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PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study
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fc_track_reads.py produces fakemovie entries in raw_read_ids #13

Closed fbemm closed 8 years ago

fbemm commented 8 years ago

I am trying to extract unlocalized reads with falcon unzip from a new assembly (falcon 0.4.1). Somehow it won't create the contig_reads.fa files anymore (000045F_reads.fa). I guess this has to do with the way reads are imported into the 0-rawreads dazzdb now. The raw_read_ids files contains something like fakemovieid instead of the original one. Known problem?

pb-jchin commented 8 years ago

yes. I have not tested the Unzip code with FALCON 0.4.1. I think @pb-cdunn has made "fake movie name" for other integration reason one time for 0.4.1. It will break the Unzip code. It is known issue.

pb-cdunn commented 8 years ago

Yes, that is a temporary work-around for the fact that fasta2DB expects one movie per .fasta. Either modify these lines to drop -pfakemoviename:

falcon_kit/bash.py:128:fasta2DB -pfakemoviename -v raw_reads -f{input_fofn_fn}
falcon_kit/bash.py:148:fasta2DB -pfakemoviename -v preads -f{input_fofn_fn}

Or use FALCON-0.4.0 for now. We will sync them fairly soon, but not today.

fbemm commented 8 years ago

Switch back to 0.4.0 already. Thanks for fast reponse. F

On 21.04.2016 21:22, Christopher Dunn wrote:

Yes, that is a temporary work-around for the fact that fasta2DB expects one movie per |.fasta|. Either modify these lines to drop |-pfakemoviename|:

|falcon_kit/bash.py:128:fasta2DB -pfakemoviename -v raw_reads -f{input_fofn_fn} falcon_kit/bash.py:148:fasta2DB -pfakemoviename -v preads -f{input_fofn_fn} |

Or use FALCON-0.4.0 for now. We will sync them fairly soon, but not today.

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pb-cdunn commented 8 years ago

0.5.0 should work with FALCON_unzip now. Please let us know if it does not.