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.