I have a kalliso-created abundance.h5 file but the filename (ES_1_high_28881_CGATGT_abundance.h5) includes information about the sample. When I try to import this file using tximport v1.10.0 I get an error. tximport thinks that the file is a .tsv file. 

However, if I create a symlink named abundance.h5, I can load that perfectly well. 

Is there a way to tell tximport that the file really is a kallisto h5 file? 

-Lucas

data <- tximport( 'ES_1_high_28881_CGATGT_abundance.h5' , type = "kallisto" , tx2gene=tx2gene , ignoreAfterBar=TRUE )
Note: importing `abundance.h5` is typically faster than `abundance.tsv`
reading in files with read_tsv
1 Error in read_tokens_(data, tokenizer, col_specs, col_names, locale_,  :
  embedded nul in string: '\0\xfbLΦ(\x98Hr1'
In addition: Warning message:
Unnamed `col_types` should have the same length as `col_names`. Using smaller of the two.

> system('ln -s ES_1_high_28881_CGATGT_abundance.h5 abundance.h5')

> data <- tximport( 'abundance.h5' , type = "kallisto", tx2gene=tx2gene , ignoreAfterBar=TRUE )
1
summarizing abundance
summarizing counts
summarizing length
summarizing inferential replicates

Always something about posting to a forum that makes me find an answer. 

This works, but is messy: 

1. load the function read_kallisto_h5() from tximport helper.R

2. set importer=read_kallisto_h5

data <- tximport(  'ES_1_high_28881_CGATGT_abundance.h5' , type = "kallisto", txOut = FALSE , tx2gene=tx2gene , ignoreAfterBar=TRUE , importer = read_kallisto_h5 )

kallisto creates a directory for each RNA sample. I would suggest that you don't rename any of the kallisto output files in the directory, because downstream functions like tximport, edgeR::catchKallisto and Sleuth assume the files have standard names. Instead, just rename the directory itself to have an informative name.