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About bioawk

Bioawk is an extension to Brian Kernighan's awk that adds support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with the column names.

Bioawk adds a new -c fmt option that specifies the input format. The behavior of bioawk will vary depending on the value of fmt.

For the formats that awk recognizes specially named variables will be created. For example for the supported sequence formats the $name, $seq and, if applicable $qual variable names may be used to access the name, sequence and quality string of the sequence record in each iteration. Here is an example of iterating over a fastq file to print the sequences:

awk -c fastx '{ print $seq }' test.fq

For known interval formats the columns can be accessed via the variables called $start, $end, $chrom (etc). For example to print the feature lenght of a file in BED format one could write:

awk -c bed '{ print $end - $start }' test.bed

One important change (and innovation) over the original awk is that bioawk will treat sequences that may span multiple lines as a single record. The parsing, implemented in C, may be several orders of magnitude faster than similar code programmed in interpreted languages: Perl, Python, Ruby.

When the format mode is header or hdr, bioawk parses named columns. It automatically adds variables whose names are taken from the first line and values from the column index. Special characters are converted to a underscore.

Bioawk also adds a few built-in functions including, as of now, and(), or(), xor(), and others (see comprehensive list below).

Detailed help is maintained in the bioawk manual page, to access it type:

man ./awk.1

Usage Examples

  1. Extract unmapped reads without header:

    awk -c sam 'and($flag,4)' aln.sam.gz
    
  2. Extract mapped reads with header:

    awk -c sam -H '!and($flag,4)'
    
  3. Reverse complement FASTA:

    awk -c fastx '{ print ">"$name;print revcomp($seq) }' seq.fa.gz
    
  4. Create FASTA from SAM (uses revcomp if FLAG & 16):

    samtools view aln.bam | \
        awk -c sam '{ s=$seq; if(and($flag, 16)) {s=revcomp($seq) } print ">"$qname"\n"s}'
    
  5. Get the %GC from FASTA:

    awk -c fastx '{ print ">"$name; print gc($seq) }' seq.fa.gz
    
  6. Get the mean Phred quality score from FASTQ:

    awk -c fastx '{ print ">"$name; print meanqual($qual) }' seq.fq.gz
    
  7. Take column name from the first line (where "age" appears in the first line of input.txt):

    awk -c header '{ print $age }' input.txt
    

Note that when "-c" is not specified and the new built-in functions are not used, bioawk should behave exactly the same as the original BWK awk. At least this is the intention. Bioawk also tries to minimize the modification to the original code base such that improvements in the future versions of BWK awk can be readily incorporated into bioawk (yes, Brian Kernighan is still maintaining his code).

New Builtin Functions

gc($seq)
Returns the GC percentage of a sequence.
meanqual($seq)
Returns the average quality of the fastq sequence.
reverse($seq)
Returns the reverse of the sequence.
revcomp($seq)
Returns the reverse complement of the sequence.
qualcount($qual, threshold)
Returns the number of quality values above the threshold parameter.
trimq(qual, beg, end, param)
Trims the quality string qual in the Sanger scale using Richard Mott's algorithm (used in Phred). The 0-based beginning and ending positions are written back to beg and end, respectively. The last argument param is the single parameter used in the algorithm, which is optional and defaults 0.05.
and(x, y)
bit AND operation (& in C)
or(x, y)
bit OR operation (| in C)
xor(x, y)
bit XOR operation (^ in C)

Recognized Formats

These formats may be passed as the -c flag:

bed
1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts
sam
1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual
vcf
1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info
gff
1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute
fastx
1:name 2:seq 3:qual

The fastx flag can handle both FASTA and FASTQ formats.

Adding New Functionality

Follow these steps when adding a new function.

  1. Add a function index (e.g. #define BIO_FFOO 102) in addon.h. The integer index must be larger than 14 in the current awk implementation (see also macros starting with "F" defined in awk.h).
  2. Add the function name and the function index in the keywords array defined in lex.c. Remember to keep the array sorted!
  3. Implement the actual function in bio_func().

Note

Bioawk may have the following limitations:

  1. To parse FASTA and FASTQ formats, bioawk replaces the line reading module of awk, which also allows bioawk to seamlessly parse gzip'ed files. However, the new line reading code does not fully mimic the original code. It may fail in corner cases. Thus when "-c" is not specified, awk falls back to the original line reading code and does not support gzip'ed input.
  2. When "-c" is in use, several strings allocated in the new line reading module are not freed in the end. These will be reported by valgrind as "still reachable". To some extend, these are not memory leaks.
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