crb-blast

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unsupported system error/bindeps config not correct

8

I'm getting an error that seems to be to do with blastplus and an unsupported system error. I'm on a mac and running Ruby v 2.3.0 and blastn: 2.10.0+. I...

katieemelianova

Using the length-evalue function for blast best hits (BH)

1

Hi! crb-blast seems to work really great - I'm finding 17-39% improvement over blastp (both with default evalue cutoffs of 10-5) in identifying RBHs between de novo squid and pygmy...

000generic

Hi, https://github.com/cboursnell/crb-blast/blob/687a3f04119d6b09339ab9b284a3f9d540bda700/crb-blast.gemspec#L19 Please bump this so that it can be compatible with bio 2.0.x.

utkarsh2102

Multiple transcripts to a single database protein in tsv output file

6

Hi! I'm working with crb-blast for the first time and was able to use it without any obvious trouble (exit status 0) - running a query squid transcriptome against target...

000generic

My transcript headers, from Trinity assembly, are in the format ">TRINITY_DN4342|c0_g1_i1", where the g indicates the gene and i indicated isoform. In my output tsv file, all the characters after...

jmpolinski

Failing tests

5

``` Failure: test: crb-blast should get number of reciprocals. (TestCRBBlast) /build/ruby-crb-blast-0.6.6/test/test_test.rb:82:in `block (2 levels) in ' expected but was diff: ? 11 ? 0 ``` ruby-crb-blast Version 0.6.6 with ncbi-blast+...

mr-c

This PR addresses the issue I filed a couple days ago. I'm not sure if this would be supported, and there might be tests that should be updated (I couldn't...

camillescott

blahah

B111_pseudos.fasta_JWJX01000035.1_pseudo_00009 9a5c_pseudos.fasta_AE003849.1_pseudo_00354 100.000 141 0 0 1 141 730 590 1.63e-72 261 141 2551 B111_pseudos.fasta_JWJX01000035.1_pseudo_00014 9a5c_pseudos.fasta_AE003849.1_pseudo_00354 100.000 624 0 0 1 624 1 624 0.0 1153 624 2551 B111_pseudos.fasta_JWJX01000035.1_pseudo_00014 9a5c_pseudos.fasta_AE003851.1_pseudo_00012...

navkahlon240