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Tryp_V.py |
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| diff -r 5e346d75ccf3 -r e7da2274c9f6 Tryp_V.py --- a/Tryp_V.py Mon Jun 03 15:59:39 2019 -0400 +++ b/Tryp_V.py Mon Jun 03 16:00:24 2019 -0400 |
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| b'@@ -1,2064 +1,292 @@\n+"""\n+ * Copyright 2018 University of Liverpool\n+ * Author: John Heap, Computational Biology Facility, UoL\n+ * Based on original scripts of Sara Silva Pereira, Institute of Infection and Global Health, UoL\n+ *\n+ * Licensed under the Apache License, Version 2.0 (the "License");\n+ * you may not use this file except in compliance with the License.\n+ * You may obtain a copy of the License at\n+ *\n+ * http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Unless required by applicable law or agreed to in writing, software\n+ * distributed under the License is distributed on an "AS IS" BASIS,\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n+ * See the License for the specific language governing permissions and\n+ * limitations under the License.\n+ *\n+ """\n \n+import matplotlib as mpl\n+mpl.use(\'Agg\')\n \n+import subprocess\n+import shutil\n+import re\n+import pandas as pd\n+import os\n \n+import sys\n \n+import matplotlib.pyplot as plt\n+from matplotlib.patches import Patch\n+import seaborn as sns\n+\n+def assembleWithVelvet(name, kmers, inslen, covcut, fastq1name,fastq2name):\n+ #argString = "velveth " + name + "_k65 65 -shortPaired -fastq " + name + "_R1.fastq " + name + "_R2.fastq"\n+ argString = "velveth " + name + "_k"+ kmers+" "+ kmers + " -shortPaired -fastq " + fastq1name+" "+fastq2name\n+ print(argString)\n+ returncode = subprocess.call(argString, shell=True)\n+ if returncode != 0:\n+ return "Error in velveth"\n+ argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -clean yes -ins_length_sd 50 -min_pair_count 20"\n+ #argString = "velvetg " + name + "_k"+kmers+" -exp_cov auto -ins_length "+inslen+" -cov_cutoff "+covcut+" -clean yes -ins_length_sd 50 -min_pair_count 20"\n+ #argString = "velvetg " + name + "_k65 -exp_cov auto -ins_length 400 -cov_cutoff 5 -clean yes -ins_length_sd 50 -min_pair_count 20"+quietString\n+ print(argString)\n+ returncode = subprocess.call(argString, shell = True)\n+ if returncode != 0:\n+ return "Error in velvetg"\n+ shutil.copyfile(name + "_k"+kmers+"//contigs.fa",name + ".fa") # my $namechange = "mv ".$input."_k65/contigs.fa ".$input.".fa";\n+ return "ok"\n \n \n-<!DOCTYPE html>\n-<html lang="en">\n- <head>\n- <meta charset="utf-8">\n- <link rel="dns-prefetch" href="https://github.githubassets.com">\n- <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com">\n- <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com">\n- <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/">\n+def blastContigs(test_name,database):\n+ print(test_name)\n+ print(database)\n+ #db_path = os.path.dirname(os.path.realpath(__file__))+database\n+ db_path = database\n+ argString = "blastn -db "+db_path+" -query "+test_name+".fa -outfmt 10 -out "+test_name+"_blast.txt"\n+ print(argString)\n+ returncode = subprocess.call(argString, shell = True)\n+ if returncode != 0:\n+ return "Error in blastall"\n+ blast_df = pd.read_csv(""+test_name+"_blast.txt")\n+ #print (blast_df)\n+ #if ($temp[2] >= 98 & & $temp[3] > 100 & & $temp[10] < 0.001){\n+ #\'qaccver saccver pident length mismatch gapopen qstart qend sstart send evalue bitscore\'\n+ blast_df.columns = [\'qaccver\', \'saccver\', \'pident\', \'length\', \'mismatch\', \'gapopen\', \'qstart\', \'qend\', \'sstart\', \'send\', \'evalue\',\'bitscore\']\n+ blastResult_df = blast_df[(blast_df[\'pident\']>=98) & (blast_df[\'length\'] > 100) & (blast_df[\'evalue\']<0.001) ]\n+ blastResult_df = blastResult_df[[\'qaccver\', \'saccver\', \'pident\']] #query accession.version, subject accession.version, Percentage of identical matches\n+\n+ return blastResult_df\n \n \n \n- <link crossorigin="anonymous" 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