3.6. reports.py - produce various metrics and reports

Reports

usage: reports.py subcommand

Sub-commands:

assembly_stats

Undocumented

usage: reports.py assembly_stats [-h]
                                 [--cov_thresholds COV_THRESHOLDS [COV_THRESHOLDS ...]]
                                 [--assembly_dir ASSEMBLY_DIR]
                                 [--assembly_tmp ASSEMBLY_TMP]
                                 [--align_dir ALIGN_DIR]
                                 samples [samples ...] outFile

Positional arguments:

samples	Sample names.
outFile	Output report file.

Options:

--cov_thresholds=(1, 5, 20, 100)
	Genome coverage thresholds to report on. (default: %(default)s)
--assembly_dir=data/02_assembly
	Directory with assembly outputs. (default: %(default)s)
--assembly_tmp=tmp/02_assembly
	Directory with assembly temp files. (default: %(default)s)
--align_dir=data/02_align_to_self
	Directory with reads aligned to own assembly. (default: %(default)s)

consolidate_bamstats

Undocumented

usage: reports.py consolidate_bamstats [-h] inFiles [inFiles ...] outFile

Positional arguments:

inFiles	Input report files.
outFile	Output report file.

consolidate_fastqc

Undocumented

usage: reports.py consolidate_fastqc [-h] inDirs [inDirs ...] outFile

Positional arguments:

inDirs	Input FASTQC directories.
outFile	Output report file.

coverage_summary

Undocumented

usage: reports.py coverage_summary [-h] [--runFile RUNFILE]
                                   [--bamstatsDir BAMSTATSDIR]
                                   coverageDir coverageSuffix outFile

Positional arguments:

coverageDir	Input coverage report directory.
coverageSuffix	Suffix of all coverage files.
outFile	Output report file.

Options:

--runFile	Link in plate info from seq runs.
--bamstatsDir	Link in read info from BAM alignments.

consolidate_coverage

Undocumented

usage: reports.py consolidate_coverage [-h] inFiles [inFiles ...] adj outFile

Positional arguments:

inFiles	Input coverage files.
adj	Report adjective.
outFile	Output report file.

consolidate_spike_count

Undocumented

usage: reports.py consolidate_spike_count [-h] inFiles [inFiles ...] outFile

Positional arguments:

inFiles	Input coverage files.
outFile	Output report file.