3.6. reports.py - produce various metrics and reportsΒΆ

Reports

usage: reports.py subcommand
Sub-commands:
assembly_stats

Undocumented

Fetch assembly-level statistics for a given sample

usage: reports.py assembly_stats [-h]
                                 [--cov_thresholds COV_THRESHOLDS [COV_THRESHOLDS ...]]
                                 [--assembly_dir ASSEMBLY_DIR]
                                 [--assembly_tmp ASSEMBLY_TMP]
                                 [--align_dir ALIGN_DIR]
                                 [--reads_dir READS_DIR]
                                 [--raw_reads_dir RAW_READS_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)
--reads_dir=data/01_per_sample
 Directory with unaligned filtered read BAMs. (default: %(default)s)
--raw_reads_dir=data/00_raw
 Directory with unaligned raw read BAMs. (default: %(default)s)
alignment_summary

Undocumented

usage: reports.py alignment_summary [-h] [--outfileName OUTFILENAME]
                                    [--printCounts]
                                    inFastaFileOne inFastaFileTwo
Positional arguments:
inFastaFileOne First fasta file for an alignment
inFastaFileTwo First fasta file for an alignment
Options:
--outfileName Output file for counts in TSV format
--printCounts=False
 Undocumented
consolidate_fastqc

Undocumented

Consolidate multiple FASTQC reports into one.

usage: reports.py consolidate_fastqc [-h] inDirs [inDirs ...] outFile
Positional arguments:
inDirs Input FASTQC directories.
outFile Output report file.
consolidate_spike_count

Undocumented

Consolidate multiple spike count reports into one.

usage: reports.py consolidate_spike_count [-h] inDir outFile
Positional arguments:
inDir Input spike count directory.
outFile Output report file.