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author johnheap
date Mon, 03 Jun 2019 16:02:02 -0400
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19:fe79425b1fa4 20:26ec953069b3
1 """
2 * Copyright 2018 University of Liverpool
3 * Author: John Heap, Computational Biology Facility, UoL
4 * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL
5 *
6 * Licensed under the Apache License, Version 2.0 (the "License");
7 * you may not use this file except in compliance with the License.
8 * You may obtain a copy of the License at
9 *
10 * http://www.apache.org/licenses/LICENSE-2.0
11 *
12 * Unless required by applicable law or agreed to in writing, software
13 * distributed under the License is distributed on an "AS IS" BASIS,
14 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15 * See the License for the specific language governing permissions and
16 * limitations under the License.
17 *
18 """
19 #import subprocess
20 #import re
21 import os
22 import sys
23 #import pandas as pd
24 #import numpy as np
25 #import seaborn as sns
26 #import matplotlib.pyplot as plt
27 #from matplotlib.mlab import PCA
28 import Tryp_G
29 import Tryp_T
30 import Tryp_V
31 import Tryp_V_T
32 import argparse
33 #Entry .sort out the arguments
34
35 pdfExport = False
36 #parser = argparse.ArgumentParser(description='Variant Antigen Profiler - the VAP.')
37 #parser.add_argument('name')
38 #parser.add_argument('-t','-T', action = 'store_true', default = False, help = "Transciptomic Pathway")
39 #parser.add_argument('-p','-P', action = 'store_true', default = False, help = "Export PDFs to HTML directory")
40 #parser.add_argument('strain')
41 #parser.add_argument('Forward_Read_File')
42 #parser.add_argument('Reverse_Read_File')
43 #parser.add_argument('htmlfile')
44 #parser.add_argument('htmlresource')
45 #parser.add_argument('heatmapFile')
46 #parser.add_argument('PCAFile')
47 #parser.add_argument('devheatmapFile')
48 #args = parser.parse_args()
49
50 #we have numerous parameters....
51 #hard code it for differnt types?
1 52
2 53
54 arguments = sys.argv
55 htmldir = arguments[len(arguments)-1] #last argument is always html_resource
56 if not os.path.exists(htmldir):
57 os.mkdir(htmldir)
58
59 if arguments[1] == 'g_assemble':
60 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
61 Tryp_G.assemble(arguments,argdict)
62 if arguments[1] == 'g_contigs':
63 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
64 Tryp_G.contigs(arguments,argdict)
65 if arguments[1] == 'transcipt':
66 argdict = {'name':2, 'pdfexport': 3, 'strain': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
67 Tryp_T.transcriptomicProcess(arguments,argdict)
68 if arguments[1] == 'v_assemble':
69 argdict = {'name':2, 'pdfexport':3, 'kmers':4,'inslen':5, 'covcut':6, 'forward':7, 'reverse':8, 'html_file':9, 'html_resource':10}
70 Tryp_V.vivax_assemble(arguments,argdict)
71 if arguments[1] == 'v_contigs':
72 argdict = {'name':2, 'pdfexport':3, 'contigs':4, 'html_file':5, 'html_resource':6}
73 Tryp_V.vivax_contigs(arguments,argdict)
74 if arguments[1] == 'v_transcript':
75 argdict = {'name':2, 'pdfexport': 3, 'refFastq': 4, 'forward': 5, 'reverse': 6, 'html_file': 7, 'html_resource': 8}
76 Tryp_V_T.transcriptomicProcess(arguments,argdict)
3 77
4 78
79 sys.exit()
5 80
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731 <tr>
732 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
733 <td id="LC4" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL</span></td>
734 </tr>
735 <tr>
736 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
737 <td id="LC5" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
738 </tr>
739 <tr>
740 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
741 <td id="LC6" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);</span></td>
742 </tr>
743 <tr>
744 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
745 <td id="LC7" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * you may not use this file except in compliance with the License.</span></td>
746 </tr>
747 <tr>
748 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
749 <td id="LC8" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * You may obtain a copy of the License at</span></td>
750 </tr>
751 <tr>
752 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
753 <td id="LC9" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
754 </tr>
755 <tr>
756 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
757 <td id="LC10" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * http://www.apache.org/licenses/LICENSE-2.0</span></td>
758 </tr>
759 <tr>
760 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
761 <td id="LC11" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
762 </tr>
763 <tr>
764 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
765 <td id="LC12" 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>
766 </tr>
767 <tr>
768 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
769 <td id="LC13" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * distributed under the License is distributed on an &quot;AS IS&quot; BASIS,</span></td>
770 </tr>
771 <tr>
772 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
773 <td id="LC14" 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>
774 </tr>
775 <tr>
776 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
777 <td id="LC15" 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>
778 </tr>
779 <tr>
780 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
781 <td id="LC16" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> * limitations under the License.</span></td>
782 </tr>
783 <tr>
784 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
785 <td id="LC17" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> *</span></td>
786 </tr>
787 <tr>
788 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
789 <td id="LC18" class="blob-code blob-code-inner js-file-line"><span class="pl-s"> <span class="pl-pds">&quot;&quot;&quot;</span></span></td>
790 </tr>
791 <tr>
792 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
793 <td id="LC19" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import subprocess</span></td>
794 </tr>
795 <tr>
796 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
797 <td id="LC20" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import re</span></td>
798 </tr>
799 <tr>
800 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
801 <td id="LC21" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> os</td>
802 </tr>
803 <tr>
804 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
805 <td id="LC22" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> sys</td>
806 </tr>
807 <tr>
808 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
809 <td id="LC23" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import pandas as pd</span></td>
810 </tr>
811 <tr>
812 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
813 <td id="LC24" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import numpy as np</span></td>
814 </tr>
815 <tr>
816 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
817 <td id="LC25" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import seaborn as sns</span></td>
818 </tr>
819 <tr>
820 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
821 <td id="LC26" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>import matplotlib.pyplot as plt</span></td>
822 </tr>
823 <tr>
824 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
825 <td id="LC27" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>from matplotlib.mlab import PCA</span></td>
826 </tr>
827 <tr>
828 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
829 <td id="LC28" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_G</td>
830 </tr>
831 <tr>
832 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
833 <td id="LC29" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_T</td>
834 </tr>
835 <tr>
836 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
837 <td id="LC30" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V</td>
838 </tr>
839 <tr>
840 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
841 <td id="LC31" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> Tryp_V_T</td>
842 </tr>
843 <tr>
844 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
845 <td id="LC32" class="blob-code blob-code-inner js-file-line"><span class="pl-k">import</span> argparse</td>
846 </tr>
847 <tr>
848 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
849 <td id="LC33" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>Entry .sort out the arguments</span></td>
850 </tr>
851 <tr>
852 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
853 <td id="LC34" class="blob-code blob-code-inner js-file-line">
854 </td>
855 </tr>
856 <tr>
857 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
858 <td id="LC35" class="blob-code blob-code-inner js-file-line">pdfExport <span class="pl-k">=</span> <span class="pl-c1">False</span></td>
859 </tr>
860 <tr>
861 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
862 <td id="LC36" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser = argparse.ArgumentParser(description=&#39;Variant Antigen Profiler - the VAP.&#39;)</span></td>
863 </tr>
864 <tr>
865 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
866 <td id="LC37" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;name&#39;)</span></td>
867 </tr>
868 <tr>
869 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
870 <td id="LC38" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;-t&#39;,&#39;-T&#39;, action = &#39;store_true&#39;, default = False, help = &quot;Transciptomic Pathway&quot;)</span></td>
871 </tr>
872 <tr>
873 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
874 <td id="LC39" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;-p&#39;,&#39;-P&#39;, action = &#39;store_true&#39;, default = False, help = &quot;Export PDFs to HTML directory&quot;)</span></td>
875 </tr>
876 <tr>
877 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
878 <td id="LC40" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;strain&#39;)</span></td>
879 </tr>
880 <tr>
881 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
882 <td id="LC41" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;Forward_Read_File&#39;)</span></td>
883 </tr>
884 <tr>
885 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
886 <td id="LC42" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;Reverse_Read_File&#39;)</span></td>
887 </tr>
888 <tr>
889 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
890 <td id="LC43" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;htmlfile&#39;)</span></td>
891 </tr>
892 <tr>
893 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
894 <td id="LC44" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;htmlresource&#39;)</span></td>
895 </tr>
896 <tr>
897 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
898 <td id="LC45" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;heatmapFile&#39;)</span></td>
899 </tr>
900 <tr>
901 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
902 <td id="LC46" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;PCAFile&#39;)</span></td>
903 </tr>
904 <tr>
905 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
906 <td id="LC47" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>parser.add_argument(&#39;devheatmapFile&#39;)</span></td>
907 </tr>
908 <tr>
909 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
910 <td id="LC48" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>args = parser.parse_args()</span></td>
911 </tr>
912 <tr>
913 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
914 <td id="LC49" class="blob-code blob-code-inner js-file-line">
915 </td>
916 </tr>
917 <tr>
918 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
919 <td id="LC50" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>we have numerous parameters....</span></td>
920 </tr>
921 <tr>
922 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
923 <td id="LC51" class="blob-code blob-code-inner js-file-line"><span class="pl-c"><span class="pl-c">#</span>hard code it for differnt types?</span></td>
924 </tr>
925 <tr>
926 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
927 <td id="LC52" class="blob-code blob-code-inner js-file-line">
928 </td>
929 </tr>
930 <tr>
931 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
932 <td id="LC53" class="blob-code blob-code-inner js-file-line">
933 </td>
934 </tr>
935 <tr>
936 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
937 <td id="LC54" class="blob-code blob-code-inner js-file-line">arguments <span class="pl-k">=</span> sys.argv</td>
938 </tr>
939 <tr>
940 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
941 <td id="LC55" class="blob-code blob-code-inner js-file-line">htmldir <span class="pl-k">=</span> arguments[<span class="pl-c1">len</span>(arguments)<span class="pl-k">-</span><span class="pl-c1">1</span>] <span class="pl-c"><span class="pl-c">#</span>last argument is always html_resource</span></td>
942 </tr>
943 <tr>
944 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
945 <td id="LC56" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> <span class="pl-k">not</span> os.path.exists(htmldir):</td>
946 </tr>
947 <tr>
948 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
949 <td id="LC57" class="blob-code blob-code-inner js-file-line"> os.mkdir(htmldir)</td>
950 </tr>
951 <tr>
952 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
953 <td id="LC58" class="blob-code blob-code-inner js-file-line">
954 </td>
955 </tr>
956 <tr>
957 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
958 <td id="LC59" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>g_assemble<span class="pl-pds">&#39;</span></span>:</td>
959 </tr>
960 <tr>
961 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
962 <td id="LC60" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>kmers<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">&#39;</span>inslen<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>covcut<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">10</span>}</td>
963 </tr>
964 <tr>
965 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
966 <td id="LC61" class="blob-code blob-code-inner js-file-line"> Tryp_G.assemble(arguments,argdict)</td>
967 </tr>
968 <tr>
969 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
970 <td id="LC62" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>g_contigs<span class="pl-pds">&#39;</span></span>:</td>
971 </tr>
972 <tr>
973 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
974 <td id="LC63" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>contigs<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">6</span>}</td>
975 </tr>
976 <tr>
977 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
978 <td id="LC64" class="blob-code blob-code-inner js-file-line"> Tryp_G.contigs(arguments,argdict)</td>
979 </tr>
980 <tr>
981 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
982 <td id="LC65" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>transcipt<span class="pl-pds">&#39;</span></span>:</td>
983 </tr>
984 <tr>
985 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
986 <td id="LC66" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>strain<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">8</span>}</td>
987 </tr>
988 <tr>
989 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
990 <td id="LC67" class="blob-code blob-code-inner js-file-line"> Tryp_T.transcriptomicProcess(arguments,argdict)</td>
991 </tr>
992 <tr>
993 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
994 <td id="LC68" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>v_assemble<span class="pl-pds">&#39;</span></span>:</td>
995 </tr>
996 <tr>
997 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
998 <td id="LC69" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>kmers<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">4</span>,<span class="pl-s"><span class="pl-pds">&#39;</span>inslen<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>covcut<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">8</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">9</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">10</span>}</td>
999 </tr>
1000 <tr>
1001 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
1002 <td id="LC70" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_assemble(arguments,argdict)</td>
1003 </tr>
1004 <tr>
1005 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
1006 <td id="LC71" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>v_contigs<span class="pl-pds">&#39;</span></span>:</td>
1007 </tr>
1008 <tr>
1009 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
1010 <td id="LC72" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>contigs<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">6</span>}</td>
1011 </tr>
1012 <tr>
1013 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
1014 <td id="LC73" class="blob-code blob-code-inner js-file-line"> Tryp_V.vivax_contigs(arguments,argdict)</td>
1015 </tr>
1016 <tr>
1017 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
1018 <td id="LC74" class="blob-code blob-code-inner js-file-line"><span class="pl-k">if</span> arguments[<span class="pl-c1">1</span>] <span class="pl-k">==</span> <span class="pl-s"><span class="pl-pds">&#39;</span>v_transcript<span class="pl-pds">&#39;</span></span>:</td>
1019 </tr>
1020 <tr>
1021 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
1022 <td id="LC75" class="blob-code blob-code-inner js-file-line"> argdict <span class="pl-k">=</span> {<span class="pl-s"><span class="pl-pds">&#39;</span>name<span class="pl-pds">&#39;</span></span>:<span class="pl-c1">2</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>pdfexport<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">3</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>refFastq<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">4</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>forward<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">5</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>reverse<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">6</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_file<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">7</span>, <span class="pl-s"><span class="pl-pds">&#39;</span>html_resource<span class="pl-pds">&#39;</span></span>: <span class="pl-c1">8</span>}</td>
1023 </tr>
1024 <tr>
1025 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
1026 <td id="LC76" class="blob-code blob-code-inner js-file-line"> Tryp_V_T.transcriptomicProcess(arguments,argdict)</td>
1027 </tr>
1028 <tr>
1029 <td id="L77" class="blob-num js-line-number" data-line-number="77"></td>
1030 <td id="LC77" class="blob-code blob-code-inner js-file-line">
1031 </td>
1032 </tr>
1033 <tr>
1034 <td id="L78" class="blob-num js-line-number" data-line-number="78"></td>
1035 <td id="LC78" class="blob-code blob-code-inner js-file-line">
1036 </td>
1037 </tr>
1038 <tr>
1039 <td id="L79" class="blob-num js-line-number" data-line-number="79"></td>
1040 <td id="LC79" class="blob-code blob-code-inner js-file-line">sys.exit()</td>
1041 </tr>
1042 <tr>
1043 <td id="L80" class="blob-num js-line-number" data-line-number="80"></td>
1044 <td id="LC80" class="blob-code blob-code-inner js-file-line">
1045 </td>
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