<span class="pl-c1">0</span>] <span class="pl-c"><span class="pl-c">#</span> 'mydata/test.fasta' -> 'test'</span></td> - </tr> - <tr> - <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> - <td id="LC96" class="blob-code blob-code-inner js-file-line"> dir_path <span class="pl-k">=</span> os.path.dirname(os.path.realpath(<span class="pl-c1">__file__</span>)) <span class="pl-c"><span class="pl-c">#</span> directory of this file</span></td> - </tr> - <tr> - <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> - <td id="LC97" class="blob-code blob-code-inner js-file-line"> refPath <span class="pl-k">=</span> dir_path <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/data/Reference/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> ref <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span>/<span class="pl-pds">"</span></span> <span class="pl-k">+</span> refBase <span class="pl-c"><span class="pl-c">#</span> eg refPath = data/Reference/Trinity/Trinity.fasta</span></td> - </tr> - <tr> - <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> - <td id="LC98" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> used for dirty # refPath = 'Trinity.fasta' # dirty one</span></td> - </tr> - <tr> - <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> - <td id="LC99" class="blob-code blob-code-inner js-file-line"> track_df <span class="pl-k">=</span> pd.read_csv(name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> - <td id="LC100" class="blob-code blob-code-inner js-file-line"> names <span class="pl-k">=</span> track_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> - <td id="LC101" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(len(names))</span></td> - </tr> - <tr> - <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> - <td id="LC102" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(names[:5])</span></td> - </tr> - <tr> - <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> - <td id="LC103" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> - <td id="LC104" class="blob-code blob-code-inner js-file-line"> nlist <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> - <td id="LC105" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> n <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(names)):</td> - </tr> - <tr> - <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> - <td id="LC106" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> names[n].find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> - <td id="LC107" class="blob-code blob-code-inner js-file-line"> nlist.append(names[n][:i])</td> - </tr> - <tr> - <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> - <td id="LC108" class="blob-code blob-code-inner js-file-line"> nameset <span class="pl-k">=</span> <span class="pl-c1">set</span>(nlist) <span class="pl-c"><span class="pl-c">#</span>get unique.</span></td> - </tr> - <tr> - <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> - <td id="LC109" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(refPath, <span class="pl-s"><span class="pl-pds">'</span>r<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> myRef:</td> - </tr> - <tr> - <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> - <td id="LC110" class="blob-code blob-code-inner js-file-line"> refData <span class="pl-k">=</span> myRef.read()</td> - </tr> - <tr> - <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> - <td id="LC111" class="blob-code blob-code-inner js-file-line"> refData<span class="pl-k">=</span> refData<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\n</span>><span class="pl-pds">'</span></span></td> - </tr> - <tr> - <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> - <td id="LC112" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> - <td id="LC113" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_for_blast.fa<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>) <span class="pl-k">as</span> outfile:</td> - </tr> - <tr> - <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> - <td id="LC114" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> trans_id <span class="pl-k">in</span> nameset:</td> - </tr> - <tr> - <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> - <td id="LC115" class="blob-code blob-code-inner js-file-line"> namepos <span class="pl-k">=</span> refData.find(trans_id)</td> - </tr> - <tr> - <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> - <td id="LC116" class="blob-code blob-code-inner js-file-line"> endpos <span class="pl-k">=</span> refData.find(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>, namepos)</td> - </tr> - <tr> - <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> - <td id="LC117" class="blob-code blob-code-inner js-file-line"> outfile.write(<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span><span class="pl-k">+</span>refData[namepos:endpos])</td> - </tr> - <tr> - <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> - <td id="LC118" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> - <td id="LC119" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> - </tr> - <tr> - <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> - <td id="LC120" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> - <td id="LC121" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">blastContigs</span>(<span class="pl-smi">test_name</span>,<span class="pl-smi">html_resource</span>, <span class="pl-smi">database</span>):</td> - </tr> - <tr> - <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> - <td id="LC122" class="blob-code blob-code-inner js-file-line"> db_path <span class="pl-k">=</span> database</td> - </tr> - <tr> - <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> - <td id="LC123" class="blob-code blob-code-inner js-file-line"> argString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>blastx -db <span class="pl-pds">"</span></span><span class="pl-k">+</span>db_path<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span> -query <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_for_blast.fa -outfmt 10 -out <span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> - <td id="LC124" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(argString)</td> - </tr> - <tr> - <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> - <td id="LC125" class="blob-code blob-code-inner js-file-line"> returncode <span class="pl-k">=</span> subprocess.call(argString, <span class="pl-v">shell</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> - <td id="LC126" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> returncode <span class="pl-k">!=</span> <span class="pl-c1">0</span>:</td> - </tr> - <tr> - <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> - <td id="LC127" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-s"><span class="pl-pds">"</span>Error in blastall<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> - <td id="LC128" class="blob-code blob-code-inner js-file-line"> blast_df <span class="pl-k">=</span> pd.read_csv(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span><span class="pl-k">+</span>test_name<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_blast.txt<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> - <td id="LC129" class="blob-code blob-code-inner js-file-line"> blast_df.columns <span class="pl-k">=</span> [<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>mismatch<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>gapopen<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>qend<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>sstart<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>send<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> - <td id="LC130" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blast_df[(blast_df[<span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>]<span class="pl-k">>=</span><span class="pl-c1">70</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>length<span class="pl-pds">'</span></span>] <span class="pl-k">></span> <span class="pl-c1">100</span>) <span class="pl-k">&</span> (blast_df[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>] <span class="pl-k"><=</span><span class="pl-c1">0.001</span>) ]</td> - </tr> - <tr> - <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> - <td id="LC131" class="blob-code blob-code-inner js-file-line"> blastResult_df <span class="pl-k">=</span> blastResult_df[[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>]] <span class="pl-c"><span class="pl-c">#</span>query accession.version, subject accession.version, Percentage of identical matches</span></td> - </tr> - <tr> - <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> - <td id="LC132" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> need to allocate the transcripts (if allocated more than once to the phylotype with least error.</span></td> - </tr> - <tr> - <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> - <td id="LC133" class="blob-code blob-code-inner js-file-line"> transcripts <span class="pl-k">=</span> blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> - <td id="LC134" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>pident<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>, <span class="pl-s"><span class="pl-pds">'</span>bitscore<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> - <td id="LC135" class="blob-code blob-code-inner js-file-line"> transSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(transcripts)</td> - </tr> - <tr> - <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> - <td id="LC136" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> t <span class="pl-k">in</span> transSet:</td> - </tr> - <tr> - <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> - <td id="LC137" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> blastResult_df[(blastResult_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> t)]</td> - </tr> - <tr> - <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> - <td id="LC138" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get one with smallest error value</span></td> - </tr> - <tr> - <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> - <td id="LC139" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(t + ":")</span></td> - </tr> - <tr> - <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> - <td id="LC140" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(temp_df)</span></td> - </tr> - <tr> - <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> - <td id="LC141" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> temp_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>evalue<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> - <td id="LC142" class="blob-code blob-code-inner js-file-line"> b_df <span class="pl-k">=</span> b_df.append(temp_df.iloc[[<span class="pl-c1">0</span>]])</td> - </tr> - <tr> - <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> - <td id="LC143" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> - <td id="LC144" class="blob-code blob-code-inner js-file-line"> b_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> - <td id="LC145" class="blob-code blob-code-inner js-file-line"> b_df.to_csv(test_name <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> - <td id="LC146" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> b_df</td> - </tr> - <tr> - <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> - <td id="LC147" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> - <td id="LC148" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> - <td id="LC149" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createMultiHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">composite_df</span>):</td> - </tr> - <tr> - <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> - <td id="LC150" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> - </tr> - <tr> - <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> - <td id="LC151" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> - <td id="LC152" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> - <td id="LC153" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> - <td id="LC154" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> - <td id="LC155" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptomes. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> - <td id="LC156" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> - <td id="LC157" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> - <td id="LC158" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> - <td id="LC159" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> - <td id="LC160" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> - <td id="LC161" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> - <td id="LC162" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> - <td id="LC163" class="blob-code blob-code-inner js-file-line"> wLists <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> - <td id="LC164" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> - <td id="LC165" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>,<span class="pl-c1">len</span>(labelList)):</td> - </tr> - <tr> - <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> - <td id="LC166" class="blob-code blob-code-inner js-file-line"> wLists.append(composite_df[labelList[j]])</td> - </tr> - <tr> - <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> - <td id="LC167" class="blob-code blob-code-inner js-file-line"> header <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(labelList[j]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></th><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> - <td id="LC168" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> - <td id="LC169" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">+</span> header</td> - </tr> - <tr> - <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> - <td id="LC170" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> - <td id="LC171" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> - <td id="LC172" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> - <td id="LC173" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> - <td id="LC174" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> - <td id="LC175" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(composite_df)):</td> - </tr> - <tr> - <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> - <td id="LC176" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phyList[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> - <td id="LC177" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> j <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>,<span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span>):</td> - </tr> - <tr> - <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> - <td id="LC178" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(j)</span></td> - </tr> - <tr> - <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> - <td id="LC179" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(wLists[j][i], <span class="pl-s"><span class="pl-pds">'</span>.4f<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> - <td id="LC180" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> - <td id="LC181" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-cce">\n</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> - <td id="LC182" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> - <td id="LC183" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> - <td id="LC184" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> - <td id="LC185" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> - <td id="LC186" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> - </tr> - <tr> - <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> - <td id="LC187" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> - <td id="LC188" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> - </tr> - <tr> - <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> - <td id="LC189" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> - </tr> - <tr> - <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> - <td id="LC190" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> - <td id="LC191" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> - <td id="LC192" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">createHTML</span>(<span class="pl-smi">tdict</span>,<span class="pl-smi">sum_df</span>):</td> - </tr> - <tr> - <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> - <td id="LC193" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource</span></td> - </tr> - <tr> - <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> - <td id="LC194" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><html><title>T<span class="pl-c1">.</span>vivax VAP <span class="pl-c1">(</span>Transcriptomic Pathway<span class="pl-c1">(</span></title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> - <td id="LC195" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span>Sample name: <span class="pl-pds">"</span></span><span class="pl-k">+</span>tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> - <td id="LC196" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><br>Transcriptomic Analysis</h3></p><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> - <td id="LC197" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><p style = 'margin-left:20%; margin-right:20%'>Legend: <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> - <td id="LC198" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptome. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> - <td id="LC199" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Weighted Frequency reflects Phylotype abundance and is expressed as <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> - <td id="LC200" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>phylotype frequencies adjusted for the combined transcript abundance. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> - <td id="LC201" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> - <td id="LC202" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>(Silva Pereira et al., 2019).</p> <span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> - <td id="LC203" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> - <td id="LC204" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> - <td id="LC205" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><table style='width:50%;table-layout: auto; margin-left:25%;text-align:center'><tr><th>Phylotype</th><span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> - <td id="LC206" class="blob-code blob-code-inner js-file-line"> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><th>Combined FPKM</th><th>Weighted Frequency</th></tr><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> - <td id="LC207" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> - <td id="LC208" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> flush out table with correct values</span></td> - </tr> - <tr> - <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> - <td id="LC209" class="blob-code blob-code-inner js-file-line"> phySeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> - <td id="LC210" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> sacSeries = sum_df['saccver']</span></td> - </tr> - <tr> - <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> - <td id="LC211" class="blob-code blob-code-inner js-file-line"> fSeries <span class="pl-k">=</span> sum_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> - <td id="LC212" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> fSeries.sum()</td> - </tr> - <tr> - <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> - <td id="LC213" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print("Total="+str(total))</span></td> - </tr> - <tr> - <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> - <td id="LC214" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum_df)):</td> - </tr> - <tr> - <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> - <td id="LC215" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(phySeries[i])</span></td> - </tr> - <tr> - <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> - <td id="LC216" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i], <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> - <td id="LC217" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">format</span>(fSeries[i]<span class="pl-k">/</span>total, <span class="pl-s"><span class="pl-pds">'</span>.2f<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> - <td id="LC218" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> - <td id="LC219" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>w = format(weightList[i], '.4f')</span></td> - </tr> - <tr> - <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> - <td id="LC220" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> - <td id="LC221" class="blob-code blob-code-inner js-file-line"> tabString <span class="pl-k">+=</span> <span class="pl-s"><span class="pl-pds">"</span><tr><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(phySeries[i]) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span> <span class="pl-k">+</span> <span class="pl-c1">str</span>(f) <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></td><td><span class="pl-pds">"</span></span><span class="pl-k">+</span><span class="pl-c1">str</span>(w)<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span></tr><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> - <td id="LC222" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> tabString <span class="pl-k">+</span> <span class="pl-s"><span class="pl-pds">"</span></table><br><br><br><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> - <td id="LC223" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><h3>Weighted Relative Frequencies of Detected Phylotypes<span class="pl-c1">.</span></h3><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> - <td id="LC224" class="blob-code blob-code-inner js-file-line"> imgString <span class="pl-k">=</span> <span class="pl-sr"><span class="pl-k">r</span><span class="pl-pds">"</span><img src = '<span class="pl-pds">"</span></span><span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> - <td id="LC225" class="blob-code blob-code-inner js-file-line"> htmlString <span class="pl-k">+=</span> imgString</td> - </tr> - <tr> - <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> - <td id="LC226" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> - <td id="LC227" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">with</span> <span class="pl-c1">open</span>(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">"</span>w<span class="pl-pds">"</span></span>) <span class="pl-k">as</span> htmlfile:</td> - </tr> - <tr> - <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> - <td id="LC228" class="blob-code blob-code-inner js-file-line"> htmlfile.write(htmlString)</td> - </tr> - <tr> - <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> - <td id="LC229" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> - <td id="LC230" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> - <td id="LC231" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> - <td id="LC232" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getPhyloNumber</span>(<span class="pl-smi">sac</span>):</td> - </tr> - <tr> - <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> - <td id="LC233" class="blob-code blob-code-inner js-file-line"> i <span class="pl-k">=</span> sac.find(<span class="pl-s"><span class="pl-pds">'</span>_<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> - <td id="LC234" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> <span class="pl-c1">int</span>(sac[<span class="pl-c1">1</span>:i])</td> - </tr> - <tr> - <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> - <td id="LC235" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> - <td id="LC236" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">combineFPMK</span>(<span class="pl-smi">tdict</span>):</td> - </tr> - <tr> - <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> - <td id="LC237" class="blob-code blob-code-inner js-file-line"> fpkm_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>.cuff/genes.fpkm_tracking<span class="pl-pds">'</span></span>, <span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span><span class="pl-cce">\t</span><span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> - <td id="LC238" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> - <td id="LC239" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')</span></td> - </tr> - <tr> - <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> - <td id="LC240" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> - </tr> - <tr> - <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> - <td id="LC241" class="blob-code blob-code-inner js-file-line"> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>].apply(<span class="pl-k">lambda</span> <span class="pl-smi">names</span>: names[:names.find(<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>)])</td> - </tr> - <tr> - <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> - <td id="LC242" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(fpkm_df.head())</span></td> - </tr> - <tr> - <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> - <td id="LC243" class="blob-code blob-code-inner js-file-line"> reducedBlast_df <span class="pl-k">=</span> pd.read_csv(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">'</span>_transcript.csv<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> - <td id="LC244" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv')</span></td> - </tr> - <tr> - <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> - <td id="LC245" class="blob-code blob-code-inner js-file-line"> saccverSet <span class="pl-k">=</span> <span class="pl-c1">set</span>(reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> - <td id="LC246" class="blob-code blob-code-inner js-file-line"> saccverList <span class="pl-k">=</span> <span class="pl-c1">list</span>(saccverSet)</td> - </tr> - <tr> - <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> - <td id="LC247" class="blob-code blob-code-inner js-file-line"> saccverList.sort()</td> - </tr> - <tr> - <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> - <td id="LC248" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(saccverList[:5])</span></td> - </tr> - <tr> - <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> - <td id="LC249" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> pd.DataFrame(<span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> - <td id="LC250" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> sv <span class="pl-k">in</span> saccverList:</td> - </tr> - <tr> - <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> - <td id="LC251" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(sv)</span></td> - </tr> - <tr> - <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> - <td id="LC252" class="blob-code blob-code-inner js-file-line"> temp_df <span class="pl-k">=</span> reducedBlast_df[reducedBlast_df[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> sv]</td> - </tr> - <tr> - <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> - <td id="LC253" class="blob-code blob-code-inner js-file-line"> qList <span class="pl-k">=</span> <span class="pl-c1">list</span>(temp_df[<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> - <td id="LC254" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> q <span class="pl-k">in</span> qList:</td> - </tr> - <tr> - <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> - <td id="LC255" class="blob-code blob-code-inner js-file-line"> f_df <span class="pl-k">=</span> fpkm_df[(fpkm_df[<span class="pl-s"><span class="pl-pds">'</span>locus<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> q)]</td> - </tr> - <tr> - <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> - <td id="LC256" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> <span class="pl-c1">len</span>(f_df) <span class="pl-k">></span> <span class="pl-c1">1</span>:</td> - </tr> - <tr> - <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> - <td id="LC257" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">'</span>WARNING MULTIPLE FPKM<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> - <td id="LC258" class="blob-code blob-code-inner js-file-line"> new_fpkm<span class="pl-k">=</span><span class="pl-c1">list</span>(f_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> - <td id="LC259" class="blob-code blob-code-inner js-file-line"> f <span class="pl-k">=</span> (new_fpkm[<span class="pl-c1">0</span>])</td> - </tr> - <tr> - <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> - <td id="LC260" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(f)</span></td> - </tr> - <tr> - <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> - <td id="LC261" class="blob-code blob-code-inner js-file-line"> new_df <span class="pl-k">=</span> new_df.append({<span class="pl-s"><span class="pl-pds">'</span>qaccver<span class="pl-pds">'</span></span>: q, <span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>: sv, <span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>: f}, <span class="pl-v">ignore_index</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> - <td id="LC262" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> new_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> - </tr> - <tr> - <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> - <td id="LC263" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> - <td id="LC264" class="blob-code blob-code-inner js-file-line"> FPKMsum_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> FPKMsum_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: getPhyloNumber(row[<span class="pl-s"><span class="pl-pds">'</span>saccver<span class="pl-pds">'</span></span>]), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> - <td id="LC265" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> - <td id="LC266" class="blob-code blob-code-inner js-file-line"> FPKMsum_df <span class="pl-k">=</span> FPKMsum_df.reset_index(<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">True</span>)</td> - </tr> - <tr> - <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> - <td id="LC267" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> - <td id="LC268" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum_df)</span></td> - </tr> - <tr> - <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> - <td id="LC269" class="blob-code blob-code-inner js-file-line"> FPKMsum_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum.csv<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> - <td id="LC270" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum_df.groupby(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum().reset_index()</td> - </tr> - <tr> - <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> - <td id="LC271" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df <span class="pl-k">=</span> FPKMsum2_df.sort_values(<span class="pl-v">by</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> - <td id="LC272" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> - <td id="LC273" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(FPKMsum2_df)</span></td> - </tr> - <tr> - <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> - <td id="LC274" class="blob-code blob-code-inner js-file-line"> FPKMsum2_df.to_csv(<span class="pl-s"><span class="pl-pds">'</span>FPKM_sum2.csv<span class="pl-pds">'</span></span>) <span class="pl-c"><span class="pl-c">#</span> in case more than one entry for a particular phylotype</span></td> - </tr> - <tr> - <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> - <td id="LC275" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> FPKMsum_df, FPKMsum2_df</td> - </tr> - <tr> - <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> - <td id="LC276" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> - <td id="LC277" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> - <td id="LC278" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> - <td id="LC279" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">normalisef</span>(<span class="pl-smi">f</span>,<span class="pl-smi">max</span>):</td> - </tr> - <tr> - <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> - <td id="LC280" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> f<span class="pl-k">/</span><span class="pl-c1">max</span></td> - </tr> - <tr> - <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> - <td id="LC281" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> - <td id="LC282" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">getComposite_sum2</span>(<span class="pl-smi">nameList</span>,<span class="pl-smi">sum2_dfs</span>):</td> - </tr> - <tr> - <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> - <td id="LC283" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> lets get a composite sum2_df from all of the sum2_dfs</span></td> - </tr> - <tr> - <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> - <td id="LC284" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> - <td id="LC285" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> - <td id="LC286" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> - </tr> - <tr> - <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> - <td id="LC287" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> - </tr> - <tr> - <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> - <td id="LC288" class="blob-code blob-code-inner js-file-line"> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_dfs[i].apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total), <span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> - <td id="LC289" class="blob-code blob-code-inner js-file-line"> pSeries <span class="pl-k">=</span> sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> - <td id="LC290" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pSeries:</td> - </tr> - <tr> - <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> - <td id="LC291" class="blob-code blob-code-inner js-file-line"> phyList.append(p) <span class="pl-c"><span class="pl-c">#</span> get all the phylotypes in this one</span></td> - </tr> - <tr> - <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> - <td id="LC292" class="blob-code blob-code-inner js-file-line"> phyList <span class="pl-k">=</span> <span class="pl-c1">list</span>(<span class="pl-c1">set</span>(phyList))</td> - </tr> - <tr> - <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> - <td id="LC293" class="blob-code blob-code-inner js-file-line"> phyList.sort()</td> - </tr> - <tr> - <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> - <td id="LC294" class="blob-code blob-code-inner js-file-line"> composite_sum2_df <span class="pl-k">=</span> pd.DataFrame(phyList, <span class="pl-v">columns</span><span class="pl-k">=</span>[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> - <td id="LC295" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">0</span>, <span class="pl-c1">len</span>(sum2_dfs)):</td> - </tr> - <tr> - <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> - <td id="LC296" class="blob-code blob-code-inner js-file-line"> wList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> - <td id="LC297" class="blob-code blob-code-inner js-file-line"> pindf <span class="pl-k">=</span> <span class="pl-c1">list</span>(sum2_dfs[i][<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> - <td id="LC298" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> print(pindf)</span></td> - </tr> - <tr> - <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> - <td id="LC299" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> phyList:</td> - </tr> - <tr> - <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> - <td id="LC300" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> p <span class="pl-k">in</span> pindf:</td> - </tr> - <tr> - <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> - <td id="LC301" class="blob-code blob-code-inner js-file-line"> df <span class="pl-k">=</span> sum2_dfs[i]</td> - </tr> - <tr> - <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> - <td id="LC302" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> df.loc[df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> p, <span class="pl-s"><span class="pl-pds">'</span>w<span class="pl-pds">'</span></span>].iloc[<span class="pl-c1">0</span>]</td> - </tr> - <tr> - <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> - <td id="LC303" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">else</span>:</td> - </tr> - <tr> - <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> - <td id="LC304" class="blob-code blob-code-inner js-file-line"> w <span class="pl-k">=</span> <span class="pl-c1">0</span></td> - </tr> - <tr> - <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> - <td id="LC305" class="blob-code blob-code-inner js-file-line"> wList.append(w)</td> - </tr> - <tr> - <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> - <td id="LC306" class="blob-code blob-code-inner js-file-line"> composite_sum2_df[nameList[i]] <span class="pl-k">=</span> wList</td> - </tr> - <tr> - <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> - <td id="LC307" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(composite_sum2_df)</span></td> - </tr> - <tr> - <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> - <td id="LC308" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>composite_sum2_df.to_csv('composite.csv')</span></td> - </tr> - <tr> - <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> - <td id="LC309" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">return</span> composite_sum2_df</td> - </tr> - <tr> - <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> - <td id="LC310" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> - <td id="LC311" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> - <td id="LC312" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doMultiBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">composite_df</span>): <span class="pl-c"><span class="pl-c">#</span>array of multiple sum2_dfs</span></td> - </tr> - <tr> - <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> - <td id="LC313" class="blob-code blob-code-inner js-file-line"> labelList <span class="pl-k">=</span> composite_df.columns.tolist()</td> - </tr> - <tr> - <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> - <td id="LC314" class="blob-code blob-code-inner js-file-line"> sampnum <span class="pl-k">=</span> <span class="pl-c1">len</span>(labelList)<span class="pl-k">-</span><span class="pl-c1">1</span></td> - </tr> - <tr> - <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> - <td id="LC315" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> need to arrange bars</span></td> - </tr> - <tr> - <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> - <td id="LC316" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> number of phylotype = len(composite_df)</span></td> - </tr> - <tr> - <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> - <td id="LC317" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>number of bars = (len(labelist)-1) +1 for space</span></td> - </tr> - <tr> - <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> - <td id="LC318" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> ytick needs to ne</span></td> - </tr> - <tr> - <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> - <td id="LC319" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> - <td id="LC320" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab10<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L321" class="blob-num js-line-number" data-line-number="321"></td> - <td id="LC321" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> - </tr> - <tr> - <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> - <td id="LC322" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> - <td id="LC323" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> - <td id="LC324" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> - <td id="LC325" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> - <td id="LC326" class="blob-code blob-code-inner js-file-line"> width <span class="pl-k">=</span> <span class="pl-c1">0.6</span></td> - </tr> - <tr> - <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> - <td id="LC327" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> np.arange(width<span class="pl-k">*</span>sampnum<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>))</td> - </tr> - <tr> - <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> - <td id="LC328" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>print(ind)</span></td> - </tr> - <tr> - <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> - <td id="LC329" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span><span class="pl-c1">0.4</span></td> - </tr> - <tr> - <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> - <td id="LC330" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> - <td id="LC331" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> - </tr> - <tr> - <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> - <td id="LC332" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> - <td id="LC333" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> - <td id="LC334" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> s <span class="pl-k">in</span> <span class="pl-c1">range</span>(<span class="pl-c1">1</span>, <span class="pl-c1">len</span>(labelList)):</td> - </tr> - <tr> - <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> - <td id="LC335" class="blob-code blob-code-inner js-file-line"> ax.barh(ind, composite_df[labelList[s]], width, <span class="pl-v">color</span><span class="pl-k">=</span>palette[s], <span class="pl-v">label</span><span class="pl-k">=</span>labelList[s])</td> - </tr> - <tr> - <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> - <td id="LC336" class="blob-code blob-code-inner js-file-line"> ind <span class="pl-k">=</span> ind <span class="pl-k">+</span> width</td> - </tr> - <tr> - <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> - <td id="LC337" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> - <td id="LC338" class="blob-code blob-code-inner js-file-line"> ax.set(<span class="pl-v">yticks</span><span class="pl-k">=</span>np.arange(width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">2</span>)<span class="pl-k">/</span><span class="pl-c1">2</span>, <span class="pl-c1">len</span>(composite_df)<span class="pl-k">*</span>width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>), width<span class="pl-k">*</span>(sampnum<span class="pl-k">+</span><span class="pl-c1">1</span>)), <span class="pl-v">yticklabels</span><span class="pl-k">=</span>composite_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span> , ylim=[(len(labelList)-1) * width - 1, len(composite_df)])</span></td> - </tr> - <tr> - <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> - <td id="LC339" class="blob-code blob-code-inner js-file-line"> ax.legend()</td> - </tr> - <tr> - <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> - <td id="LC340" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L341" class="blob-num js-line-number" data-line-number="341"></td> - <td id="LC341" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L342" class="blob-num js-line-number" data-line-number="342"></td> - <td id="LC342" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L343" class="blob-num js-line-number" data-line-number="343"></td> - <td id="LC343" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> - </tr> - <tr> - <td id="L344" class="blob-num js-line-number" data-line-number="344"></td> - <td id="LC344" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L345" class="blob-num js-line-number" data-line-number="345"></td> - <td id="LC345" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L346" class="blob-num js-line-number" data-line-number="346"></td> - <td id="LC346" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> - </tr> - <tr> - <td id="L347" class="blob-num js-line-number" data-line-number="347"></td> - <td id="LC347" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> - </tr> - <tr> - <td id="L348" class="blob-num js-line-number" data-line-number="348"></td> - <td id="LC348" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L349" class="blob-num js-line-number" data-line-number="349"></td> - <td id="LC349" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.92</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> - </tr> - <tr> - <td id="L350" class="blob-num js-line-number" data-line-number="350"></td> - <td id="LC350" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> - </tr> - <tr> - <td id="L351" class="blob-num js-line-number" data-line-number="351"></td> - <td id="LC351" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L352" class="blob-num js-line-number" data-line-number="352"></td> - <td id="LC352" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L353" class="blob-num js-line-number" data-line-number="353"></td> - <td id="LC353" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L354" class="blob-num js-line-number" data-line-number="354"></td> - <td id="LC354" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L355" class="blob-num js-line-number" data-line-number="355"></td> - <td id="LC355" class="blob-code blob-code-inner js-file-line"> plt.show()</td> - </tr> - <tr> - <td id="L356" class="blob-num js-line-number" data-line-number="356"></td> - <td id="LC356" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> - </tr> - <tr> - <td id="L357" class="blob-num js-line-number" data-line-number="357"></td> - <td id="LC357" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L358" class="blob-num js-line-number" data-line-number="358"></td> - <td id="LC358" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L359" class="blob-num js-line-number" data-line-number="359"></td> - <td id="LC359" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L360" class="blob-num js-line-number" data-line-number="360"></td> - <td id="LC360" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">doBarChart</span>(<span class="pl-smi">tdict</span>, <span class="pl-smi">sum2_df</span>):</td> - </tr> - <tr> - <td id="L361" class="blob-num js-line-number" data-line-number="361"></td> - <td id="LC361" class="blob-code blob-code-inner js-file-line"> cmap <span class="pl-k">=</span> plt.cm.get_cmap(<span class="pl-s"><span class="pl-pds">'</span>tab20<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L362" class="blob-num js-line-number" data-line-number="362"></td> - <td id="LC362" class="blob-code blob-code-inner js-file-line"> palette <span class="pl-k">=</span> [cmap(i) <span class="pl-k">for</span> i <span class="pl-k">in</span> <span class="pl-c1">range</span>(cmap.N)]</td> - </tr> - <tr> - <td id="L363" class="blob-num js-line-number" data-line-number="363"></td> - <td id="LC363" class="blob-code blob-code-inner js-file-line"> title <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">"</span>Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L364" class="blob-num js-line-number" data-line-number="364"></td> - <td id="LC364" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Phylotype abundance is expressed as phylotype frequencies adjusted <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L365" class="blob-num js-line-number" data-line-number="365"></td> - <td id="LC365" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>for combined transcript abundance. <span class="pl-pds">"</span></span> \</td> - </tr> - <tr> - <td id="L366" class="blob-num js-line-number" data-line-number="366"></td> - <td id="LC366" class="blob-code blob-code-inner js-file-line"> <span class="pl-s"><span class="pl-pds">"</span>Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019).<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L367" class="blob-num js-line-number" data-line-number="367"></td> - <td id="LC367" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> get a list of phylotype, create equivalent of saccver, get a list of</span></td> - </tr> - <tr> - <td id="L368" class="blob-num js-line-number" data-line-number="368"></td> - <td id="LC368" class="blob-code blob-code-inner js-file-line"> maxFPKM <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].max()</td> - </tr> - <tr> - <td id="L369" class="blob-num js-line-number" data-line-number="369"></td> - <td id="LC369" class="blob-code blob-code-inner js-file-line"> total <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>].sum()</td> - </tr> - <tr> - <td id="L370" class="blob-num js-line-number" data-line-number="370"></td> - <td id="LC370" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L371" class="blob-num js-line-number" data-line-number="371"></td> - <td id="LC371" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Normalised<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], maxFPKM),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L372" class="blob-num js-line-number" data-line-number="372"></td> - <td id="LC372" class="blob-code blob-code-inner js-file-line"> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> sum2_df.apply(<span class="pl-k">lambda</span> <span class="pl-smi">row</span>: normalisef(row[<span class="pl-s"><span class="pl-pds">'</span>FPKM<span class="pl-pds">'</span></span>], total),<span class="pl-v">axis</span><span class="pl-k">=</span><span class="pl-c1">1</span>)</td> - </tr> - <tr> - <td id="L373" class="blob-num js-line-number" data-line-number="373"></td> - <td id="LC373" class="blob-code blob-code-inner js-file-line"> pList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L374" class="blob-num js-line-number" data-line-number="374"></td> - <td id="LC374" class="blob-code blob-code-inner js-file-line"> phList <span class="pl-k">=</span> []</td> - </tr> - <tr> - <td id="L375" class="blob-num js-line-number" data-line-number="375"></td> - <td id="LC375" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">for</span> p <span class="pl-k">in</span> pList:</td> - </tr> - <tr> - <td id="L376" class="blob-num js-line-number" data-line-number="376"></td> - <td id="LC376" class="blob-code blob-code-inner js-file-line"> phList.append(<span class="pl-c1">str</span>(p))</td> - </tr> - <tr> - <td id="L377" class="blob-num js-line-number" data-line-number="377"></td> - <td id="LC377" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L378" class="blob-num js-line-number" data-line-number="378"></td> - <td id="LC378" class="blob-code blob-code-inner js-file-line"> fList <span class="pl-k">=</span> sum2_df[<span class="pl-s"><span class="pl-pds">'</span>Weighted<span class="pl-pds">'</span></span>]</td> - </tr> - <tr> - <td id="L379" class="blob-num js-line-number" data-line-number="379"></td> - <td id="LC379" class="blob-code blob-code-inner js-file-line"> ysize <span class="pl-k">=</span> <span class="pl-c1">len</span>(phList)<span class="pl-k">*</span><span class="pl-c1">0.3</span></td> - </tr> - <tr> - <td id="L380" class="blob-num js-line-number" data-line-number="380"></td> - <td id="LC380" class="blob-code blob-code-inner js-file-line"> fig, ax <span class="pl-k">=</span> plt.subplots(<span class="pl-v">figsize</span><span class="pl-k">=</span>(<span class="pl-c1">10</span>,ysize))</td> - </tr> - <tr> - <td id="L381" class="blob-num js-line-number" data-line-number="381"></td> - <td id="LC381" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L382" class="blob-num js-line-number" data-line-number="382"></td> - <td id="LC382" class="blob-code blob-code-inner js-file-line"> ax.barh(phList, fList, <span class="pl-v">color</span><span class="pl-k">=</span>palette)</td> - </tr> - <tr> - <td id="L383" class="blob-num js-line-number" data-line-number="383"></td> - <td id="LC383" class="blob-code blob-code-inner js-file-line"> ax.set_ylabel(<span class="pl-s"><span class="pl-pds">'</span>Phylotype<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L384" class="blob-num js-line-number" data-line-number="384"></td> - <td id="LC384" class="blob-code blob-code-inner js-file-line"> ax.invert_yaxis() <span class="pl-c"><span class="pl-c">#</span> labels read top-to-bottom</span></td> - </tr> - <tr> - <td id="L385" class="blob-num js-line-number" data-line-number="385"></td> - <td id="LC385" class="blob-code blob-code-inner js-file-line"> ax.set_xlabel(<span class="pl-s"><span class="pl-pds">'</span>Weighted Phylotype Frequency<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L386" class="blob-num js-line-number" data-line-number="386"></td> - <td id="LC386" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L387" class="blob-num js-line-number" data-line-number="387"></td> - <td id="LC387" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.text(-0.3, -0.15, title, va="top", wrap="True")</span></td> - </tr> - <tr> - <td id="L388" class="blob-num js-line-number" data-line-number="388"></td> - <td id="LC388" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span>plt.tight_layout()</span></td> - </tr> - <tr> - <td id="L389" class="blob-num js-line-number" data-line-number="389"></td> - <td id="LC389" class="blob-code blob-code-inner js-file-line"> plt.subplots_adjust(<span class="pl-v">bottom</span><span class="pl-k">=</span><span class="pl-c1">0.1</span>, <span class="pl-v">top</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>, <span class="pl-v">left</span><span class="pl-k">=</span><span class="pl-c1">0.15</span>, <span class="pl-v">right</span><span class="pl-k">=</span><span class="pl-c1">0.9</span>)</td> - </tr> - <tr> - <td id="L390" class="blob-num js-line-number" data-line-number="390"></td> - <td id="LC390" class="blob-code blob-code-inner js-file-line"> ax.set_title(title, <span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-c1">0</span>, <span class="pl-v">wrap</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>True<span class="pl-pds">'</span></span>,<span class="pl-v">ha</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">'</span>left<span class="pl-pds">'</span></span>,)</td> - </tr> - <tr> - <td id="L391" class="blob-num js-line-number" data-line-number="391"></td> - <td id="LC391" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L392" class="blob-num js-line-number" data-line-number="392"></td> - <td id="LC392" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>_phylotypes.png<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L393" class="blob-num js-line-number" data-line-number="393"></td> - <td id="LC393" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">if</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">'</span>PDF_Yes<span class="pl-pds">'</span></span>:</td> - </tr> - <tr> - <td id="L394" class="blob-num js-line-number" data-line-number="394"></td> - <td id="LC394" class="blob-code blob-code-inner js-file-line"> plt.savefig(tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">+</span> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]<span class="pl-k">+</span><span class="pl-s"><span class="pl-pds">"</span>phylotypes.pdf<span class="pl-pds">"</span></span>)</td> - </tr> - <tr> - <td id="L395" class="blob-num js-line-number" data-line-number="395"></td> - <td id="LC395" class="blob-code blob-code-inner js-file-line"> <span class="pl-c"><span class="pl-c">#</span> plt.show()</span></td> - </tr> - <tr> - <td id="L396" class="blob-num js-line-number" data-line-number="396"></td> - <td id="LC396" class="blob-code blob-code-inner js-file-line"> <span class="pl-k">pass</span></td> - </tr> - <tr> - <td id="L397" class="blob-num js-line-number" data-line-number="397"></td> - <td id="LC397" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L398" class="blob-num js-line-number" data-line-number="398"></td> - <td id="LC398" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span> argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}</span></td> - </tr> - <tr> - <td id="L399" class="blob-num js-line-number" data-line-number="399"></td> - <td id="LC399" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L400" class="blob-num js-line-number" data-line-number="400"></td> - <td id="LC400" class="blob-code blob-code-inner js-file-line"><span class="pl-k">def</span> <span class="pl-en">transcriptomicProcess</span>(<span class="pl-smi">args</span>,<span class="pl-smi">argdict</span>):</td> - </tr> - <tr> - <td id="L401" class="blob-num js-line-number" data-line-number="401"></td> - <td id="LC401" class="blob-code blob-code-inner js-file-line"> tdict <span class="pl-k">=</span> {}</td> - </tr> - <tr> - <td id="L402" class="blob-num js-line-number" data-line-number="402"></td> - <td id="LC402" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L403" class="blob-num js-line-number" data-line-number="403"></td> - <td id="LC403" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L404" class="blob-num js-line-number" data-line-number="404"></td> - <td id="LC404" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L405" class="blob-num js-line-number" data-line-number="405"></td> - <td id="LC405" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L406" class="blob-num js-line-number" data-line-number="406"></td> - <td id="LC406" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>vivax_trans_database<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span></td> - </tr> - <tr> - <td id="L407" class="blob-num js-line-number" data-line-number="407"></td> - <td id="LC407" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>pdf<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>pdfexport<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L408" class="blob-num js-line-number" data-line-number="408"></td> - <td id="LC408" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_file<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L409" class="blob-num js-line-number" data-line-number="409"></td> - <td id="LC409" class="blob-code blob-code-inner js-file-line"> tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>] <span class="pl-k">=</span> args[argdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>]]</td> - </tr> - <tr> - <td id="L410" class="blob-num js-line-number" data-line-number="410"></td> - <td id="LC410" class="blob-code blob-code-inner js-file-line"> </td> - </tr> - <tr> - <td id="L411" class="blob-num js-line-number" data-line-number="411"></td> - <td id="LC411" class="blob-code blob-code-inner js-file-line"> uploadUserReferenceFastq(tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>])</td> - </tr> - <tr> - <td id="L412" class="blob-num js-line-number" data-line-number="412"></td> - <td id="LC412" class="blob-code blob-code-inner js-file-line"> transcriptMapping(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>forward<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>reverse<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses bowtie</span></td> - </tr> - <tr> - <td id="L413" class="blob-num js-line-number" data-line-number="413"></td> - <td id="LC413" class="blob-code blob-code-inner js-file-line"> processSamFiles(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses samtools</span></td> - </tr> - <tr> - <td id="L414" class="blob-num js-line-number" data-line-number="414"></td> - <td id="LC414" class="blob-code blob-code-inner js-file-line"> transcriptAbundance(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>uses cufflinks -> ?.cuff/*.*</span></td> - </tr> - <tr> - <td id="L415" class="blob-num js-line-number" data-line-number="415"></td> - <td id="LC415" class="blob-code blob-code-inner js-file-line"> transcriptsForBlast(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>refFastq<span class="pl-pds">'</span></span>]) <span class="pl-c"><span class="pl-c">#</span>creates name+4blast.fa</span></td> - </tr> - <tr> - <td id="L416" class="blob-num js-line-number" data-line-number="416"></td> - <td id="LC416" class="blob-code blob-code-inner js-file-line"> blastContigs(tdict[<span class="pl-s"><span class="pl-pds">'</span>name<span class="pl-pds">'</span></span>], tdict[<span class="pl-s"><span class="pl-pds">'</span>html_resource<span class="pl-pds">'</span></span>], <span class="pl-s"><span class="pl-pds">'</span>data/vivax/Database/Phylotype_typeseqs.fas<span class="pl-pds">'</span></span>)</td> - </tr> - <tr> - <td id="L417" class="blob-num js-line-number" data-line-number="417"></td> - <td id="LC417" class="blob-code blob-code-inner js-file-line"> sum_df, sum2_df <span class="pl-k">=</span> combineFPMK(tdict)</td> - </tr> - <tr> - <td id="L418" class="blob-num js-line-number" data-line-number="418"></td> - <td id="LC418" class="blob-code blob-code-inner js-file-line"> doBarChart(tdict, sum2_df)</td> - </tr> - <tr> - <td id="L419" class="blob-num js-line-number" data-line-number="419"></td> - <td id="LC419" class="blob-code blob-code-inner js-file-line"> createHTML(tdict, sum_df)</td> - </tr> - <tr> - <td id="L420" class="blob-num js-line-number" data-line-number="420"></td> - <td id="LC420" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L421" class="blob-num js-line-number" data-line-number="421"></td> - <td id="LC421" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L422" class="blob-num js-line-number" data-line-number="422"></td> - <td id="LC422" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-c1">__name__</span> <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">"</span>__main__<span class="pl-pds">"</span></span>:</td> - </tr> - <tr> - <td id="L423" class="blob-num js-line-number" data-line-number="423"></td> - <td id="LC423" class="blob-code blob-code-inner js-file-line"> <span class="pl-c1">exit</span>()</td> - </tr> - <tr> - <td id="L424" class="blob-num js-line-number" data-line-number="424"></td> - <td id="LC424" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> - <tr> - <td id="L425" class="blob-num js-line-number" data-line-number="425"></td> - <td id="LC425" class="blob-code blob-code-inner js-file-line"> -</td> - </tr> -</table> - - <details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true"> - <summary class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1" aria-label="Inline file action toolbar"> - <svg class="octicon octicon-kebab-horizontal" viewBox="0 0 13 16" version="1.1" width="13" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M1.5 9a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zm5 0a1.5 1.5 0 1 0 0-3 1.5 1.5 0 0 0 0 3zM13 7.5a1.5 1.5 0 1 1-3 0 1.5 1.5 0 0 1 3 0z"/></svg> - </summary> - <details-menu> - <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2" style="width:185px"> - <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-lines" style="cursor:pointer;" data-original-text="Copy lines">Copy lines</clipboard-copy></li> - <li><clipboard-copy role="menuitem" class="dropdown-item" id="js-copy-permalink" 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class="js-global-screen-reader-notice sr-only"></div> - - </body> -</html> - +""" +* Galaxy Version + + * Copyright 2019 University of Liverpool + * Author John Heap, Computational Biology Facility, UoL + * Based on original scripts of Sara Silva Silva Pereira, Institute of Infection and Global Health, UoL + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * + """ + + +import subprocess +import pandas as pd +import re +import os +import sys +import shutil +# import matplotlib as mpl +# mpl.use('Agg') +import matplotlib.pyplot as plt +import numpy as np + + + + +# copies the user provided Fasta file to data/reference/file/file.fasta +def uploadUserReferenceFastq(refFastq): + refBase = os.path.basename(refFastq) + ref = os.path.splitext(refBase)[0] # 'mydata/test.fasta' -> 'test' + dir_path = os.path.dirname(os.path.realpath(__file__)) # directory of this file + refDir = dir_path + "/data/Reference/" + ref #propose putting file in '/data/reference/ref/ + if not os.path.isdir(refDir): # if directory data/Reference/ref doesn't exist + os.mkdir(refDir) + refPath = refDir+"/" + shutil.copy(refFastq, refPath + refBase) #copy reference file into the directory + argString = "bowtie2-build " + refPath + refBase+" "+refPath+ref + print("Building the bowtie2 reference files.") + subprocess.call(argString, shell=True) + return + +def transcriptMapping(inputname, refFastq, forwardFN, reverseFN): + # where is our Reference data? + refBase = os.path.basename(refFastq) + ref = os.path.splitext(refBase)[0] + dir_path = os.path.dirname(os.path.realpath(__file__)) + refDir = dir_path + "/data/Reference/" + ref + "/" + refName = refDir + ref + # now have reference file so we can proceed with the transcript mapping via bowtie2 + argString = "bowtie2 -x "+refName+" -1 "+forwardFN+" -2 "+reverseFN+" -S "+inputname+".sam" + print(argString) + subprocess.call(argString, shell=True) #outputs a name.sam file + return + + + +def processSamFiles(inputname): + cur_path = os.getcwd() + samName = cur_path+"/"+inputname + argString = "samtools view -bS "+inputname+".sam > "+samName+".bam" + print(argString) + subprocess.call(argString, shell=True) + + argString = "samtools sort "+samName+".bam -o "+samName+".sorted" + print("argstring = "+argString) + subprocess.call(argString, shell=True) + + argString = "samtools index "+samName+".sorted "+samName+".sorted.bai" + print("argstring = " + argString) + subprocess.call(argString, shell=True) + return #we have saved out the relevent name.bam, name.sorted and name.sorted.bai files + +# we will not have the .gtf file so call cufflinks without -G option +def transcriptAbundance(inputname): + argString = "cufflinks -o "+inputname+".cuff -u -p 8 "+inputname+".sorted" + subprocess.call(argString, shell = True) + os.remove(inputname+".sorted") #remove name.sorted + os.remove(inputname+".sorted.bai") + os.remove(inputname+".bam") + return + +def transcriptsForBlast(name, refFastq): + # quick and dirty just to see. + refBase = os.path.basename(refFastq) + ref = os.path.splitext(refBase)[0] # 'mydata/test.fasta' -> 'test' + dir_path = os.path.dirname(os.path.realpath(__file__)) # directory of this file + refPath = dir_path + "/data/Reference/" + ref + "/" + refBase # eg refPath = data/Reference/Trinity/Trinity.fasta + # used for dirty # refPath = 'Trinity.fasta' # dirty one + track_df = pd.read_csv(name+'.cuff/genes.fpkm_tracking', sep='\t') + names = track_df['locus'] + # print(len(names)) + # print(names[:5]) + + nlist = [] + for n in range(0,len(names)): + i = names[n].find(':') + nlist.append(names[n][:i]) + nameset = set(nlist) #get unique. + with open(refPath, 'r') as myRef: + refData = myRef.read() + refData= refData+'\n>' + + with open(name + '_for_blast.fa', 'w') as outfile: + for trans_id in nameset: + namepos = refData.find(trans_id) + endpos = refData.find('>', namepos) + outfile.write('>'+refData[namepos:endpos]) + + pass + +def blastContigs(test_name,html_resource, database): + db_path = database + argString = "blastx -db "+db_path+" -query "+test_name+"_for_blast.fa -outfmt 10 -out "+test_name+"_blast.txt" + print(argString) + returncode = subprocess.call(argString, shell=True) + if returncode != 0: + return "Error in blastall" + blast_df = pd.read_csv(""+test_name+"_blast.txt") + blast_df.columns = ['qaccver', 'saccver', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue','bitscore'] + blastResult_df = blast_df[(blast_df['pident']>=70) & (blast_df['length'] > 100) & (blast_df['evalue'] <=0.001) ] + blastResult_df = blastResult_df[['qaccver', 'saccver', 'pident', 'evalue', 'bitscore']] #query accession.version, subject accession.version, Percentage of identical matches + # need to allocate the transcripts (if allocated more than once to the phylotype with least error. + transcripts = blastResult_df['qaccver'] + b_df = pd.DataFrame(columns=['qaccver', 'saccver', 'pident', 'evalue', 'bitscore']) + transSet = set(transcripts) + for t in transSet: + temp_df = blastResult_df[(blastResult_df['qaccver'] == t)] + # get one with smallest error value + #print(t + ":") + #print(temp_df) + temp_df = temp_df.sort_values(by=['evalue']) + b_df = b_df.append(temp_df.iloc[[0]]) + + b_df.sort_values(by=['qaccver']) + b_df.to_csv(test_name + '_transcript.csv') + return b_df + + +def createMultiHTML(tdict,composite_df): + labelList = composite_df.columns.tolist() + htmlString = r"<html><title>T.vivax VAP (Transcriptomic Pathway(</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3>" + htmlString += r"Sample name: "+tdict['name'] + htmlString += r"<br>Transcriptomic Analysis</h3></p>" + htmlString += "<p style = 'margin-left:20%; margin-right:20%'>Legend: " \ + "Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptomes. " \ + "Weighted Frequency reflects Phylotype abundance and is expressed as " \ + "phylotype frequencies adjusted for the combined transcript abundance. " \ + "Data was produced with VAPPER-Variant Antigen Profiler " \ + "(Silva Pereira et al., 2019).</p> " + htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>" + + header = r"<table style='width:50%;margin-left:25%;text-align:center'><tr><th>Phylotype</th>" + wLists = [] + + for j in range(1,len(labelList)): + wLists.append(composite_df[labelList[j]]) + header += r"<th>" + str(labelList[j]) + "</th>" + + htmlString += "</tr>\n" + header + tabString = "" + phyList = composite_df['Phylotype'] + + + + for i in range(0, len(composite_df)): + tabString += "<tr><td>" + str(phyList[i]) + "</td>" + for j in range(0,len(labelList)-1): + #print(j) + f = format(wLists[j][i], '.4f') + tabString += "<td>" + str(f) + "</td>" + tabString += "</tr>\n" + + htmlString += tabString + "</table><br><br><br><br><br>" + htmlString += r"<h3>Weighted Relative Frequencies of Detected Phylotypes.</h3>" + imgString = r"<img src = '"+ tdict['name']+"_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br>" + htmlString += imgString + + with open(tdict['html_file'], "w") as htmlfile: + htmlfile.write(htmlString) + + +def createHTML(tdict,sum_df): + #assumes imgs are heatmap.png, dheatmap.png, vapPCA.png and already in htmlresource + htmlString = r"<html><title>T.vivax VAP (Transcriptomic Pathway(</title><body><div style='text-align:center'><h2><i>Trypanosoma vivax</i> Variant Antigen Profile</h2><h3>" + htmlString += r"Sample name: "+tdict['name'] + htmlString += r"<br>Transcriptomic Analysis</h3></p>" + htmlString += "<p style = 'margin-left:20%; margin-right:20%'>Legend: " \ + "Variant Antigen Profile of a <i>Trypanosoma vivax</i> transcriptome. " \ + "Weighted Frequency reflects Phylotype abundance and is expressed as " \ + "phylotype frequencies adjusted for the combined transcript abundance. " \ + "Data was produced with VAPPER-Variant Antigen Profiler " \ + "(Silva Pereira et al., 2019).</p> " + htmlString += r"<style> table, th, tr, td {border: 1px solid black; border-collapse: collapse;}</style>" + + htmlString += r"<table style='width:50%;table-layout: auto; margin-left:25%;text-align:center'><tr><th>Phylotype</th>" \ + r"<th>Combined FPKM</th><th>Weighted Frequency</th></tr>" + tabString = "" + # flush out table with correct values + phySeries = sum_df['Phylotype'] + # sacSeries = sum_df['saccver'] + fSeries = sum_df['FPKM'] + total = fSeries.sum() + # print("Total="+str(total)) + for i in range(0, len(sum_df)): + # print(phySeries[i]) + f = format(fSeries[i], '.2f') + w = format(fSeries[i]/total, '.2f') + + #w = format(weightList[i], '.4f') + + tabString += "<tr><td>" + str(phySeries[i]) + "</td><td>" + str(f) + "</td><td>"+str(w)+"</tr>" + htmlString += tabString + "</table><br><br><br><br><br>" + htmlString += r"<h3>Weighted Relative Frequencies of Detected Phylotypes.</h3>" + imgString = r"<img src = '"+ tdict['name']+"_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br>" + htmlString += imgString + + with open(tdict['html_file'], "w") as htmlfile: + htmlfile.write(htmlString) + + + +def getPhyloNumber(sac): + i = sac.find('_') + return int(sac[1:i]) + +def combineFPMK(tdict): + fpkm_df = pd.read_csv(tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') + + #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t') + #print(fpkm_df.head()) + fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')]) + #print(fpkm_df.head()) + reducedBlast_df = pd.read_csv(tdict['name']+'_transcript.csv') + # reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv') + saccverSet = set(reducedBlast_df['saccver']) + saccverList = list(saccverSet) + saccverList.sort() + # print(saccverList[:5]) + new_df = pd.DataFrame(columns=['qaccver','saccver','FPKM']) + for sv in saccverList: + #print(sv) + temp_df = reducedBlast_df[reducedBlast_df['saccver'] == sv] + qList = list(temp_df['qaccver']) + for q in qList: + f_df = fpkm_df[(fpkm_df['locus'] == q)] + if len(f_df) > 1: + print('WARNING MULTIPLE FPKM') + new_fpkm=list(f_df['FPKM']) + f = (new_fpkm[0]) + # print(f) + new_df = new_df.append({'qaccver': q, 'saccver': sv, 'FPKM': f}, ignore_index=True) + FPKMsum_df = new_df.groupby('saccver')['FPKM'].sum().reset_index() + + FPKMsum_df['Phylotype'] = FPKMsum_df.apply(lambda row: getPhyloNumber(row['saccver']), axis=1) + FPKMsum_df = FPKMsum_df.sort_values(by=['Phylotype']) + FPKMsum_df = FPKMsum_df.reset_index(drop=True) + + # print(FPKMsum_df) + FPKMsum_df.to_csv('FPKM_sum.csv') + FPKMsum2_df = FPKMsum_df.groupby('Phylotype')['FPKM'].sum().reset_index() + FPKMsum2_df = FPKMsum2_df.sort_values(by=['Phylotype']) + + # print(FPKMsum2_df) + FPKMsum2_df.to_csv('FPKM_sum2.csv') # in case more than one entry for a particular phylotype + return FPKMsum_df, FPKMsum2_df + + + +def normalisef(f,max): + return f/max + +def getComposite_sum2(nameList,sum2_dfs): + # lets get a composite sum2_df from all of the sum2_dfs + phyList = [] + + for i in range(0, len(sum2_dfs)): + total = sum2_dfs[i]['FPKM'].sum() + sum2_dfs[i]['w'] = sum2_dfs[i].apply(lambda row: normalisef(row['FPKM'], total), axis=1) + pSeries = sum2_dfs[i]['Phylotype'] + for p in pSeries: + phyList.append(p) # get all the phylotypes in this one + phyList = list(set(phyList)) + phyList.sort() + composite_sum2_df = pd.DataFrame(phyList, columns=['Phylotype']) + for i in range(0, len(sum2_dfs)): + wList = [] + pindf = list(sum2_dfs[i]['Phylotype']) + # print(pindf) + for p in phyList: + if p in pindf: + df = sum2_dfs[i] + w = df.loc[df['Phylotype'] == p, 'w'].iloc[0] + else: + w = 0 + wList.append(w) + composite_sum2_df[nameList[i]] = wList + #print(composite_sum2_df) + #composite_sum2_df.to_csv('composite.csv') + return composite_sum2_df + + +def doMultiBarChart(tdict, composite_df): #array of multiple sum2_dfs + labelList = composite_df.columns.tolist() + sampnum = len(labelList)-1 +# need to arrange bars +# number of phylotype = len(composite_df) +#number of bars = (len(labelist)-1) +1 for space +# ytick needs to ne + + cmap = plt.cm.get_cmap('tab10') + palette = [cmap(i) for i in range(cmap.N)] + title = "Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptomes. " \ + "Phylotype abundance is expressed as phylotype frequencies adjusted " \ + "for combined transcript abundance. " \ + "Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019)." + width = 0.6 + ind = np.arange(width*sampnum/2, len(composite_df)*width*(sampnum+1), width*(sampnum+1)) + #print(ind) + ysize = len(composite_df)*0.4 + + fig, ax = plt.subplots(figsize=(10,ysize)) + + + for s in range(1, len(labelList)): + ax.barh(ind, composite_df[labelList[s]], width, color=palette[s], label=labelList[s]) + ind = ind + width + + ax.set(yticks=np.arange(width*(sampnum+2)/2, len(composite_df)*width*(sampnum+1), width*(sampnum+1)), yticklabels=composite_df['Phylotype']) # , ylim=[(len(labelList)-1) * width - 1, len(composite_df)]) + ax.legend() + + + ax.set_ylabel('Phylotype') + ax.invert_yaxis() # labels read top-to-bottom + ax.set_xlabel('Weighted Phylotype Frequency') + + # plt.text(-0.3, -0.15, title, va="top", wrap="True") + #plt.tight_layout() + + plt.subplots_adjust(bottom=0.1, top=0.92, left=0.15, right=0.9) + ax.set_title(title, x=0, wrap='True',ha='left',) + + plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png") + if tdict['pdf'] == 'PDF_Yes': + plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf") + plt.show() + pass + + + +def doBarChart(tdict, sum2_df): + cmap = plt.cm.get_cmap('tab20') + palette = [cmap(i) for i in range(cmap.N)] + title = "Legend: Variant Antigen Profile of a $\itTrypanosoma$ $\itvivax$ transcriptome. " \ + "Phylotype abundance is expressed as phylotype frequencies adjusted " \ + "for combined transcript abundance. " \ + "Data was produced with VAPPER-Variant Antigen Profiler (Silva Pereira et al., 2019)." + # get a list of phylotype, create equivalent of saccver, get a list of + maxFPKM = sum2_df['FPKM'].max() + total = sum2_df['FPKM'].sum() + + sum2_df['Normalised'] = sum2_df.apply(lambda row: normalisef(row['FPKM'], maxFPKM),axis=1) + sum2_df['Weighted'] = sum2_df.apply(lambda row: normalisef(row['FPKM'], total),axis=1) + pList = sum2_df['Phylotype'] + phList = [] + for p in pList: + phList.append(str(p)) + + fList = sum2_df['Weighted'] + ysize = len(phList)*0.3 + fig, ax = plt.subplots(figsize=(10,ysize)) + + ax.barh(phList, fList, color=palette) + ax.set_ylabel('Phylotype') + ax.invert_yaxis() # labels read top-to-bottom + ax.set_xlabel('Weighted Phylotype Frequency') + + # plt.text(-0.3, -0.15, title, va="top", wrap="True") + #plt.tight_layout() + plt.subplots_adjust(bottom=0.1, top=0.9, left=0.15, right=0.9) + ax.set_title(title, x=0, wrap='True',ha='left',) + + plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png") + if tdict['pdf'] == 'PDF_Yes': + plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf") + # plt.show() + pass + +# argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8} + +def transcriptomicProcess(args,argdict): + tdict = {} + tdict['name'] = args[argdict['name']] + tdict['refFastq'] = args[argdict['refFastq']] + tdict['forward'] = args[argdict['forward']] + tdict['reverse'] = args[argdict['reverse']] + tdict['vivax_trans_database'] = 'data/vivax/Database/Phylotype_typeseqs.fas' + tdict['pdf'] = args[argdict['pdfexport']] + tdict['html_file'] = args[argdict['html_file']] + tdict['html_resource'] = args[argdict['html_resource']] + + uploadUserReferenceFastq(tdict['refFastq']) + transcriptMapping(tdict['name'], tdict['refFastq'], tdict['forward'], tdict['reverse']) #uses bowtie + processSamFiles(tdict['name']) #uses samtools + transcriptAbundance(tdict['name']) #uses cufflinks -> ?.cuff/*.* + transcriptsForBlast(tdict['name'], tdict['refFastq']) #creates name+4blast.fa + blastContigs(tdict['name'], tdict['html_resource'], 'data/vivax/Database/Phylotype_typeseqs.fas') + sum_df, sum2_df = combineFPMK(tdict) + doBarChart(tdict, sum2_df) + createHTML(tdict, sum_df) + + +if __name__ == "__main__": + exit() + +