From 55339ed99124279edba92ff68bb5725d1cefc677 Mon Sep 17 00:00:00 2001 From: krt7 Date: Mon, 26 Mar 2018 11:52:27 -0400 Subject: [PATCH] updated mutation_loci file with minor edits, modified mv of failed fastq files --- bin/coverage_estimator.py | 2 +- bin/mutation_loci.txt | 4 ++-- scripts/UVP | 2 +- scripts/UVP.py | 11 ++--------- 4 files changed, 6 insertions(+), 13 deletions(-) diff --git a/bin/coverage_estimator.py b/bin/coverage_estimator.py index 67dad20..f8973e0 100755 --- a/bin/coverage_estimator.py +++ b/bin/coverage_estimator.py @@ -21,6 +21,6 @@ av_depth = depth/count perc_cov = float((count/4411532.00)*100.00) perc_cov_str = "{0:.2f}".format(perc_cov) -print "Unified Analysis Pipeline Version: UVPv2.4.1\n" +print "Unified Analysis Pipeline Version: UVPv2.5.1\n" print "Average Genome Coverage Depth: " + str(av_depth) print "Percentage of Reference genome covered: " + perc_cov_str diff --git a/bin/mutation_loci.txt b/bin/mutation_loci.txt index e021489..ba9a00c 100644 --- a/bin/mutation_loci.txt +++ b/bin/mutation_loci.txt @@ -41,7 +41,7 @@ ndh upstream Rv1854c upstream 2103043 2103183 intergenic reverse katG upstream Rv1908c upstream 2156112 2156148 intergenic reverse furA upstream Rv1909c upstream 2156593 2156705 intergenic reverse Rv1979c upstream Rv1979c upstream 2223165 2223342 intergenic reverse -erm(37) upstream erm(37) upstream 2231455 2231679 intergenic forward +erm(37) upstream Rv1988 upstream 2231455 2231679 intergenic forward pncA upstream Rv2043 upstream 2289242 2289281 intergenic reverse blaC upstream Rv2068c upstream 2326810 2326943 intergenic reverse mshC upstream Rv2130c upstream 2392460 2392516 intergenic reverse @@ -74,7 +74,7 @@ gidB upstream Rv3919c upstream 4408203 4408333 intergenic reverse ppsA upstream Rv2931 upstream 3243697 3245444 CDS forward mas upstream Rv2940c upstream 3282716 3283334 intergenic reverse Rv0191 upstream Rv0191 upstream 222162 222288 intergenic forward -Rv3008 upstream Rv3008 upstram 3366451 3366643 intergenic forward +Rv3008 upstream Rv3008 upstream 3366451 3366643 intergenic forward Rv1667c upstream Rv1667c upstream 1894231 1895342 CDS reverse proZ upstream Rv3756c upstream 4202614 4203299 CDS reverse clpC1 upstream Rv3596c upstream 4040705 4040878 intergenic reverse diff --git a/scripts/UVP b/scripts/UVP index c4e1dbe..bdfc9df 100755 --- a/scripts/UVP +++ b/scripts/UVP @@ -30,7 +30,7 @@ if __name__ == '__main__': group6 = parser.add_argument_group('Optional', '') group6.add_argument('-v', '--verbose', action='store_true', help='Produce status updates of the run.') group6.add_argument('-h', '--help', action='help', help='Show this help message and exit') - group6.add_argument('--version', action='version', version='%(prog)s v2.4.1', + group6.add_argument('--version', action='version', version='%(prog)s v2.5.1', help='Show program\'s version number and exit') diff --git a/scripts/UVP.py b/scripts/UVP.py index 0d605e8..52eebd7 100644 --- a/scripts/UVP.py +++ b/scripts/UVP.py @@ -150,10 +150,7 @@ def runVali(self): if lined.startswith("Returning"): comments = lined.split(":") if comments[2] != " FASTQ_SUCCESS": - self.__CallCommand('mv', ['mv', self.input, self.flog]) - self.__CallCommand('mv', ['mv', self.fOut, self.flog]) - if self.paired: - self.__CallCommand('mv', ['mv', self.input2, self.flog]) + self.__CallCommand('mv', ['mv', self.fOut, self.flog]) self.__logFH.write("Input not in fastq format\n") i = datetime.now() self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input: " + self.input + "\t" + "not in fastq format\n") @@ -212,15 +209,11 @@ def runKraken(self): cov += float(fields[0]) fh1.close() if cov < 90: - self.__CallCommand('mv', ['mv', self.input, self.flog]) self.__CallCommand('mv', ['mv', self.fOut, self.flog]) self.__CallCommand('rm', ['rm', self.kraken + "/kraken.txt"]) self.__logFH.write("not species specific\n") i = datetime.now() self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input:" + "\t" + self.input + "\t" + "not species specific\n") - if self.paired: - self.__CallCommand('mv', ['mv', self.input2, self.flog]) - self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input:" + "\t" + self.input2 + "\t" + "not species specific\n") sys.exit(2) """ Aligners """ @@ -448,7 +441,7 @@ def runLineage(self): lined = line.rstrip("\r\n") i = datetime.now() if "No Informative SNPs" in lined: - self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input:" + "\t" + self.name + "\t" + "no clear lineage classification\n") + self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input:" + "\t" + self.name + "\t" + "no MTBC lineage detected\n") self.__unclear = "positive" elif "no precise lineage" in lined: self.__logFH2.write(i.strftime('%Y/%m/%d %H:%M:%S') + "\t" + "Input:" + "\t" + self.name + "\t" + "no clear lineage classification\n")