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Saturday, July 20, 2013

install bioawk in unbuntu

Bioawk is written by Heng Li, and it can handle formats like:
     1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts
    1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual
    1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info
    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 4:comment

 I followed the tutorial here

my first try did not work

tommy@tommy-ThinkPad-T420:~$ git clone git:// && cd bioawk && make && mv awk bioawk && sudo cp bioawk /usr/local/bin/
Cloning into 'bioawk'...
remote: Counting objects: 163, done.
remote: Compressing objects: 100% (89/89), done.
remote: Total 163 (delta 95), reused 136 (delta 74)
Receiving objects: 100% (163/163), 112.32 KiB, done.
Resolving deltas: 100% (95/95), done.
yacc -d awkgram.y
make: yacc: Command not found
make: *** [ytab.o] Error 127

It looks like I do not have  yacc or bison (the GNU
equivalent) installed.

tommy@tommy-ThinkPad-T420:~/bioawk$ sudo synaptic

search yacc, and install the bison.

after that, it worked.

tommy@tommy-ThinkPad-T420:~/bioawk$ bioawk
usage: bioawk [-F fs] [-v var=value] [-c fmt] [-H] [-f progfile | 'prog'] [file ...]

a quick tutorial for git:

1 comment:

  1. Hello,

    I am trying to convert the .faa format protein sequences into OrthoMCL readable format (organism_ID|protein_ID) using the bioawk -c fastx '{ print ">GMI1000|"$name; print $seq }'. I am only getting the results with around 900 sequences out of 4000. I found that bioawk is not reading the sequences from first 3000 proteins in the .faa format.
    Is there any way to solve this problem?

    Thank you very much in advance!!