API

seqtools.utils

seqtools.utils.fileOpen(fname, mode='rt', encoding='latin-1')

Open a file, including gzip files

Parameters:

• fname – The filename to open. Gzip files are distinguished by ending in ‘.gz’
• mode – File mode for opening [default ‘r’]

Returns:

An open file handle

Note: the gzip module in python is REALLY slow, so this function uses subprocess and command-line gzip instead.

seqtools.utils.revcomp(sequence)

Reverse complement a string

Parameters:sequence – The DNA string (all caps)

This function includes a caching mechanism, so watch memory usage!

seqtools.utils.sortVcfBySequence(vcf, seqnames, seqmap=None)

Sort a tabixed VCF file by sequence names

>>> import vcf
>>> v = vcf.Reader('vcf.gz')
>>> from seqtools.utils import sortVcfBySequence
>>> w = vcf.Writer(open('sorted.vcf','w'),v)
>>> faifile = open('ucsc.hg19.fasta.fai')
>>> seqnames = [x.split('   ')[0] for x in faifile]
>>> for rec in sortVcfBySequence(v,seqnames):
    w.write_record(rec)
>>> w.close()
>>> v.close()

seqtools.fastq

class seqtools.fastq.FastqRecord(header, sequence, line3, quality)

Very simple fastq class containing header, sequence, line3, and quality as strings

class seqtools.fastq.FastqRecord(header, sequence, line3, quality)

Very simple fastq class containing header, sequence, line3, and quality as strings

class seqtools.fastq.Fastq(fname)

close()

name()

seqtools.varscan

parse VCF output from VarScan and fix the ALT column to adhere with VCF specifications

seqtools.varscan.fixLine(line)

Fix a varscan VCF line

Prints the output to stdout. Fixes the ALT column and also fixes the FREQ field to be a floating point value, easier for filtering.

Parameters:line – a pre-split and stripped varscan line

seqtools.varscan.fixVarscanVcfFile(iterable)

Takes an interator over a varscan VCF file and returns an iterator over fixed VCF lines, including header.

Parameters:iterable – any iterable of the VCF lines Returns:An iterator over fixed VCF lines

Usage is like so:

>>> from seqtools.varscan import fixVarscanVcfFile
>>> varscan = fixVarscanVcfFile(open('filename.vcf','r'))
>>> for line in varscan:
    print line

seqtools.vcf

seqtools.demultiplexer

seqtools.strucvar

seqtools.strucvar.crest.crestLineToBedLines(crestline, extrastring=None)

Takes a line from a CREST file and turns it into two BED lines

Parameters:

• crestline – a single string representing the CREST output
• extrastring – a single string to concatenate to the bed output, useful for including sample information, etc.

Returns:

a string containing the two bed lines