def loadFastqc(infile, outfile): '''load FASTQC stats into database.''' track = P.snip(infile, ".fastqc") filename = os.path.join(PARAMS["exportdir"], "fastqc", track + "*_fastqc", "fastqc_data.txt") PipelineReadqc.loadFastqc(filename, database_url=PARAMS["database"]["url"]) IOTools.touch_file(outfile)
def buildExperimentLevelReadQuality(infiles, outfile): """Collate per sequence read qualities for all replicates per experiment. Replicates are the last part of a filename, eg. Experiment-R1, Experiment-R2, etc. """ PipelineReadqc.buildExperimentReadQuality(infiles, outfile, "fastqc.dir")
def buildExperimentLevelReadQuality(infiles, outfile): """ Collate per sequence read qualities for all replicates per experiment. Replicates are the last part of a filename, eg. Experiment-R1, Experiment-R2, etc. """ exportdir = os.path.join(PARAMS["exportdir"], "fastqc") PipelineReadqc.buildExperimentReadQuality(infiles, outfile, exportdir)
def loadFastqc(infile, outfile): '''load FASTQC stats into database.''' track = P.snip(infile, ".fastqc") filename = os.path.join( PARAMS["exportdir"], "fastqc", track + "*_fastqc", "fastqc_data.txt") PipelineReadqc.loadFastqc(filename, backend=PARAMS["database_backend"], database=PARAMS["database_name"], host=PARAMS["database_host"], username=PARAMS["database_username"], password=PARAMS["database_password"], port=PARAMS["database_port"]) P.touch(outfile)
def loadFastqc(infile, outfile): '''load FASTQC stats into database.''' track = P.snip(infile.replace("processed.dir/", ""), ".fastqc") filename = os.path.join( PARAMS["exportdir"], "fastqc", track + "*_fastqc", "fastqc_data.txt") PipelineReadqc.loadFastqc(filename, backend=PARAMS["database_backend"], database=PARAMS["database_name"], host=PARAMS["database_host"], username=PARAMS["database_username"], password=PARAMS["database_password"], port=PARAMS["database_port"]) P.touch(outfile)
def summarizeFastqScreen(infiles, outfiles): all_files = [] for infile in infiles: all_files.extend(glob.glob(IOTools.snip(infile, "screen") + "*_screen.txt")) if len(all_files) == 0: E.warn("no fastqcscreen results to concatenate") for x in outfiles: IOTools.touch_file(x) return df_summary, df_details = PipelineReadqc.read_fastq_screen( all_files) df_summary.to_csv(outfiles[0], sep="\t", index=True) df_details.to_csv(outfiles[1], sep="\t", index=True)
def summarizeFastQC(infiles, outfiles): all_files = [] for infile in infiles: track = P.snip(infile, ".fastqc") all_files.extend( glob.glob(os.path.join(track + "*_fastqc", "fastqc_data.txt"))) dfs = PipelineReadqc.read_fastqc(all_files) for key, df in dfs.items(): fn = re.sub("basic_statistics", key, outfiles[0]) E.info("writing to {}".format(fn)) with IOTools.open_file(fn, "w") as outf: df.to_csv(outf, sep="\t", index=True)
def buildFastQCSummaryBasicStatistics(infiles, outfile): '''load fastqc summaries into a single table.''' exportdir = os.path.join(PARAMS["exportdir"], "fastqc") PipelineReadqc.buildFastQCSummaryBasicStatistics(infiles, outfile, exportdir)
def buildFastQCSummaryStatus(infiles, outfile): '''load FastQC status summaries into a single table.''' PipelineReadqc.buildFastQCSummaryStatus(infiles, outfile, "fastqc.dir")
def buildFastQCSummaryStatus(infiles, outfile): """load fastqc status summaries into a single table.""" exportdir = os.path.join(PARAMS["exportdir"], "fastqc") PipelineReadqc.buildFastQCSummaryStatus(infiles, outfile, exportdir)