Bug in parseFasta ??

[ptranvan]

Hi,

Using that command:

blobtools create -i sm.scafSeq -t assembly_se_uniref.daa.tagc -t assembly_se_nt.blastn -y soap --nodes nodes.dmp --names names.dmp

I got an error:

[STATUS] : Parsing FASTA - sm.scafSeq Traceback (most recent call last): File "blobtools/create.py", line 56, in blobDb.parseFasta(fasta_f, fasta_type) File "blobtools/lib/BtCore.py", line 265, in parseFasta cov = BtIO.parseCovFromHeader(fasta_type, blObj.name) File "blobtools/lib/BtIO.py", line 146, in parseCovFromHeader return float(temp[2]/(temp[1]+1-75))

Do you have any solution ??

[DRL]

Hi ptranvan,

is sm.scafSeq a FASTA file generated by soap? could you sent me a selection of the headers in the FASTA file to see what goes on there?

cheers,

dom

[ptranvan]

Thanks for your quick answer.

Is has been assembled with soapdenovo2: The header looks like this:

scaffold1 43.4 scaffold2 36.2 scaffold3 12.8

[DRL]

Hi ptravan,

we usually don't use either soap or abyss so I wasn't aware that this didn't work properly.

Due to the structure of the code and the general behaviour of other bioinformatic tools, there is no easy way of fixing the parsing for abyss and soap (AFAIK they are the only assemblers that have spaces in their headers).

Hence I will drop the support for coverage parsing for these two assemblers.

In order to run blobtools with your assembly you can just generate a simple coverage file using the following one-liner:

grep '^>' assembly.fna | sed 's/^>//g' | awk '{print $1 "\t" $2}' > assembly.cov

and then just provide the cov file with -c assembly.cov (without the option -y soap)

cheers,

dom