lcdblib.parse package

Submodules

lcdblib.parse.atropos module

lcdblib.parse.atropos.parse_atropos(sample, file)

Parse atropos.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.bamtools module

lcdblib.parse.bamtools.parse_bamtools_stats(sample, file)

Parse bamtools stats.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.dupradar module

lcdblib.parse.dupradar.parse_dupradar(sample, file)

Parser for dupradar.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.fastq_screen module

lcdblib.parse.fastq_screen.parse_fqscreen(sample, file)

Parser fastq screen summary table.

Adapted from multiqc.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

Returns:

pandas.DataFrame

Return type:

A single row dataframe.

lcdblib.parse.fastqc module

Quick and dirty Fastqc parser

class lcdblib.parse.fastqc.FastQC(id, filename)

Bases: object

items()

keys()

classmethod parse_from_zip(id, filename)

Parse from ZipFile.

values()

class lcdblib.parse.fastqc.FastQCBlock(block)

Bases: object

lcdblib.parse.fastqc.parse_fastqc(sample, file, field='')

Parse fastqc zip file.

Takes a zip file and makes a FastQC object.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.
• field (str) – Name of specific Fastqc section to return. Look at lcdblib.parse.fastqc.FastQC.keys() for a list of possible names.

Returns:

• lcdblib.parse.fastqc.FastQC or lcdblib.parse.fastqc.FastQCBlock if field
• is provided.

lcdblib.parse.fastqc.parse_fastqc_adapter_content(sample, file)

Parse fastqc Adapter Content. :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_basic_stats(sample, file)

Parse fastqc Basic Stats :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_kmer_content(sample, file)

Parse fastqc Kmer Content :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_overrepresented_seq(sample, file)

Parse fastqc Overrepresente Sequence :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_per_base_n_content(sample, file)

Parse fastqc Per Base N Content :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_per_base_seq_content(sample, file)

Parse fastqc Per Base Seq Content :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_per_base_seq_quality(sample, file)

Parse fastqc Per Base Quality :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_per_seq_gc_content(sample, file)

Parse fastqc Per Seq GC Content :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_per_seq_quality(sample, file)

Parse fastqc Per Seq Quality.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.fastqc.parse_fastqc_seq_dup_level(sample, file)

Parse fastqc Seq Duplication Level :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.parse_fastqc_sequence_length(sample, file)

Parse fastqc Sequence Length :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.fastqc.split_ranges(df)

Split ranges into bases.

Fastqc sometimes collapses bases into ranges, this splits them back out.

lcdblib.parse.featurecounts module

lcdblib.parse.featurecounts.parse_featureCounts_counts(sample, file)

Parser for featurecounts counts table.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.featurecounts.parse_featureCounts_summary(sample, file)

Parse featurecounts summary table

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.picard module

lcdblib.parse.picard.parse_picardCollect_hist(sample, file)

Parser for picard collectRNAMetrics summary.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.picard.parse_picardCollect_summary(sample, file)

Parser for picard collectRNAMetrics summary.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.picard.parse_picard_markduplicate_metrics(sample, file)

Parser for picard markduplicates.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.rseqc module

lcdblib.parse.rseqc.parse_bamStat(sample, file)

Parse rseqc bam stat.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.rseqc.parse_geneBodyCoverage(sample, file)

Parse rseqc genebody coverage.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.rseqc.parse_inferExperiment(sample, file)

Parse rseqc infer expeirment. :param sample: Sample name which will be added as row index. :type sample: str :param file: Path to the fastqc zip file. :type file: str

lcdblib.parse.rseqc.parse_tin(sample, file)

Parse rseqc tin.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

lcdblib.parse.samtools module

lcdblib.parse.samtools.parse_samtools_stats(sample, file)

Parse samtools stats.

Parameters:

• sample (str) – Sample name which will be added as row index.
• file (str) – Path to the fastqc zip file.

Module contents