awk 'NR==FNR{array[">"$1]=(">" $1 "_length_in_kmers=" $3
"_mode_kmer_coverage=" $6 "_nucleotideLength=");next} {if($1 in
array){$1=array[$1]}}1'
/path/to/BiologicalAbundances/_DeNovoAssembly/Contigs.tsv Contigs.fasta
> contigs_annoated.fasta
On 11/21/2013 4:24 PM, Rick White wrote:
Hello Sebastien,
Could you suggest a way to do it?
Cheers
Rick
On Thu, Nov 21, 2013 at 1:20 PM, Sébastien Boisvert
<sebastien.boisver...@ulaval.ca
<mailto:sebastien.boisver...@ulaval.ca>> wrote:
On 21/11/13 01:43 PM, Rick White wrote:
Hello,
For MG-RAST upload it has two problems from Ray outputs.
The space between contig and number with unique sequence
number for example.
>contig-3000000**508 nucleotides
And, it needs coverage information for
>sequence_number_1_*[cov=2]*
CTAGCGCACATAGCATTCAGCGTAGCAGTCACTAGTACGTAGTACGTACC
>sequence_number_2_*[cov=4]*
ACGTAGCTCACTCCAGTAGCAGGTACGTCGAGAAGACGTCTAGTCATCAT
I was wondering if there was a quick command to add the
coverage information to the contig file and remove the space.
The mode coverage is available in:
RayOutput/
BiologicalAbundances/
_DenovoAssembly/
Contigs.tsv
You would probably need more than a awk command to rewrite the
headers though.
Cheers and many thanks
Rick
--
Richard Allen White III M.S.
PhD Candidate - Suttle Lab
Department of Microbiology & Immunology
The University of British Columbia
Vancouver, BC, Canada
cell. 604-440-5150 <tel:604-440-5150> <tel:604-440-5150
<tel:604-440-5150>>
http://www.ocgy.ubc.ca/~suttle/
<http://www.ocgy.ubc.ca/%7Esuttle/>
<http://www.ocgy.ubc.ca/%7Esuttle/>
--
Richard Allen White III M.S.
PhD Candidate - Suttle Lab
Department of Microbiology & Immunology
The University of British Columbia
Vancouver, BC, Canada
cell. 604-440-5150
http://www.ocgy.ubc.ca/~suttle/ <http://www.ocgy.ubc.ca/%7Esuttle/>
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