def bowtie2Align(
index, outFile, read1, read2 = None, bowtie2Path = 'bowtie2',
threads = 1, readGroup = 1, sampleName = None, libraryID = None,
platform = None, discordant = False, mixed = False, upto = None,
maxInsert = None, check = True, samtoolsPath = 'samtools',
memory = 2, nameSort = False
):
''' Function to generate command to peform Bowtie2 Alignment of
paired FASTQ files. Function takes 9 arguments:
1) index - Suffix of Bowtie2 index.
2) outSam - Name of output SAM file.
3) read1 - Read1 FASTQ file.
4) read2 - Read2 FASTQ file.
5) path - Path to Bowtie2 executable.
6) threads - Number of thread to use.
7) discordant - Boolean; whether to output discordant pairs.
8) mixed - Boolean; whether to output mixed pairs.
9) upto - Number of reads to align
10) check - Boolean; whether to check for index entensions.
'''
# Check for index extensions
if not isinstance(check, bool):
raise TypeError('check argument must be bool')
if check:
suffixes = ['.1.bt2', '.2.bt2', '.3.bt2', '.4.bt2', '.rev.1.bt2',
'.rev.2.bt2']
for s in suffixes:
if not os.path.isfile(index + s):
raise IOError('Index file %s no found' %(index + s))
# Check and process discordant
if not isinstance(discordant, bool):
raise TypeError('discordant argument must be bool')
if discordant:
discordant = ''
else:
discordant = '--no-discordant'
# Check mixed
if not isinstance(mixed, bool):
raise TypeError('mixed argument must be bool')
if mixed:
mixed = ''
else:
mixed = '--no-mixed'
# Check upto argument
if not upto is None:
if not isinstance(upto, int):
raise TypeError('upto argument must be integer')
if upto < 1:
raise ValueError('upto argument must be >= 1')
# Check maximum insert argument
if not maxInsert is None:
if not isinstance(maxInsert, int):
raise TypeError('maxInsert argument must be integer')
if maxInsert < 1:
raise ValueError('maxInsert argument must be >= 1')
# Check outut file name and generate intermediate file names
if outFile.endswith('.sam'):
outSam = outFile
outBam = ''
elif outFile.endswith('.bam'):
outBam = outFile
outSam = outFile[:-4] + '.sam'
else:
raise ValueError("'outFile' argument must end '.sam' or '.bam'")
# Join multiple fastq files
if isinstance(read1, list):
read1 = ','.join(read1)
if isinstance(read2, list):
read2 = ','.join(read2)
# Create initial command
bowtie2Command = [bowtie2Path, '--phred33', '--very-sensitive', mixed,
discordant, '-p', str(threads), '-x', index, '-S', outSam]
# Extend command depending on if read2 is applied
if read2:
bowtie2Command.extend(['-1', read1, '-2', read2])
else:
bowtie2Command.extend(['-U', read1])
# Supplement additional commands
if upto:
bowtie2Command.extend(['-u', str(upto)])
if maxInsert:
bowtie2Command.extend(['-X', str(maxInsert)])
# Add read group data
if readGroup:
# Create read group list
rgList = ['--rg-id', str(readGroup)]
if sampleName:
rgList.extend(['--rg', 'SM:' + str(sampleName)])
if libraryID:
rgList.extend(['--rg', 'LB:' + str(libraryID)])
if platform:
rgList.extend(['--rg', 'PL:' + str(platform)])
# Add list to command
bowtie2Command.extend(rgList)
# Concatenate bowtie2Command command
bowtie2Command = filter(None, bowtie2Command)
bowtie2Command = ' '.join(bowtie2Command)
# Supplement BWA command with sort command
if outBam:
sortCommand = samtools.sort(inFile = outSam, outFile = outBam,
name = nameSort, memory = memory, delete = True,
path = samtoolsPath, threads = threads)
completeCommand = bowtie2Command + ' && ' + sortCommand
else:
completeCommand = bowtie2Command
# Return complete command
return(completeCommand)
def bowtie2Align(
index, outFile, read1, read2 = None, bowtie2Path = 'bowtie2',
threads = 1, readGroup = 1, sampleName = None, libraryID = None,
platform = None, discordant = False, mixed = False, upto = None,
maxInsert = None, check = True, samtoolsPath = 'samtools',
memory = '2', nameSort = False
):
''' Function to generate command to peform Bowtie2 Alignment of
paired FASTQ files. Function takes 9 arguments:
1) index - Suffix of Bowtie2 index.
2) outSam - Name of output SAM file.
3) read1 - Read1 FASTQ file.
4) read2 - Read2 FASTQ file.
5) path - Path to Bowtie2 executable.
6) threads - Number of thread to use.
7) discordant - Boolean; whether to output discordant pairs.
8) mixed - Boolean; whether to output mixed pairs.
9) upto - Number of reads to align
10) check - Boolean; whether to check for index entensions.
'''
# Check for index extensions
if not isinstance(check, bool):
raise TypeError('check argument must be bool')
if check:
suffixes = ['.1.bt2', '.2.bt2', '.3.bt2', '.4.bt2', '.rev.1.bt2',
'.rev.2.bt2']
for s in suffixes:
if not os.path.isfile(index + s):
raise IOError('Index file %s no found' %(index + s))
# Check and process discordant
if not isinstance(discordant, bool):
raise TypeError('discordant argument must be bool')
if discordant:
discordant = ''
else:
discordant = '--no-discordant'
# Check mixed
if not isinstance(mixed, bool):
raise TypeError('mixed argument must be bool')
if mixed:
mixed = ''
else:
mixed = '--no-mixed'
# Check upto argument
if not upto is None:
if not isinstance(upto, int):
raise TypeError('upto argument must be integer')
if upto < 1:
raise ValueError('upto argument must be >= 1')
# Check maximum insert argument
if not maxInsert is None:
if not isinstance(maxInsert, int):
raise TypeError('maxInsert argument must be integer')
if maxInsert < 1:
raise ValueError('maxInsert argument must be >= 1')
# Check outut file name and generate intermediate file names
if outFile.endswith('.sam'):
outSam = outFile
outBam = ''
elif outFile.endswith('.bam'):
outBam = outFile
outSam = outFile[:-4] + '.sam'
else:
raise ValueError("'outFile' argument must end '.sam' or '.bam'")
# Join multiple fastq files
if isinstance(read1, list):
read1 = ','.join(read1)
if isinstance(read2, list):
read2 = ','.join(read2)
# Create initial command
bowtie2Command = [bowtie2Path, '--phred33', '--very-sensitive', mixed,
discordant, '-p', str(threads), '-x', index, '-S', outSam]
# Extend command depending on if read2 is applied
if read2:
bowtie2Command.extend(['-1', read1, '-2', read2])
else:
bowtie2Command.extend(['-U', read1])
# Supplement additional commands
if upto:
bowtie2Command.extend(['-u', str(upto)])
if maxInsert:
bowtie2Command.extend(['-X', str(maxInsert)])
# Add read group data
if readGroup:
# Create read group list
rgList = ['--rg-id', str(readGroup)]
if sampleName:
rgList.extend(['--rg', 'SM:' + str(sampleName)])
if libraryID:
rgList.extend(['--rg', 'LB:' + str(libraryID)])
if platform:
rgList.extend(['--rg', 'PL:' + str(platform)])
# Add list to command
bowtie2Command.extend(rgList)
# Concatenate bowtie2Command command
bowtie2Command = filter(None, bowtie2Command)
bowtie2Command = ' '.join(bowtie2Command)
# Supplement BWA command with sort command
if outBam:
sortCommand = samtools.sort(inFile = outSam, outFile = outBam,
name = nameSort, memory = memory, delete = True,
path = samtoolsPath, threads = threads)
completeCommand = bowtie2Command + ' && ' + sortCommand
else:
completeCommand = bowtie2Command
# Return complete command
return(completeCommand)
def bwaMemAlign(
index, outFile, read1, read2 = None, bwaPath = 'bwa', threads = 1,
readGroup = '1', sampleName = None, libraryID = None, platform = None,
markSecondary = True, check = True, samtoolsPath = 'samtools',
memory = '2', nameSort = False
):
''' Function to generate command to perform BWA mem alignment of single
end or paired end FASTQ files. If the supplied output file name ends with
'.bam' then a sorted BAM file will be generated else if the file names
ends with '.sam' a sam file is returned. Function takes the following 14
arguments:
Args:
index (str)- Full path BWA index prefix.
outFile (str)- Full path to output sam or bam file.
read1 (str)- Read1 FASTQ file.
read2 (str)- Read2 FASTQ file.
bwaPath (str)- BWA exectuable.
threads (int)- Number of threads to use.
readGroup (str)- Read group to be used in SAM/BAM.
sampleName (str)- Name of sample to be used in header.
libraryID (str)- Library ID to be used in SAM/BAM.
platform (str)- Platform to be used in SAM/BAM.
markSecondary (bool)- Mark secondary alignments.
check (bool)- Check for index extensions and output directory.
samtoolsPath (str)- Samtools executable.
memory (int)- Gigabytes of memory to use in generating BAM file.
nameSort (bool)- Generate a name sorted BAM file.
Returns:
bwaCommand (str)- Command to perform BWA alignment.
Raises:
IOError - If index suffixes or output directory are absent.
TypeError - If arguments are of the wrong type.
ValueError - If arguments have an unexpected value.
'''
# Check index extensions and output directory, if required
if not isinstance(check, bool):
raise TypeError('check argument must be bool')
if check:
suffixes = ['.amb', '.ann', '.bwt', '.pac', '.sa']
for s in suffixes:
if not os.path.isfile(index + s):
raise IOError('Genome index file %s no found' %(index + s))
if not os.path.isdir(os.path.dirname(outFile)):
raise IOError('Could not find output directory {}'.format(
os.path.dirname(outFile)))
# Check outut file name and generate intermediate file names
if outFile.endswith('.sam'):
outSam = outFile
outBam = ''
elif outFile.endswith('.bam'):
outBam = outFile
outSam = outFile[:-4] + '.sam'
else:
raise ValueError('outFile argument must end .sam or .bam')
# Process secondary command
if not isinstance(markSecondary, bool):
raise TypeError('markSecondary argument must be bool')
if markSecondary:
markSecondary = '-M'
else:
markSecondary = ''
# Process multiple input fastq files
if isinstance(read1, list):
read1 = "'< zcat " + ' '.join(read1) + "'"
if isinstance(read2, list):
read2 = "'< zcat " + ' '.join(read2) + "'"
# Create command
bwaCommand = [bwaPath, 'mem', markSecondary ,'-t', str(threads),
index, read1, read2]
# Remove missing elements from command
bwaCommand = filter(None, bwaCommand)
# Add read group data
if readGroup:
# Create read group string
rgString = "'@RG\\tID:" + str(readGroup)
if sampleName:
rgString += '\\tSM:' + str(sampleName)
if libraryID:
rgString += '\\tLB:' + str(libraryID)
if platform:
rgString += '\\tPL:' + str(platform)
rgString += "'"
# Add string to command
bwaCommand.insert(2,rgString)
bwaCommand.insert(2,'-R')
# Complete BWA command
bwaCommand = '%s > %s' %(' '.join(bwaCommand), outSam)
# Supplement BWA command with sort command, if required, and return
if outBam:
sortCommand = samtools.sort(inFile = outSam, outFile = outBam,
name = nameSort, memory = memory, delete = True,
path = samtoolsPath, threads = threads)
bwaCommand = bwaCommand + ' && ' + sortCommand
return(bwaCommand)
def bwaMemAlign(
index, outFile, read1, read2 = None, bwaPath = 'bwa', threads = 1,
readGroup = '1', sampleName = None, libraryID = None, platform = None,
markSecondary = True, check = True, samtoolsPath = 'samtools',
memory = '2', nameSort = False
):
''' Function to generate command to perform BWA mem alignment of single
end or paired end FASTQ files. If the supplied output file name ends with
'.bam' then a sorted BAM file will be generated else if the file names
ends with '.sam' a sam file is returned. Function takes the following 14
arguments:
Args:
index (str)- Full path BWA index prefix.
outFile (str)- Full path to output sam or bam file.
read1 (str)- Read1 FASTQ file.
read2 (str)- Read2 FASTQ file.
bwaPath (str)- BWA exectuable.
threads (int)- Number of threads to use.
readGroup (str)- Read group to be used in SAM/BAM.
sampleName (str)- Name of sample to be used in header.
libraryID (str)- Library ID to be used in SAM/BAM.
platform (str)- Platform to be used in SAM/BAM.
markSecondary (bool)- Mark secondary alignments.
check (bool)- Check for index extensions and output directory.
samtoolsPath (str)- Samtools executable.
memory (int)- Gigabytes of memory to use in generating BAM file.
nameSort (bool)- Generate a name sorted BAM file.
Returns:
bwaCommand (str)- Command to perform BWA alignment.
Raises:
IOError - If index suffixes or output directory are absent.
TypeError - If arguments are of the wrong type.
ValueError - If arguments have an unexpected value.
'''
# Check index extensions and output directory, if required
if not isinstance(check, bool):
raise TypeError('check argument must be bool')
if check:
suffixes = ['.amb', '.ann', '.bwt', '.pac', '.sa']
for s in suffixes:
if not os.path.isfile(index + s):
raise IOError('Genome index file %s no found' %(index + s))
if not os.path.isdir(os.path.dirname(outFile)):
raise IOError('Could not find output directory {}'.format(
os.path.dirname(outFile)))
# Check outut file name and generate intermediate file names
if outFile.endswith('.sam'):
outSam = outFile
outBam = ''
elif outFile.endswith('.bam'):
outBam = outFile
outSam = outFile[:-4] + '.sam'
else:
raise ValueError('outFile argument must end .sam or .bam')
# Process secondary command
if not isinstance(markSecondary, bool):
raise TypeError('markSecondary argument must be bool')
if markSecondary:
markSecondary = '-M'
else:
markSecondary = ''
# Create command
bwaCommand = [bwaPath, 'mem', markSecondary ,'-t', str(threads),
index, read1, read2]
# Remove missing elements from coomand
bwaCommand = filter(None, bwaCommand)
# Add read group data
if readGroup:
# Create read group string
rgString = "'@RG\\tID:" + str(readGroup)
if sampleName:
rgString += '\\tSM:' + str(sampleName)
if libraryID:
rgString += '\\tLB:' + str(libraryID)
if platform:
rgString += '\\tPL:' + str(platform)
rgString += "'"
# Add string to command
bwaCommand.insert(2,rgString)
bwaCommand.insert(2,'-R')
# Complete BWA command
bwaCommand = '%s > %s' %(' '.join(bwaCommand), outSam)
# Supplement BWA command with sort command, if required, and return
if outBam:
sortCommand = samtools.sort(inFile = outSam, outFile = outBam,
name = nameSort, memory = memory, delete = True,
path = samtoolsPath, threads = threads)
bwaCommand = bwaCommand + ' && ' + sortCommand
return(bwaCommand)
