Package ngstk Documentation

Package exports

Class UnsupportedFiletypeException

Restrict domain of file types.

def count_fail_reads(file_name, paired_end, prog_path)

Count the number of reads that failed platform/vendor quality checks.

Parameters:

• file_name (str): name/path to file to examine
• paired_end (``): this parameter is ignored; samtools automaticallycorrectly responds depending on the data in the bamfile; we leave the option here just for consistency, since all the other counting functions require the parameter; this makes it easier to swap counting functions during pipeline development.
• prog_path (str): path to main program/tool to use for the counting

Returns:

• int: count of failed reads

def count_flag_reads(file_name, flag, paired_end, prog_path)

Counts the number of reads with the specified flag.

Parameters:

• file_name (str): name/path to file to examine
• flag (str int |): SAM flag value to be read
• paired_end (``): this parameter is ignored; samtools automaticallycorrectly responds depending on the data in the bamfile; we leave the option here just for consistency, since all the other counting functions require the parameter; this makes it easier to swap counting functions during pipeline development.
• prog_path (str): path to main program/tool to use for the counting

Returns:

• str: terminal-like text output

def count_lines(file_name)

Uses the command-line utility wc to count the number of lines in a file.

For MacOS, must strip leading whitespace from wc.

Parameters:

• file_name (str): name of file whose lines are to be counted

Returns:

• str: terminal-like text output

def count_lines_zip(file_name)

Count number of lines in a zipped file.

This function eses the command-line utility wc to count the number of lines in a file. For MacOS, strip leading whitespace from wc.

Parameters:

• file_name (str): path to file in which to count lines

Returns:

• str: terminal-like text output

def count_reads(file_name, paired_end, prog_path)

Count reads in a file.

Paired-end reads count as 2 in this function. For paired-end reads, this function assumes that the reads are split into 2 files, so it divides line count by 2 instead of 4. This will thus give an incorrect result if your paired-end fastq files are in only a single file (you must divide by 2 again).

Parameters:

• file_name (str): Name/path of file whose reads are to be counted.
• paired_end (bool): Whether the file contains paired-end reads.
• prog_path (str): path to main program/tool to use for the counting

Returns:

• str: terminal-like text output (if input is SAM/BAM), or actualcount value (if input isn't SAM/BAM)

def get_file_size(filename)

Get size of all files in gigabytes (Gb).

Parameters:

• filename (str | collections.Iterable[str]): A space-separatedstring or list of space-separated strings of absolute file paths.

Returns:

• float: size of file(s), in gigabytes.

def get_input_ext(input_file)

Get the extension of the input_file.

This function assumes you're using .bam, .fastq/.fq, or .fastq.gz/.fq.gz.

Parameters:

• input_file (str): name/path of file for which to get extension

Returns:

• str: standardized extension

Raises:

• ubiquerg.ngs.UnsupportedFiletypeException: if the given file nameor path has an extension that's not supported

def is_fastq(file_name)

Determine whether indicated file appears to be in FASTQ format.

Parameters:

• file_name (str): Name/path of file to check as FASTQ.

Returns:

• bool: Whether indicated file appears to be in FASTQ format, zippedor unzipped.

def is_gzipped_fastq(file_name)

Determine whether indicated file appears to be a gzipped FASTQ.

Parameters:

• file_name (str): Name/path of file to check as gzipped FASTQ.

Returns:

• bool: Whether indicated file appears to be in gzipped FASTQ format.

def is_sam_or_bam(file_name)

Determine whether a file appears to be in a SAM format.

Parameters:

• file_name (str): Name/path of file to check as SAM-formatted.

Returns:

• bool: Whether file appears to be SAM-formatted

def is_unzipped_fastq(file_name)

Determine whether indicated file appears to be an unzipped FASTQ.

Parameters:

• file_name (str): Name/path of file to check as unzipped FASTQ.

Returns:

• bool: Whether indicated file appears to be in unzipped FASTQ format.

def parse_ftype(input_file)

Checks determine filetype from extension.

Parameters:

• input_file (str): String to check.

Returns:

• str: filetype (extension without dot prefix)

Raises:

• UnsupportedFiletypeException: if file does not appear of asupported type

def peek_read_lengths_and_paired_counts_from_bam(bam, sample_size)

Counting read lengths and paired reads in a sample from a BAM.

Parameters:

• bam (str): path to BAM file to examine
• sample_size (int): number of reads to look at for estimation

Returns:

• defaultdict[int, int], int: read length observation counts, andnumber of paired reads observed

Raises:

• OSError:

def samtools_view(file_name, param, prog_path, postpend='')

Run samtools view, with flexible parameters and post-processing.

This is used to implement the various read counting functions.

Parameters:

• file_name (str): name/path of reads tile to use
• param (str): String of parameters to pass to samtools view
• prog_path (str): path to the samtools program
• postpend (str): String to append to the samtools command;useful to add cut, sort, wc operations to the samtools view output.

Returns:

• str: terminal-like text output

Version Information: ngstk v0.0.1pre2, generated by lucidoc v0.4.3