| Previous changeset 0:e28c965eeed4 (2014-01-27) Next changeset 2:d2cf2c0c8a11 (2014-11-12) |
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Commit message:
Uploaded form GH |
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modified:
rgFastQC.py rgFastQC.xml test-data/fastqc_report.html tool_dependencies.xml |
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added:
test-data/fastqc_customlimits.txt test-data/fastqc_data.txt test-data/fastqc_data2.txt test-data/fastqc_report2.html |
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| diff -r e28c965eeed4 -r 8fae48caaf06 rgFastQC.py --- a/rgFastQC.py Mon Jan 27 09:29:14 2014 -0500 +++ b/rgFastQC.py Tue Nov 11 12:46:27 2014 -0500 |
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| b'@@ -1,83 +1,52 @@\n """\n-# May 2013 ross added check for bogus gz extension - fastqc gets confused\n-# added sanitizer for user supplied name\n-# removed shell and make cl a sequence for Popen call\n-# ross lazarus August 10 2012 in response to anon insecurity report\n-wrapper for fastqc\n+Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.\n+\n+Changes implemented from tmcgowan at\n+https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc\n+and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc\n+with minor changes and bug fixes\n \n-called as\n- <command interpreter="python">\n- rgFastqc.py -i $input_file -d $html_file.files_path -o $html_file -n "$out_prefix"\n- </command>\n+SYNOPSIS\n+\n+ rgFastQC.py -i input_file -j input_file.name -o output_html_file [-d output_directory]\n+ [-f fastq|bam|sam] [-n job_name] [-c contaminant_file] [-e fastqc_executable]\n \n-\n+EXAMPLE (generated by Galaxy)\n \n-Current release seems overly intolerant of sam/bam header strangeness\n-Author notified...\n-\n+ rgFastQC.py -i path/dataset_1.dat -j 1000gsample.fastq -o path/dataset_3.dat -d path/job_working_directory/subfolder\n+ -f fastq -n FastQC -c path/dataset_2.dat -e fastqc\n \n """\n+\n import re\n import os\n-import sys\n+import shutil\n import subprocess\n import optparse\n-import shutil\n import tempfile\n+import glob\n+import gzip\n+import bz2\n import zipfile\n-import gzip\n-\n \n-def getFileString(fpath, outpath):\n- """\n- format a nice file size string\n- """\n- size = \'\'\n- fp = os.path.join(outpath, fpath)\n- s = \'? ?\'\n- if os.path.isfile(fp):\n- n = float(os.path.getsize(fp))\n- if n > 2**20:\n- size = \' (%1.1f MB)\' % (n/2**20)\n- elif n > 2**10:\n- size = \' (%1.1f KB)\' % (n/2**10)\n- elif n > 0:\n- size = \' (%d B)\' % (int(n))\n- s = \'%s %s\' % (fpath, size) \n- return s\n-\n-\n-class FastQC():\n- """wrapper\n- """\n- \n+class FastQCRunner(object):\n \n def __init__(self,opts=None):\n- assert opts <> None\n- self.opts = opts\n- \n+ \'\'\'\n+ Initializes an object to run FastQC in Galaxy. To start the process, use the function run_fastqc()\n+ \'\'\'\n \n- def run_fastqc(self):\n- """\n- In batch mode fastqc behaves not very nicely - will write to a new folder in\n- the same place as the infile called [infilebasename]_fastqc\n- rlazarus@omics:/data/galaxy/test$ ls FC041_1_sequence_fastqc\n- duplication_levels.png fastqc_icon.png per_base_n_content.png per_sequence_gc_content.png summary.txt\n- error.png fastqc_report.html per_base_quality.png per_sequence_quality.png tick.png\n- fastqc_data.txt per_base_gc_content.png per_base_sequence_content.png sequence_length_distribution.png warning.png\n+ # Check whether the options are specified and saves them into the object\n+ assert opts != None\n+ self.opts = opts\n \n- """\n- serr = \'\'\n- dummy,tlog = tempfile.mkstemp(prefix=\'rgFastQC\',suffix=".log",dir=self.opts.outputdir)\n- sout = open(tlog, \'w\')\n- fastq = os.path.basename(self.opts.input)\n- cl = [self.opts.executable,\'--outdir=%s\' % self.opts.outputdir]\n- if self.opts.informat in [\'sam\',\'bam\']:\n- cl.append(\'--f=%s\' % self.opts.informat)\n- if self.opts.contaminants <> None :\n- cl.append(\'--contaminants=%s\' % self.opts.contaminants)\n- # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30\n- # use a symlink in a temporary directory so that the FastQC report reflects the history input file name\n+ def prepare_command_line(self):\n+ \'\'\'\n+ Develops the Commandline to run FastQC in Galaxy\n+ \'\'\'\n+ \n+ # Check whether a given file compression format is valid\n+ # This prevents uncompression of already uncompressed files\n infname = self.opts.inputfilename\n'..b'at is the case, please tell the relevant Galaxy administrator that it can be snarfed from<br/>\\n\',\n- \'http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/<br/>\\n\',]\n- return res,1,serr\n- self.fix_fastqcimages(odpath)\n- flist = os.listdir(self.opts.outputdir) # these have now been fixed\n- excludefiles = [\'tick.png\',\'warning.png\',\'fastqc_icon.png\',\'error.png\']\n- flist = [x for x in flist if not x in excludefiles]\n- for i in range(len(rep)): # need to fix links to Icons and Image subdirectories in lastest fastqc code - ugh\n- rep[i] = rep[i].replace(\'Icons/\',\'\')\n- rep[i] = rep[i].replace(\'Images/\',\'\')\n-\n- html = self.fix_fastqc(rep,flist,runlog)\n- return html,retval,serr\n- \n-\n- \n- def fix_fastqc(self,rep=[],flist=[],runlog=[]):\n- """ add some of our stuff to the html\n- """\n- bodyindex = len(rep) -1 # hope they don\'t change this\n- footrow = bodyindex - 1 \n- footer = rep[footrow]\n- rep = rep[:footrow] + rep[footrow+1:]\n- res = [\'<div class="module"><h2>Files created by FastQC</h2><table cellspacing="2" cellpadding="2">\\n\']\n- flist.sort()\n- for i,f in enumerate(flist):\n- if not(os.path.isdir(f)):\n- fn = os.path.split(f)[-1]\n- res.append(\'<tr><td><a href="%s">%s</a></td></tr>\\n\' % (fn,getFileString(fn, self.opts.outputdir)))\n- res.append(\'</table>\\n\') \n- res.append(\'<a href="http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/">FastQC documentation and full attribution is here</a><br/><hr/>\\n\')\n- res.append(\'FastQC was run by Galaxy using the rgenetics rgFastQC wrapper - see http://bitbucket.org/rgenetics for details and licensing\\n</div>\')\n- res.append(footer)\n- fixed = rep[:bodyindex] + res + rep[bodyindex:]\n- return fixed # with our additions\n-\n-\n- def fix_fastqcimages(self,odpath):\n- """ Galaxy wants everything in the same files_dir\n- """\n- icpath = os.path.join(odpath,\'Icons\')\n- impath = os.path.join(odpath,\'Images\')\n- for adir in [icpath,impath,odpath]:\n- if os.path.exists(adir):\n- flist = os.listdir(adir) # get all files created\n- for f in flist:\n- if not os.path.isdir(os.path.join(adir,f)):\n- sauce = os.path.join(adir,f)\n- dest = os.path.join(self.opts.outputdir,f)\n- shutil.move(sauce,dest)\n- os.rmdir(adir)\n-\n- \n \n if __name__ == \'__main__\':\n op = optparse.OptionParser()\n op.add_option(\'-i\', \'--input\', default=None)\n- op.add_option(\'-j\', \'--inputfilename\', default=None) \n+ op.add_option(\'-j\', \'--inputfilename\', default=None)\n op.add_option(\'-o\', \'--htmloutput\', default=None)\n+ op.add_option(\'-t\', \'--textoutput\', default=None)\n op.add_option(\'-d\', \'--outputdir\', default="/tmp/shortread")\n op.add_option(\'-f\', \'--informat\', default=\'fastq\')\n op.add_option(\'-n\', \'--namejob\', default=\'rgFastQC\')\n op.add_option(\'-c\', \'--contaminants\', default=None)\n+ op.add_option(\'-l\', \'--limits\', default=None)\n op.add_option(\'-e\', \'--executable\', default=\'fastqc\')\n opts, args = op.parse_args()\n- assert opts.input <> None\n+ \n+ assert opts.input != None\n+ assert opts.inputfilename != None\n+ assert opts.htmloutput != None\n assert os.path.isfile(opts.executable),\'##rgFastQC.py error - cannot find executable %s\' % opts.executable\n if not os.path.exists(opts.outputdir): \n os.makedirs(opts.outputdir)\n- f = FastQC(opts)\n- html,retval,serr = f.run_fastqc()\n- f = open(opts.htmloutput, \'w\')\n- f.write(\'\'.join(html))\n- f.close()\n- if retval <> 0:\n- print >> sys.stderr, serr # indicate failure\n- \n \n-\n+ fastqc_runner = FastQCRunner(opts)\n+ fastqc_runner.run_fastqc()\n\\ No newline at end of file\n' |
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| diff -r e28c965eeed4 -r 8fae48caaf06 rgFastQC.xml --- a/rgFastQC.xml Mon Jan 27 09:29:14 2014 -0500 +++ b/rgFastQC.xml Tue Nov 11 12:46:27 2014 -0500 |
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| @@ -1,13 +1,16 @@ -<tool name="FastQC:Read QC" id="fastqc" version="0.52"> +<tool name="FastQC:Read QC" id="fastqc" version="0.62"> <description>reports using FastQC</description> <command interpreter="python"> - rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$JAVA_JAR_PATH/fastqc" + rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -t "$text_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "\$FASTQC_JAR_PATH/fastqc" #if $contaminants.dataset and str($contaminants) > '' -c "$contaminants" #end if +#if $limits.dataset and str($limits) > '' +-l "$limits" +#end if </command> <requirements> - <requirement type="package" version="0.10.1">FastQC</requirement> + <requirement type="package" version="0.11.2">FastQC</requirement> </requirements> <inputs> <param format="fastqsanger,fastq,bam,sam" name="input_file" type="data" label="Short read data from your current history" /> @@ -18,10 +21,13 @@ </sanitizer> </param> <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list" - help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/> + help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/> + <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file" + help="a file that specifies which submodules are to be executed (default=all) and also specifies the thresholds for the each submodules warning parameter" /> </inputs> <outputs> - <data format="html" name="html_file" label="${out_prefix}_${input_file.name}.html" /> + <data format="html" name="html_file" label="${out_prefix}_${input_file.name}_Webpage.html" /> + <data format="txt" name="text_file" label="${out_prefix}_${input_file.name}_RawData.txt" /> </outputs> <tests> <test> @@ -29,6 +35,14 @@ <param name="out_prefix" value="fastqc_out" /> <param name="contaminants" value="fastqc_contaminants.txt" ftype="tabular" /> <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="100"/> + <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="100"/> + </test> + <test> + <param name="input_file" value="1000gsample.fastq" /> + <param name="out_prefix" value="fastqc_out" /> + <param name="limits" value="fastqc_customlimits.txt" ftype="txt" /> + <output name="html_file" file="fastqc_report2.html" ftype="html" lines_diff="100"/> + <output name="text_file" file="fastqc_data2.txt" ftype="txt" lines_diff="100"/> </test> </tests> <help> @@ -65,6 +79,7 @@ The contaminants file parameter was borrowed from the independently developed fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. +Adaption to version 0.11.2 by T. McGowan. ----- @@ -77,9 +92,11 @@ This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. It will also take an optional file containing a list of contaminants information, in the form of -a tab-delimited file with 2 columns, name and sequence. +a tab-delimited file with 2 columns, name and sequence. As another option the tool takes a custom +limits.txt file that allows setting the warning thresholds for the different modules and also specifies +which modules to include in the output. -The tool produces a single HTML output file that contains all of the results, including the following: +The tool produces a basic text and a HTML output file that contain all of the results, including the following: - Basic Statistics - Per base sequence quality |
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| diff -r e28c965eeed4 -r 8fae48caaf06 test-data/fastqc_customlimits.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_customlimits.txt Tue Nov 11 12:46:27 2014 -0500 |
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| @@ -0,0 +1,84 @@ +# For each of the modules you can choose to not run that +# module at all by setting the value below to 1 for the +# modules you want to remove. +duplication ignore 1 +kmer ignore 0 +n_content ignore 0 +overrepresented ignore 0 +quality_base ignore 0 +sequence ignore 0 +gc_sequence ignore 0 +quality_sequence ignore 1 +tile ignore 1 +sequence_length ignore 0 +adapter ignore 0 + +# For the duplication module the value is the percentage +# remaining after deduplication. Measured levels below +# these limits trigger the warning / error. +duplication warn 70 +duplication error 50 + +# For the kmer module the filter is on the -log10 binomial +# pvalue for the most significant Kmer, so 5 would be +# 10^-5 = p<0.00001 +kmer warn 2 +kmer error 5 + +# For the N module the filter is on the percentage of Ns +# at any position in the library +n_content warn 5 +n_content error 20 + +# For the overrepresented seqs the warn value sets the +# threshold for the overrepresented sequences to be reported +# at all as the proportion of the library which must be seen +# as a single sequence +overrepresented warn 0.001 +overrepresented error 1 + +# The per base quality filter uses two values, one for the value +# of the lower quartile, and the other for the value of the +# median quality. Failing either of these will trigger the alert +quality_base_lower warn 10 +quality_base_lower error 5 +quality_base_median warn 50 +quality_base_median error 20 + +# The per base sequence content module tests the maximum deviation +# between A and T or C and G +sequence warn 2 +sequence error 5 + +# The per sequence GC content tests the maximum deviation between +# the theoretical distribution and the real distribution +gc_sequence warn 15 +gc_sequence error 30 + +# The per sequence quality module tests the phred score which is +# most frequently observed +quality_sequence warn 27 +quality_sequence error 20 + +# The per tile module tests the maximum phred score loss between +# and individual tile and the average for that base across all tiles +tile warn 5 +tile error 10 + +# The sequence length module tests are binary, so the values here +# simply turn them on or off. The actual tests warn if you have +# sequences of different length, and error if you have sequences +# of zero length. + +sequence_length warn 1 +sequence_length error 1 + +# The adapter module's warnings and errors are based on the +# percentage of reads in the library which have been observed +# to contain an adapter associated Kmer at any point + +adapter warn 5 +adapter error 10 + + + \ No newline at end of file |
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| diff -r e28c965eeed4 -r 8fae48caaf06 test-data/fastqc_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data.txt Tue Nov 11 12:46:27 2014 -0500 |
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| b'@@ -0,0 +1,934 @@\n+##FastQC\t0.11.2\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000gsample.fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t5000\n+Sequences flagged as poor quality\t0\n+Sequence length\t54\n+%GC\t43\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t28.9946\t31.0\t27.0\t33.0\t22.0\t34.0\n+2\t28.486\t30.0\t26.0\t32.0\t21.0\t33.0\n+3\t28.5272\t30.0\t26.0\t32.0\t21.0\t34.0\n+4\t28.6252\t30.0\t26.0\t32.0\t22.0\t33.0\n+5\t28.4804\t30.0\t26.0\t32.0\t21.0\t33.0\n+6\t28.5128\t30.0\t26.0\t32.0\t22.0\t33.0\n+7\t28.4102\t30.0\t26.0\t32.0\t21.0\t33.0\n+8\t28.4674\t30.0\t26.0\t32.0\t22.0\t33.0\n+9\t28.182\t30.0\t26.0\t32.0\t21.0\t33.0\n+10\t28.0908\t30.0\t26.0\t32.0\t21.0\t33.0\n+11\t28.1876\t30.0\t26.0\t32.0\t21.0\t33.0\n+12\t28.1742\t30.0\t26.0\t32.0\t21.0\t33.0\n+13\t27.923\t30.0\t25.0\t32.0\t20.0\t33.0\n+14\t27.8984\t29.0\t25.0\t32.0\t21.0\t33.0\n+15\t27.6112\t29.0\t25.0\t32.0\t20.0\t33.0\n+16\t27.6638\t29.0\t25.0\t32.0\t20.0\t33.0\n+17\t27.5734\t29.0\t25.0\t32.0\t20.0\t33.0\n+18\t27.6348\t29.0\t25.0\t32.0\t20.0\t33.0\n+19\t27.6526\t29.0\t25.0\t32.0\t20.0\t33.0\n+20\t27.2716\t29.0\t24.0\t32.0\t19.0\t33.0\n+21\t27.2642\t29.0\t25.0\t31.0\t19.0\t33.0\n+22\t26.881\t28.0\t24.0\t31.0\t19.0\t33.0\n+23\t26.8124\t28.0\t24.0\t31.0\t19.0\t33.0\n+24\t26.8204\t28.0\t24.0\t31.0\t19.0\t33.0\n+25\t26.6606\t28.0\t24.0\t31.0\t18.0\t33.0\n+26\t26.3806\t28.0\t23.0\t31.0\t18.0\t33.0\n+27\t25.947\t28.0\t23.0\t31.0\t17.0\t33.0\n+28\t25.7446\t27.0\t22.0\t31.0\t16.0\t33.0\n+29\t25.6856\t27.0\t22.0\t31.0\t16.0\t33.0\n+30\t25.5228\t27.0\t22.0\t31.0\t16.0\t33.0\n+31\t25.354\t27.0\t22.0\t30.0\t16.0\t32.0\n+32\t25.1656\t27.0\t22.0\t30.0\t16.0\t32.0\n+33\t25.0164\t26.0\t21.0\t30.0\t15.0\t32.0\n+34\t24.75\t26.0\t21.0\t30.0\t15.0\t32.0\n+35\t24.3926\t26.0\t21.0\t30.0\t15.0\t32.0\n+36\t24.1122\t25.0\t20.0\t30.0\t14.0\t32.0\n+37\t23.8612\t25.0\t20.0\t29.0\t13.0\t32.0\n+38\t23.7544\t25.0\t20.0\t29.0\t13.0\t32.0\n+39\t23.485\t25.0\t19.0\t29.0\t13.0\t32.0\n+40\t23.1984\t24.0\t19.0\t29.0\t13.0\t32.0\n+41\t23.0976\t24.0\t19.0\t29.0\t13.0\t32.0\n+42\t22.9212\t24.0\t19.0\t28.0\t13.0\t31.0\n+43\t22.5172\t24.0\t18.0\t28.0\t12.0\t31.0\n+44\t22.3234\t23.0\t18.0\t28.0\t12.0\t31.0\n+45\t22.1372\t23.0\t18.0\t28.0\t11.0\t31.0\n+46\t22.2166\t23.0\t18.0\t28.0\t11.0\t31.0\n+47\t22.075\t23.0\t18.0\t28.0\t11.0\t31.0\n+48\t21.4592\t22.0\t17.0\t27.0\t11.0\t31.0\n+49\t21.0954\t22.0\t16.0\t27.0\t10.0\t30.0\n+50\t20.9356\t22.0\t16.0\t27.0\t10.0\t30.0\n+51\t20.6152\t21.0\t15.0\t27.0\t9.0\t30.0\n+52\t20.6588\t21.0\t16.0\t27.0\t9.0\t30.0\n+53\t19.5852\t20.0\t14.0\t25.0\t9.0\t29.0\n+54\t19.9424\t21.0\t14.0\t26.0\t7.0\t30.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1\t1\t0.4542485249902164\n+1\t2\t0.02493171505959424\n+1\t3\t0.004493134032774293\n+1\t4\t0.6119404948560927\n+1\t5\t0.5283275008594686\n+1\t6\t0.3741933003058371\n+1\t7\t-0.2985554485298749\n+1\t8\t0.6040181642739206\n+1\t9\t0.43795745033596845\n+1\t10\t0.05327706110314523\n+1\t11\t0.8097461135057031\n+1\t12\t0.9171964750225641\n+1\t13\t1.0716973449965757\n+1\t14\t0.562649938864773\n+1\t15\t0.5112535943737946\n+1\t16\t0.7098461441939676\n+1\t17\t0.3989886413671577\n+1\t18\t0.2351551176870892\n+1\t19\t0.002716666680861124\n+1\t20\t-0.5270840838615776\n+1\t21\t0.08959510509382795\n+1\t22\t-0.6322238602545553\n+1\t23\t-0.8566085860715056\n+1\t24\t-0.8167218970288026\n+1\t25\t0.7728199138173544\n+1\t26\t-0.26898877195552373\n+1\t27\t-0.7734079986509634\n+1\t28\t0.46313879073469266\n+1\t29\t-1.0803714983510417\n+1\t30\t-0.9107347156963463\n+1\t31\t-1.1279249650605188\n+1\t32\t0.03588141895047414\n+1\t33\t-0.3276409211703317\n+1\t34\t0.07833890179158587\n+1\t35\t-0.8393131051954583\n+1\t36\t-1.024889600311596\n+1\t37\t-1.4177418858492992\n+1\t38\t-1.912918888443187\n+1\t39\t-1.880569234686881\n+1\t40\t-0.9901560786471286\n+1\t41\t-1.9499635516515283\n+1\t42\t-2.3754765893384793\n+1\t43\t-1.6682056704307335\n+1\t44\t-2.2432919652101226\n+1\t45\t-2.1214550638335794\n+1\t46\t-1.6941624871292404\n+1\t47\t-2.261740586778952\n+1\t48\t-0.47246064535067234\n+1\t49\t-1.345180096970381\n+1\t50\t-1.3012642855865373\n+1\t51\t-1.6748103331735038\n+1\t52\t-1.4936238782530324\n+1\t53\t-0.9900326328970834\n+1\t54\t-0.9042724595665739\n+2\t1\t0.27305194379363584\n+2\t2\t-0.40803531790744074\n+2\t3\t-1.054114924575284\n+2\t4\t0.02463890755450393\n+2\t5\t-1.0899875174555511\n+2\t6\t-0.7630472369346997\n+2\t7\t-1.2563088062832328\n+2\t8\t0.09022085047'..b'6171233\t28.985797159431886\t27.545509101820365\t22.064412882576516\n+45\t21.86\t29.28\t26.740000000000002\t22.12\n+46\t21.26\t27.54\t27.74\t23.46\n+47\t21.628651460584233\t28.271308523409367\t28.051220488195277\t22.048819527811126\n+48\t21.279999999999998\t28.439999999999998\t26.400000000000002\t23.880000000000003\n+49\t21.044208841768352\t29.045809161832363\t27.185437087417487\t22.724544908981798\n+50\t21.82873149259704\t28.15126050420168\t26.810724289715886\t23.209283713485394\n+51\t21.028411364545818\t27.73109243697479\t28.011204481792717\t23.229291716686674\n+52\t21.824364872974595\t30.146029205841167\t25.94518903780756\t22.084416883376676\n+53\t21.164232846569313\t28.325665133026607\t28.045609121824366\t22.464492898579717\n+54\t21.53907976692787\t27.024311834438418\t26.90375728350412\t24.5328511151296\n+>>END_MODULE\n+>>Per sequence GC content\twarn\n+#GC Content\tCount\n+0\t3.0\n+1\t5.0\n+2\t7.0\n+3\t7.0\n+4\t7.0\n+5\t5.0\n+6\t2.0\n+7\t1.0\n+8\t1.5\n+9\t2.0\n+10\t1.5\n+11\t1.0\n+12\t2.5\n+13\t4.0\n+14\t4.0\n+15\t4.0\n+16\t5.0\n+17\t6.0\n+18\t11.0\n+19\t19.5\n+20\t23.0\n+21\t37.5\n+22\t52.0\n+23\t61.0\n+24\t70.0\n+25\t79.0\n+26\t88.0\n+27\t117.5\n+28\t147.0\n+29\t159.5\n+30\t172.0\n+31\t203.0\n+32\t243.0\n+33\t252.0\n+34\t290.0\n+35\t328.0\n+36\t330.0\n+37\t332.0\n+38\t332.5\n+39\t333.0\n+40\t342.0\n+41\t351.0\n+42\t343.5\n+43\t336.0\n+44\t318.5\n+45\t279.5\n+46\t258.0\n+47\t254.5\n+48\t251.0\n+49\t234.5\n+50\t218.0\n+51\t209.5\n+52\t201.0\n+53\t198.5\n+54\t196.0\n+55\t177.0\n+56\t162.5\n+57\t167.0\n+58\t147.0\n+59\t127.0\n+60\t106.5\n+61\t86.0\n+62\t85.0\n+63\t84.0\n+64\t61.5\n+65\t39.0\n+66\t42.5\n+67\t46.0\n+68\t34.0\n+69\t17.0\n+70\t12.0\n+71\t14.0\n+72\t16.0\n+73\t12.5\n+74\t9.0\n+75\t6.5\n+76\t4.0\n+77\t4.5\n+78\t5.0\n+79\t5.0\n+80\t5.0\n+81\t3.0\n+82\t1.0\n+83\t1.0\n+84\t1.0\n+85\t1.0\n+86\t1.0\n+87\t1.0\n+88\t1.0\n+89\t1.0\n+90\t2.0\n+91\t3.0\n+92\t2.5\n+93\t2.0\n+94\t2.0\n+95\t3.0\n+96\t4.0\n+97\t5.0\n+98\t6.0\n+99\t3.5\n+100\t1.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.0\n+2\t0.0\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10\t0.0\n+11\t0.0\n+12\t0.0\n+13\t0.0\n+14\t0.0\n+15\t0.0\n+16\t0.0\n+17\t0.0\n+18\t0.0\n+19\t0.0\n+20\t0.0\n+21\t0.0\n+22\t0.0\n+23\t0.0\n+24\t0.0\n+25\t0.0\n+26\t0.04\n+27\t0.02\n+28\t0.0\n+29\t0.02\n+30\t0.0\n+31\t0.0\n+32\t0.04\n+33\t0.02\n+34\t0.02\n+35\t0.02\n+36\t0.02\n+37\t0.04\n+38\t0.02\n+39\t0.04\n+40\t0.0\n+41\t0.06\n+42\t0.06\n+43\t0.02\n+44\t0.02\n+45\t0.0\n+46\t0.0\n+47\t0.04\n+48\t0.0\n+49\t0.02\n+50\t0.04\n+51\t0.04\n+52\t0.02\n+53\t0.02\n+54\t0.45999999999999996\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+54\t5000.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\tpass\n+#Total Deduplicated Percentage\t99.52\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t99.81913183279742\t99.33999999999999\n+2\t0.08038585209003216\t0.16\n+3\t0.04019292604501608\t0.12\n+4\t0.0\t0.0\n+5\t0.02009646302250804\t0.1\n+6\t0.0\t0.0\n+7\t0.04019292604501608\t0.27999999999999997\n+8\t0.0\t0.0\n+9\t0.0\t0.0\n+>10\t0.0\t0.0\n+>50\t0.0\t0.0\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\twarn\n+#Sequence\tCount\tPercentage\tPossible Source\n+CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAAT\t7\t0.13999999999999999\tIllumina Paired End PCR Primer 2 (96% over 33bp)\n+CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC\t7\t0.13999999999999999\tIllumina Paired End PCR Primer 2 (100% over 35bp)\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\n+1\t0.0\t0.0\t0.0\n+2\t0.02\t0.0\t0.0\n+3\t0.02\t0.0\t0.0\n+4\t0.02\t0.0\t0.0\n+5\t0.02\t0.0\t0.0\n+6\t0.02\t0.0\t0.0\n+7\t0.02\t0.0\t0.0\n+8\t0.02\t0.0\t0.0\n+9\t0.02\t0.0\t0.0\n+10\t0.02\t0.0\t0.0\n+11\t0.02\t0.0\t0.0\n+12\t0.02\t0.0\t0.0\n+13\t0.02\t0.0\t0.0\n+14\t0.02\t0.0\t0.0\n+15\t0.02\t0.0\t0.0\n+16\t0.02\t0.0\t0.0\n+17\t0.02\t0.0\t0.0\n+18\t0.02\t0.0\t0.0\n+19\t0.06\t0.0\t0.0\n+20\t0.36\t0.0\t0.0\n+21\t0.36\t0.0\t0.0\n+22\t0.36\t0.0\t0.0\n+23\t0.36\t0.0\t0.0\n+24\t0.36\t0.0\t0.0\n+25\t0.4\t0.0\t0.0\n+26\t0.4\t0.0\t0.0\n+27\t0.42\t0.0\t0.0\n+28\t0.62\t0.0\t0.0\n+29\t0.66\t0.0\t0.0\n+30\t0.68\t0.0\t0.0\n+31\t0.68\t0.0\t0.0\n+32\t0.68\t0.0\t0.0\n+33\t0.68\t0.0\t0.0\n+34\t0.7\t0.0\t0.0\n+35\t0.76\t0.0\t0.0\n+36\t0.8\t0.0\t0.0\n+37\t0.88\t0.0\t0.0\n+38\t1.0\t0.0\t0.0\n+39\t1.12\t0.0\t0.0\n+40\t1.22\t0.0\t0.0\n+41\t1.38\t0.0\t0.0\n+42\t1.48\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\tpass\n+>>END_MODULE\n' |
| b |
| diff -r e28c965eeed4 -r 8fae48caaf06 test-data/fastqc_data2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_data2.txt Tue Nov 11 12:46:27 2014 -0500 |
| b |
| b'@@ -0,0 +1,5859 @@\n+##FastQC\t0.11.2\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\t1000gsample.fastq\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t5000\n+Sequences flagged as poor quality\t0\n+Sequence length\t54\n+%GC\t43\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t28.9946\t31.0\t27.0\t33.0\t22.0\t34.0\n+2\t28.486\t30.0\t26.0\t32.0\t21.0\t33.0\n+3\t28.5272\t30.0\t26.0\t32.0\t21.0\t34.0\n+4\t28.6252\t30.0\t26.0\t32.0\t22.0\t33.0\n+5\t28.4804\t30.0\t26.0\t32.0\t21.0\t33.0\n+6\t28.5128\t30.0\t26.0\t32.0\t22.0\t33.0\n+7\t28.4102\t30.0\t26.0\t32.0\t21.0\t33.0\n+8\t28.4674\t30.0\t26.0\t32.0\t22.0\t33.0\n+9\t28.182\t30.0\t26.0\t32.0\t21.0\t33.0\n+10\t28.0908\t30.0\t26.0\t32.0\t21.0\t33.0\n+11\t28.1876\t30.0\t26.0\t32.0\t21.0\t33.0\n+12\t28.1742\t30.0\t26.0\t32.0\t21.0\t33.0\n+13\t27.923\t30.0\t25.0\t32.0\t20.0\t33.0\n+14\t27.8984\t29.0\t25.0\t32.0\t21.0\t33.0\n+15\t27.6112\t29.0\t25.0\t32.0\t20.0\t33.0\n+16\t27.6638\t29.0\t25.0\t32.0\t20.0\t33.0\n+17\t27.5734\t29.0\t25.0\t32.0\t20.0\t33.0\n+18\t27.6348\t29.0\t25.0\t32.0\t20.0\t33.0\n+19\t27.6526\t29.0\t25.0\t32.0\t20.0\t33.0\n+20\t27.2716\t29.0\t24.0\t32.0\t19.0\t33.0\n+21\t27.2642\t29.0\t25.0\t31.0\t19.0\t33.0\n+22\t26.881\t28.0\t24.0\t31.0\t19.0\t33.0\n+23\t26.8124\t28.0\t24.0\t31.0\t19.0\t33.0\n+24\t26.8204\t28.0\t24.0\t31.0\t19.0\t33.0\n+25\t26.6606\t28.0\t24.0\t31.0\t18.0\t33.0\n+26\t26.3806\t28.0\t23.0\t31.0\t18.0\t33.0\n+27\t25.947\t28.0\t23.0\t31.0\t17.0\t33.0\n+28\t25.7446\t27.0\t22.0\t31.0\t16.0\t33.0\n+29\t25.6856\t27.0\t22.0\t31.0\t16.0\t33.0\n+30\t25.5228\t27.0\t22.0\t31.0\t16.0\t33.0\n+31\t25.354\t27.0\t22.0\t30.0\t16.0\t32.0\n+32\t25.1656\t27.0\t22.0\t30.0\t16.0\t32.0\n+33\t25.0164\t26.0\t21.0\t30.0\t15.0\t32.0\n+34\t24.75\t26.0\t21.0\t30.0\t15.0\t32.0\n+35\t24.3926\t26.0\t21.0\t30.0\t15.0\t32.0\n+36\t24.1122\t25.0\t20.0\t30.0\t14.0\t32.0\n+37\t23.8612\t25.0\t20.0\t29.0\t13.0\t32.0\n+38\t23.7544\t25.0\t20.0\t29.0\t13.0\t32.0\n+39\t23.485\t25.0\t19.0\t29.0\t13.0\t32.0\n+40\t23.1984\t24.0\t19.0\t29.0\t13.0\t32.0\n+41\t23.0976\t24.0\t19.0\t29.0\t13.0\t32.0\n+42\t22.9212\t24.0\t19.0\t28.0\t13.0\t31.0\n+43\t22.5172\t24.0\t18.0\t28.0\t12.0\t31.0\n+44\t22.3234\t23.0\t18.0\t28.0\t12.0\t31.0\n+45\t22.1372\t23.0\t18.0\t28.0\t11.0\t31.0\n+46\t22.2166\t23.0\t18.0\t28.0\t11.0\t31.0\n+47\t22.075\t23.0\t18.0\t28.0\t11.0\t31.0\n+48\t21.4592\t22.0\t17.0\t27.0\t11.0\t31.0\n+49\t21.0954\t22.0\t16.0\t27.0\t10.0\t30.0\n+50\t20.9356\t22.0\t16.0\t27.0\t10.0\t30.0\n+51\t20.6152\t21.0\t15.0\t27.0\t9.0\t30.0\n+52\t20.6588\t21.0\t16.0\t27.0\t9.0\t30.0\n+53\t19.5852\t20.0\t14.0\t25.0\t9.0\t29.0\n+54\t19.9424\t21.0\t14.0\t26.0\t7.0\t30.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1\t1\t0.4542485249902164\n+1\t2\t0.02493171505959424\n+1\t3\t0.004493134032774293\n+1\t4\t0.6119404948560927\n+1\t5\t0.5283275008594686\n+1\t6\t0.3741933003058371\n+1\t7\t-0.2985554485298749\n+1\t8\t0.6040181642739206\n+1\t9\t0.43795745033596845\n+1\t10\t0.05327706110314523\n+1\t11\t0.8097461135057031\n+1\t12\t0.9171964750225641\n+1\t13\t1.0716973449965757\n+1\t14\t0.562649938864773\n+1\t15\t0.5112535943737946\n+1\t16\t0.7098461441939676\n+1\t17\t0.3989886413671577\n+1\t18\t0.2351551176870892\n+1\t19\t0.002716666680861124\n+1\t20\t-0.5270840838615776\n+1\t21\t0.08959510509382795\n+1\t22\t-0.6322238602545553\n+1\t23\t-0.8566085860715056\n+1\t24\t-0.8167218970288026\n+1\t25\t0.7728199138173544\n+1\t26\t-0.26898877195552373\n+1\t27\t-0.7734079986509634\n+1\t28\t0.46313879073469266\n+1\t29\t-1.0803714983510417\n+1\t30\t-0.9107347156963463\n+1\t31\t-1.1279249650605188\n+1\t32\t0.03588141895047414\n+1\t33\t-0.3276409211703317\n+1\t34\t0.07833890179158587\n+1\t35\t-0.8393131051954583\n+1\t36\t-1.024889600311596\n+1\t37\t-1.4177418858492992\n+1\t38\t-1.912918888443187\n+1\t39\t-1.880569234686881\n+1\t40\t-0.9901560786471286\n+1\t41\t-1.9499635516515283\n+1\t42\t-2.3754765893384793\n+1\t43\t-1.6682056704307335\n+1\t44\t-2.2432919652101226\n+1\t45\t-2.1214550638335794\n+1\t46\t-1.6941624871292404\n+1\t47\t-2.261740586778952\n+1\t48\t-0.47246064535067234\n+1\t49\t-1.345180096970381\n+1\t50\t-1.3012642855865373\n+1\t51\t-1.6748103331735038\n+1\t52\t-1.4936238782530324\n+1\t53\t-0.9900326328970834\n+1\t54\t-0.9042724595665739\n+2\t1\t0.27305194379363584\n+2\t2\t-0.40803531790744074\n+2\t3\t-1.054114924575284\n+2\t4\t0.02463890755450393\n+2\t5\t-1.0899875174555511\n+2\t6\t-0.7630472369346997\n+2\t7\t-1.2563088062832328\n+2\t8\t0.0902208504'..b'TTGTCTCTTTAAAAGACTTTTATT\t1\t0.02\tNo Hit\n+AAAAGTTTATAGAAGACCTTAAAATGACTCTTTTTAAATGTATTTTCCACCAGG\t1\t0.02\tNo Hit\n+ACAGTTAACCATGCTGACCTCCTTCTTTTTGCCATTGCCTTTCTGGCTGAGTTG\t1\t0.02\tNo Hit\n+CATCAGCTGTGTGCTGGGCACATTAGTTGAGCACTATGCATGGGATCTAGGAAC\t1\t0.02\tNo Hit\n+AAAGCCAACATGTTTTTCCTCCACTGCTTTAAAGGATCATCAATAGGGACGGCA\t1\t0.02\tNo Hit\n+CACCAGAGTTTCCTCTGGCTTCGCCCTGCCCAGGCGTAGTTCACCATCTTTCGG\t1\t0.02\tNo Hit\n+ATGAAGTTGCTGCCAGATTTCATAATACGTTAGAACTGGTTTAAACCCCCCCCC\t1\t0.02\tNo Hit\n+AATCGATACCACAGAAATAAAAAAGATTATTCAGGGCTACTATAAACATCTTCA\t1\t0.02\tNo Hit\n+TTGTTAGGATTCAAAGCAGCTTTGGTGAATATAAATCAACATACAACTCTGATT\t1\t0.02\tNo Hit\n+TGCAAGTGGATATCTGGACCAAGTTGGGGCCTTACTTCGAAACGGGTATATCTT\t1\t0.02\tNo Hit\n+ATACCAGAGGCTTTGATCTTTGGCCCTCATCTCACAACGCTCAGGGATATGACT\t1\t0.02\tNo Hit\n+TGAGTGAGGTTCACCAAGAGCAGTGGTTCTCAAACCCGAGTGTGCATCCGAATC\t1\t0.02\tNo Hit\n+ACCAAAATACCAGTTACCAGCTTTTTAAAAAAAGCAACAACTAACAATGGTAGG\t1\t0.02\tNo Hit\n+CATAAGGCTGGGTGTGGTGGCTCATGCCTGTCATCGCAGCTCTTTGGGAGGCCG\t1\t0.02\tNo Hit\n+TCTACCCTGCCGGCACATCCTAATTAATTTAGGTTTGGAACGCTGTGTGCCAAT\t1\t0.02\tNo Hit\n+GGGCGACTCATGTTTGGGTGAGCAGCTGCCACCACTCCTTGTCATGTGCAGAGC\t1\t0.02\tNo Hit\n+CAGTGAAGTCACATCCCAATTACTTAATGCCCACGTACTGGTTGACAGCTCACT\t1\t0.02\tNo Hit\n+CATTGCATTCCATTCCATTCCATTCCCCTGCACTCGCGTTGATTCCATTCCATT\t1\t0.02\tNo Hit\n+GACTACTTAATTCCATTTATGTGATCAATTTTAGAGTAAGTGTTGTGTGGCGAT\t1\t0.02\tNo Hit\n+AATCAATCTGCTGTGACCAAACTCACCACCTCATCCTTCCACCCCAAATCAACT\t1\t0.02\tNo Hit\n+AGGAACCAACACACATGCTTTACATAAGCCATCTTATTTAAATTTTGCCATCGC\t1\t0.02\tNo Hit\n+TCAATTTTCTTGGTTGTAGTAATGGTATGTGGTTATGTAGGAAATGTAGATATT\t1\t0.02\tNo Hit\n+GACCAACAAGCAGACTATAGCATATTTGGAGTCACTGTATTAGGATTTTCCAGA\t1\t0.02\tNo Hit\n+TTCTCATTGAACTCTAGATTTTTGCCTGCTGTGGATAATCAAAAGATCTGGCTG\t1\t0.02\tNo Hit\n+TGGAGTCGAATGGAATGGACTGGAATGGAATGGATTCGAATGGAATCGAATGGA\t1\t0.02\tNo Hit\n+AGGTAAGAAGTCTGGTTGCCCCAGATACTATTGCTGATGTTTTGCTAAGCAGTT\t1\t0.02\tNo Hit\n+TAACTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGTTCAACGCACACCTCAC\t1\t0.02\tNo Hit\n+CAACAAAAGGAATAAGGATTTTAGTAACACTGTTGTACATGGATTATTTCATAC\t1\t0.02\tNo Hit\n+TTTTGGTTTTTGTGCCTTTATTTGTGGATCCTGGTTTGTTCTGTGGTAATACCC\t1\t0.02\tNo Hit\n+GACTTCTAACCCTAATTGGCTATCACGCTCACTATCCACATGTCTTCCTGAGTC\t1\t0.02\tNo Hit\n+AAACAGGGACAATTTGACTTCCTCTTTTCCTAATTGAATACCCTTTATTTCCTT\t1\t0.02\tNo Hit\n+CCCCAGGTGACAGTCTGGACCGGGATTCCAGAAGAAAGACCTAGATTATTCCTC\t1\t0.02\tNo Hit\n+AAGGGAAGAAACAACCTACAGAATGGAAGGAAATATTTGCACATAGTATATCTG\t1\t0.02\tNo Hit\n+AATCCTTCTTCACTGCGTAGCACCTTGCAGAACATTTGCACATATTAGGCTCTT\t1\t0.02\tNo Hit\n+AATAACACACCAAGATCAACTACGGTTTATTTCATGGATAAGAATGCAAGAATT\t1\t0.02\tNo Hit\n+GACTTTATTATAGCCATTATATTTTGTGTAAGAATAGCACCAATATATTGATAA\t1\t0.02\tNo Hit\n+AAATATCAGAGTTTCCGAGGCAAAAAGTTAATGTTTGTCTCTAGTCATTTGGAA\t1\t0.02\tNo Hit\n+CTTGAAGGGTAGTTTGGTGAGATAGGACTTATTTTATTTCTTTGAATACATACT\t1\t0.02\tNo Hit\n+AATTACTCACAGTTCAGCACGGCTGGGCGGCCTCAGGAAACTTATAATCATGGG\t1\t0.02\tNo Hit\n+CATGAGGCAGACACTGTTGATTGCTAAAAAGTAGTCACTCCTGCTTTCTTCCTT\t1\t0.02\tNo Hit\n+TTTTTCTCAACTAAGAATTTGAAAGATATTCCGATTTATATCTAGTGTTTTAAG\t1\t0.02\tNo Hit\n+TAGGGTCATTATAGATATAGTTAGATAAGATGAGGTCATATTGAAGCAGGATGG\t1\t0.02\tNo Hit\n+TTAGTGAAGCTCTCAAACCACTGAAGATTTTTTTCTTTCAAACGTTTCGAACTC\t1\t0.02\tNo Hit\n+GCAACCCACTCCAGGGCCTCCTCTCTCCTAGGAGCTGGGCAGACAACAGGACAC\t1\t0.02\tNo Hit\n+TCTACTGCCTGCACTGCCTTTTCATCTAGCTCCAATTTATATTCTTGTAGTTTA\t1\t0.02\tNo Hit\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\n+1\t0.0\t0.0\t0.0\n+2\t0.02\t0.0\t0.0\n+3\t0.02\t0.0\t0.0\n+4\t0.02\t0.0\t0.0\n+5\t0.02\t0.0\t0.0\n+6\t0.02\t0.0\t0.0\n+7\t0.02\t0.0\t0.0\n+8\t0.02\t0.0\t0.0\n+9\t0.02\t0.0\t0.0\n+10\t0.02\t0.0\t0.0\n+11\t0.02\t0.0\t0.0\n+12\t0.02\t0.0\t0.0\n+13\t0.02\t0.0\t0.0\n+14\t0.02\t0.0\t0.0\n+15\t0.02\t0.0\t0.0\n+16\t0.02\t0.0\t0.0\n+17\t0.02\t0.0\t0.0\n+18\t0.02\t0.0\t0.0\n+19\t0.06\t0.0\t0.0\n+20\t0.36\t0.0\t0.0\n+21\t0.36\t0.0\t0.0\n+22\t0.36\t0.0\t0.0\n+23\t0.36\t0.0\t0.0\n+24\t0.36\t0.0\t0.0\n+25\t0.4\t0.0\t0.0\n+26\t0.4\t0.0\t0.0\n+27\t0.42\t0.0\t0.0\n+28\t0.62\t0.0\t0.0\n+29\t0.66\t0.0\t0.0\n+30\t0.68\t0.0\t0.0\n+31\t0.68\t0.0\t0.0\n+32\t0.68\t0.0\t0.0\n+33\t0.68\t0.0\t0.0\n+34\t0.7\t0.0\t0.0\n+35\t0.76\t0.0\t0.0\n+36\t0.8\t0.0\t0.0\n+37\t0.88\t0.0\t0.0\n+38\t1.0\t0.0\t0.0\n+39\t1.12\t0.0\t0.0\n+40\t1.22\t0.0\t0.0\n+41\t1.38\t0.0\t0.0\n+42\t1.48\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\tpass\n+>>END_MODULE\n' |
| b |
| diff -r e28c965eeed4 -r 8fae48caaf06 test-data/fastqc_report.html --- a/test-data/fastqc_report.html Mon Jan 27 09:29:14 2014 -0500 +++ b/test-data/fastqc_report.html Tue Nov 11 12:46:27 2014 -0500 |
| [ |
| b'@@ -1,1809 +1,2 @@\n-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Strict//EN">\n-<html>\n-<head><title>dataset_1.dat FastQC Report</title>\n-\n-<style type="text/css">\n-\n- @media screen {\n- div.summary {\n- width: 18em;\n- position:fixed;\n- top: 3em;\n- margin:1em 0 0 1em;\n- }\n- \n- div.main {\n- display:block;\n- position:absolute;\n- overflow:auto;\n- height:auto;\n- width:auto;\n- top:4.5em;\n- bottom:2.3em;\n- left:18em;\n- right:0;\n- border-left: 1px solid #CCC;\n- padding:0 0 0 1em;\n- background-color: white;\n- z-index:1;\n- }\n- \n- div.header {\n- background-color: #EEE;\n- border:0;\n- margin:0;\n- padding: 0.5em;\n- font-size: 200%;\n- font-weight: bold;\n- position:fixed;\n- width:100%;\n- top:0;\n- left:0;\n- z-index:2;\n- }\n-\n- div.footer {\n- background-color: #EEE;\n- border:0;\n- margin:0;\n-\tpadding:0.5em;\n- height: 1.3em;\n-\toverflow:hidden;\n- font-size: 100%;\n- font-weight: bold;\n- position:fixed;\n- bottom:0;\n- width:100%;\n- z-index:2;\n- }\n- \n- img.indented {\n- margin-left: 3em;\n- }\n- }\n- \n- @media print {\n-\timg {\n-\t\tmax-width:100% !important;\n-\t\tpage-break-inside: avoid;\n-\t}\n-\th2, h3 {\n-\t\tpage-break-after: avoid;\n-\t}\n-\tdiv.header {\n- background-color: #FFF;\n- }\n-\t\n- }\n- \n- body { \n- font-family: sans-serif; \n- color: #000; \n- background-color: #FFF;\n- border: 0;\n- margin: 0;\n- padding: 0;\n- }\n- \n- div.header {\n- border:0;\n- margin:0;\n- padding: 0.5em;\n- font-size: 200%;\n- font-weight: bold;\n- width:100%;\n- } \n- \n- #header_title {\n- display:inline-block;\n- float:left;\n- clear:left;\n- }\n- #header_filename {\n- display:inline-block;\n- float:right;\n- clear:right;\n- font-size: 50%;\n- margin-right:2em;\n- text-align: right;\n- }\n-\n- div.header h3 {\n- font-size: 50%;\n- margin-bottom: 0;\n- }\n- \n- div.summary ul {\n- padding-left:0;\n- list-style-type:none;\n- }\n- \n- div.summary ul li img {\n- margin-bottom:-0.5em;\n- margin-top:0.5em;\n- }\n-\t \n- div.main {\n- background-color: white;\n- }\n- \n- div.module {\n- padding-bottom:1.5em;\n- padding-top:1.5em;\n- }\n-\t \n- div.footer {\n- background-color: #EEE;\n- border:0;\n- margin:0;\n- padding: 0.5em;\n- font-size: 100%;\n- font-weight: bold;\n- width:100%;\n- }\n-\n-\n- a {\n- color: #000080;\n- }\n-\n- a:hover {\n- color: #800000;\n- }\n- \n- h2 {\n- color: #800000;\n- padding-bottom: 0;\n- margin-bottom: 0;\n- clear:left;\n- }\n-\n- table { \n- margin-left: 3em;\n- text-align: center;\n- }\n- \n- th { \n- text-align: center;\n- background-color: #000080;\n- color: #FFF;\n- padding: 0.4em;\n- } \n- \n- td { \n- font-family: monospace; \n- text-align: left;\n- background-color: #EEE;\n- color: #000;\n- padding: 0.4em;\n- }\n-\n- img {\n- padding-top: 0;\n- margin-top: 0;\n- border-top: 0;\n- }\n-\n- \n- p {\n- padding-top: 0;\n- margin-top: 0;\n- }\n- \n-</style>\n-\n-</head>\n-<body>\n-<div class="header">\n-<div id="header_title"><img src="fastqc_icon.png" alt="FastQC">FastQC Report</div>\n-<div id="header_filename">\n-Wed 16 Nov 2011<br />\n-dataset_1.dat\n-</div>\n-</div>\n-<div class="summary">\n-<h2>Summary</h2>\n-<ul>\n-<li><img src="tick.png" alt="[PASS]"> <a href="#M0">Basic Statistics</a></li>\n-<li><img src="warning.png" alt="[WARNING]"> <a href="#M1">Per base sequence quality</a></li>\n-<li><img src="warning.png" alt="[WARNING]"> <a href="#M2">Per sequence quality scores</a></li>\n-<li><img src="warning.png" alt="[WARNING]"> <a href="#M3">Per base sequence content</a></li>\n-<li><img src="tick.png" alt="[PASS]"> <a href="#M4">Per base GC content</a></li>\n-<li><img src="warning.png" alt="[WARNING]"> <a href="#M5">Per sequence GC content</a></li>\n-<li><img src="tick.png" alt="[PASS]"> <a href="#M6">Per base N content</a></li>\n-<li><img src="tick.png" alt="[PASS]"> <a href="#M7">Sequence Length Distribution</a></li>\n-<li><img src="tick.png" alt="[PASS]"> <a href="#M8">Sequence Duplication Levels</a></li>\n-<li><img src="warn'..b'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" height="600" width="800"></p></div><div class="module"><h2 id="M11"><img alt="[OK]" src="data:image/png;base64,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">Kmer Content</h2><p>No overrepresented Kmers</p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.2)</div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r e28c965eeed4 -r 8fae48caaf06 test-data/fastqc_report2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_report2.html Tue Nov 11 12:46:27 2014 -0500 |
| [ |
| b'@@ -0,0 +1,2 @@\n+<html><head>\n+<meta http-equiv="content-type" content="text/html; charset=windows-1252"></head><body>1000gsample.fastq FastQC Report<div class="header"><div id="header_title"><img alt="FastQC" src="data:image/png;base64,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">FastQC Report</div><div id="header_filename">Thu 23 Oct 2014<br>1000gsample.fastq</div></div><div class="summary"><h2>Summary</h2><ul><li><img alt="[PASS]" src="data:image/png;base64,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"><a href="#M0">Basic Statistics</a></li><li><img alt="[WARNING]" src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAYAAABzenr0AAAEpklEQVR42s1XfUyUdRz/URrktNpaW/aHW1LLNdN0+U9WSzdfcq31/uLrWvZP+Y/2T+mc54GplSCOt4CBgqicpICGwokvSYkc3B3nQJxmBSo0K6fsiJe759Pn+zzccRx3xyGwvO07fvye5/f9fH7f90cBUP+nDP+QSd1XZ1LT6hPU/FqzWi4ia9mTZ2NGwLZZ'..b'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" height="600" width="800"></p></div><div class="module"><h2 id="M11"><img alt="[OK]" src="data:image/png;base64,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">Kmer Content</h2><p>No overrepresented Kmers</p></div></div><div class="footer">Produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">FastQC</a> (version 0.11.2)</div></body></html>\n\\ No newline at end of file\n' |
| b |
| diff -r e28c965eeed4 -r 8fae48caaf06 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jan 27 09:29:14 2014 -0500 +++ b/tool_dependencies.xml Tue Nov 11 12:46:27 2014 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="FastQC" version="0.10.1"> - <repository changeset_revision="4c650e5219e0" name="package_fastqc_0_10_1" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="FastQC" version="0.11.2"> + <repository changeset_revision="4b65f6e39cb0" name="package_fastqc_0_11_2" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |