{"id":2915,"date":"2019-03-29T15:57:25","date_gmt":"2019-03-29T15:57:25","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2915"},"modified":"2019-03-29T15:58:57","modified_gmt":"2019-03-29T15:58:57","slug":"bioawk","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/bioawk\/","title":{"rendered":"bioawk"},"content":{"rendered":"

Overview<\/h2>\n

Bioawk is an extension created by Heng Li<\/a> of Brian Kernighan’s awk<\/a> which adds the support of several common biological data formats, including optionally gzip’ed BED, GFF, SAM, VCF, FASTA\/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input\/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.<\/p>\n

Latest version dated 27-08-2013 is installed on the CSF. Bioawk does not have a version number hence date of github commit is used to identify versions.<\/p>\n

Restrictions on use<\/h2>\n

No licence information available.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

module load apps\/gcc\/bioawk\/27-08-2013<\/pre>\n
Running the application<\/h2>\n
Please do not run bioawk on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\nmodule load apps\/gcc\/bioawk\/27-08-2013\r\nbioawk -Hc sam '!and($flag,4)'<\/code><\/pre>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
bioawk is not designed to run in parallel. If you need to run multiple similar jobs then please consider using job arrays<\/a>.<\/p>\n
Examples of usage:<\/h3>\n
    \n
  1. List the supported formats:\n
    bioawk -c help\r\n<\/code><\/pre>\n<\/li>\n
  2. Extract unmapped reads without header:\n
    bioawk -c sam 'and($flag,4)' aln.sam.gz\r\n<\/code><\/pre>\n<\/li>\n
  3. Extract mapped reads with header:\n
    bioawk -Hc sam '!and($flag,4)'\r\n<\/code><\/pre>\n<\/li>\n
  4. Reverse complement FASTA:\n
    bioawk -c fastx '{print \">\"$name;print revcomp($seq)}' seq.fa.gz<\/code><\/pre>\n<\/li>\n<\/ol>\n
    Further examples can be found on the bioawk help page<\/a>.<\/p>\n
    Recognized Formats<\/h3>\n
    These formats may be passed as the -c flag:<\/p>\n
    \n
    bed<\/dt>\n
    1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts<\/dd>\n
    sam<\/dt>\n
    1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual<\/dd>\n
    vcf<\/dt>\n
    1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info<\/dd>\n
    gff<\/dt>\n
    1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute<\/dd>\n
    fastx<\/dt>\n
    1:name 2:seq 3:qual<\/dd>\n<\/dl>\n
    The fastx flag can handle both FASTA and FASTQ formats.<\/p>\n
    Further info<\/h2>\n