biolockj.util

Class SeqUtil

java.lang.Object

biolockj.util.SeqUtil

public class SeqUtil
extends Object

This utility helps interact with FastA and FastQ sequence files.

Field Summary

Fields

Modifier and Type	Field and Description
static String	FASTA_HEADER_DEFAULT_DELIM Default 1st character for a FASTA file: ">"
static String	ILLUMINA_FW_READ_IND Illumina forward read indicator found in sequence header
static String	ILLUMINA_RV_READ_IND Illumina reverse read indicator found in sequence header

Method Summary

Modifier and Type	Method and Description
static long	countNumReads(File seqFile) Method counts number of reads in the given sequence file by counting the number of lines and dividing by the number of lines/sample (fasta=2, fastq=4)
static String	getHeader(String line) Extract the header from the first line of a read (parse to first space).
static Set<String>	getHeaders(File seq) Return the header of each read in the sequence file.
static Set<String>	getHeaders(File fwRead, File rvRead) Get valid headers found in both forward and reverse read.
static String	getIupacBase(String base) Return regex version of IUPAC DNA substitution bases so that only ACGT values are used.
static int	getNumLinesPerRead() Return number of lines per read (for fasta return 2, for fastq return 4)
static long	getNumReads(long numLines) Return number of reads given number of lines in a sample.
static Map<File,File>	getPairedReads(Collection<File> files) Paired reads must have a unique file suffix to identify forward and reverse reads.
static String	getReadDirectionSuffix(File file) Return read direction indicator for forward or reverse read if found in the file name.
static String	getReadDirectionSuffix(String fileName) Return read direction indicator for forward or reverse read if found in the file name.
static String	getSampleId(String value) Method extracts Sample ID from the name param.
static List<File>	getSeqFiles(Collection<File> files) Return only sequence files for sample IDs found in the metadata file. If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
static List<String>	getSeqHeaderChars() Get all sequence header characters for fasta and fastq files.
static String	getSeqType() Get sequence type
static void	initialize() Initialize Config params set by SeqUtil.
protected static void	initSeqParams() Set "input.ignoreFiles", , and Ignore the metadata file Config."metadata.filePath" If Config pipeline contains biolockj.module.seq or biolockj.module.classifier BioModules, ignore non-(fasta/fastq) files found in Constants.INPUT_DIRS
static boolean	isFastA() Return TRUE if input files are in FastA format.
static boolean	isFastQ() Return TRUE if input files are in FastQ format.
static boolean	isForwardRead(String name) Return TRUE if reads are unpaired or if name does not contain the reverse read file suffix:
static boolean	isGzipped(String fileName) Determine if file is gzipped based on its file extension. Any file ending with ".gz" is treated as a gzipped file.
static Boolean	isMultiplexed() Check current state of sequence data.
static boolean	isSeqFile(File file) Verify 1st character of sequence header and mask 1st sequence for valid DNA/RNA bases "acgtu"
static boolean	isSeqModule(BioModule module) Check the module to determine if it generated sequence file output.
static boolean	piplineHasSeqInput() Return TRUE if pipeline input files are sequence files.
protected static void	registerPairedReadStatus() Inspect the pipeline input files to determine if input includes paired reads.
static String	reverseComplement(String dna) Return the DNA reverse compliment for the input dna parameter.
static String	scanFirstLine(BufferedReader reader, File file) This method returns the 1st non-empty line and moves the BufferedReader pointer to this line.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTA_HEADER_DEFAULT_DELIM

public static final String FASTA_HEADER_DEFAULT_DELIM

Default 1st character for a FASTA file: ">"

See Also:

Constant Field Values

ILLUMINA_FW_READ_IND

public static final String ILLUMINA_FW_READ_IND

Illumina forward read indicator found in sequence header

See Also:

Constant Field Values

ILLUMINA_RV_READ_IND

public static final String ILLUMINA_RV_READ_IND

Illumina reverse read indicator found in sequence header

See Also:

Constant Field Values

Method Detail

countNumReads

public static long countNumReads(File seqFile)
                          throws Exception

Method counts number of reads in the given sequence file by counting the number of lines and dividing by the number of lines/sample (fasta=2, fastq=4)

Parameters:

seqFile - Sequence file

Returns:

Number of reads in seqFile

Throws:

Exception - if errors occur

getHeader

public static String getHeader(String line)

Extract the header from the first line of a read (parse to first space). This part of the header line will be identical on forward and reverse reads, so can be used to find matching pairs of reads.

To extract the header, trim to the Illumina read direction indicator, if it exists, otherwise to the 1st space. Method recognizes the headers: " 1:N:" and " 2:N:"

Parameters:

line - Sequence line

Returns:

Sequence header

getHeaders

public static Set<String> getHeaders(File seq)
                              throws Exception

Return the header of each read in the sequence file.

Parameters:

seq - Fasta or Fastq file

Returns:

Set of sequence headers

Throws:

Exception - if unable to parse the seq file

getHeaders

public static Set<String> getHeaders(File fwRead,
                                     File rvRead)
                              throws Exception

Get valid headers found in both forward and reverse read.

Parameters:

fwRead - Forward read sequence file

rvRead - Reverse read sequence file

Returns:

Sequence headers found in both files

Throws:

Exception - if I/O errors occur

getIupacBase

public static String getIupacBase(String base)

Return regex version of IUPAC DNA substitution bases so that only ACGT values are used. For example, if base = "Y", return "[CT]", if base = "A", return "A".
Function returns base in the same case as the input parameter.

Parameters:

base - DNA Base

Returns:

regex version of IUPAC DNA substitution bases

getNumLinesPerRead

public static int getNumLinesPerRead()
                              throws Exception

Return number of lines per read (for fasta return 2, for fastq return 4)

Returns:

2 or 4

Throws:

Exception - if unable to determine sequence format

getNumReads

public static long getNumReads(long numLines)
                        throws Exception

Return number of reads given number of lines in a sample.

Parameters:

numLines - Total number of lines in sample

Returns:

Number of reads

Throws:

Exception - if number of reads cannot be determined

getPairedReads

public static Map<File,File> getPairedReads(Collection<File> files)
                                     throws Exception

Paired reads must have a unique file suffix to identify forward and reverse reads. Parameter files read and a map with forward read file names as keys and matching reverse reads as the map return value

Parameters:

files - List of paired read files

Returns:

Map with key=fwRead and val=rvRead

Throws:

ConfigViolationException - if unpaired reads are found and Config. = "Y"

Exception - if other errors occur

getReadDirectionSuffix

public static String getReadDirectionSuffix(File file)
                                     throws Exception

Return read direction indicator for forward or reverse read if found in the file name.

Parameters:

file - Sequence file

Returns:

Forward or reverse read file suffix

Throws:

Exception - if errors occur

getReadDirectionSuffix

public static String getReadDirectionSuffix(String fileName)
                                     throws Exception

Return read direction indicator for forward or reverse read if found in the file name.

Parameters:

fileName - Sequence file name

Returns:

Forward or reverse read file suffix

Throws:

Exception - if errors occur

getSampleId

public static String getSampleId(String value)
                          throws Exception

Method extracts Sample ID from the name param. Possibly input is a file name so remove file extensions. If demultiplexing (RDP/Kraken support this option), input is a sequence header. If Config."metadata.fileNameColumn" is supplied, then possible return values are limited to the given samples ids, or "" if the file is not in the filename column.

Parameters:

value - File name or sequence header

Returns:

Sample ID

Throws:

Exception - if unable to determine Sample ID

getSeqFiles

public static List<File> getSeqFiles(Collection<File> files)
                              throws Exception

Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.

Parameters:

files - List of input files

Returns:

Module input sequence files

Throws:

Exception - if no input files are found

getSeqHeaderChars

public static final List<String> getSeqHeaderChars()
                                            throws Exception

Get all sequence header characters for fasta and fastq files.

Returns:

List of sequence header 1st character options

Throws:

Exception - if unable to determine sequence type

getSeqType

public static String getSeqType()
                         throws ConfigNotFoundException

Get sequence type

Returns:

sequence typ (fasta/fastq/NA)

Throws:

ConfigNotFoundException - if property is undefined

initialize

public static void initialize()
                       throws Exception

Initialize Config params set by SeqUtil.

Throws:

Exception - if runtime errors occur

isFastA

public static boolean isFastA()
                       throws Exception

Return TRUE if input files are in FastA format.

Returns:

TRUE if input files are in FastA format

Throws:

Exception - if unable to determine sequence type

isFastQ

public static boolean isFastQ()
                       throws Exception

Return TRUE if input files are in FastQ format.

Returns:

TRUE if input files are in FastQ format

Throws:

Exception - if unable to determine sequence type

isForwardRead

public static boolean isForwardRead(String name)

Return TRUE if reads are unpaired or if name does not contain the reverse read file suffix:

Parameters:

name - Name of file

Returns:

TRUE for unpaired or forward reads

isGzipped

public static boolean isGzipped(String fileName)

Determine if file is gzipped based on its file extension.
Any file ending with ".gz" is treated as a gzipped file.

Parameters:

fileName - File name

Returns:

TRUE if file name ends with .gz

isMultiplexed

public static Boolean isMultiplexed()
                             throws ConfigFormatException

Check current state of sequence data.

Returns:

Boolean TRUE if multiplexed

Throws:

ConfigFormatException - if property assignment is invalid

isSeqFile

public static boolean isSeqFile(File file)
                         throws Exception

Verify 1st character of sequence header and mask 1st sequence for valid DNA/RNA bases "acgtu"

Parameters:

file - File

Returns:

TRUE if file is a squence file

Throws:

Exception - if errors occur

isSeqModule

public static boolean isSeqModule(BioModule module)

Check the module to determine if it generated sequence file output.

Parameters:

module - BioModule

Returns:

TRUE if module generated OTU count files

piplineHasSeqInput

public static boolean piplineHasSeqInput()
                                  throws Exception

Return TRUE if pipeline input files are sequence files.

Returns:

TRUE if pipeline input files are sequence files.

Throws:

Exception - if errors occur

reverseComplement

public static String reverseComplement(String dna)
                                throws Exception

Return the DNA reverse compliment for the input dna parameter.

Parameters:

dna - DNA base sequence

Returns:

DNA reverse complement

Throws:

Exception - if sequence contains a non-standard letter (only ACGT accepted)

scanFirstLine

public static String scanFirstLine(BufferedReader reader,
                                   File file)
                            throws Exception

This method returns the 1st non-empty line and moves the BufferedReader pointer to this line. By passing the reader, subsequent calls to reader.readLine() will pick up from here.

Parameters:

reader - BufferedReader reader for sequence file

file - Sequence file read by the BufferedReader (used for log and error messages)

Returns:

String First non-empty line

Throws:

Exception - if errors occur

initSeqParams

protected static void initSeqParams()
                             throws Exception

Set "input.ignoreFiles", , and

• Ignore the metadata file Config."metadata.filePath"
• If Config pipeline contains biolockj.module.seq or biolockj.module.classifier BioModules, ignore non-(fasta/fastq) files found in Constants.INPUT_DIRS

Throws:

Exception - if Constants.INPUT_DIRS undefined or file reader I/O Exception occurs

registerPairedReadStatus

protected static void registerPairedReadStatus()
                                        throws Exception

Inspect the pipeline input files to determine if input includes paired reads.

Throws:

Exception - if unable to determine if reads are paired