peak_anno : several errors encountered in example file (rst)

[dputhier]

    make html -j 4                                                              ✔  ⚙  10172  22:29:25
    Running Sphinx v1.8.3
    loading translations [en]... done
    making output directory...
    building [mo]: targets for 0 po files that are out of date
    building [html]: targets for 16 source files that are out of date
    updating environment: 16 added, 0 changed, 0 removed
    reading sources... [100%] sequence
    waiting for workers...
    WARNING: Unexpected return code 1 from command 'gtftk get_example -d mini_real | gtftk peak_anno -m gene_biotype -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38.genome -D -n  -if example_pa_02.png'
    WARNING: Unexpected return code 1 from command 'gtftk get_example -d mini_real |  gtftk join_attr -H -j mini_real_counts_ENCFF630HEX.tsv -k gene_name -n exprs -t gene | gtftk discretize_key -k exprs -p -d exprs_class -n 6   | gtftk peak_anno -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38.genome -D -n -m exprs_class -if example_pa_03.png'
    WARNING: Unexpected return code 1 from command 'gtftk get_example -d mini_real | gtftk add_exon_nb -k exon_nbr | gtftk discretize_key -p -d exon_nbr_cat -n 5  -k exon_nbr | gtftk peak_anno -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38.genome -D -n -m exon_nbr_cat -if example_pa_04.png'
    looking for now-outdated files... none found
    pickling environment... done
    checking consistency... done
    preparing documents... done
    writing output... [100%] sequence
    waiting for workers...
    generating indices... genindex py-modindex
    writing additional pages... search
    copying images... [100%] _static/example_13.png
    copying static files... done
    copying extra files... done
    dumping search index in English (code: en) ... done
    dumping object inventory... done
    build succeeded, 3 warnings.

    The HTML pages are in build/html.

    Build finished. The HTML pages are in build/html.

[qferre]

I think this is because these peak_anno commands used the old (completely different except from the name) peak_anno. I can tell because it has the '-D' command line option, and I have no idea what it is.

[dputhier]

-D is a command wise argument to delete dates in output file names (see gtftk peak_anno -h). This argument works with the current version. These examples should work.

[dputhier]

Changing the png output to pdf.

[qferre]

Then what does "WARNING: Unexpected return code 1" mean ? When I try to run the first example manually in a terminal, gtftk says it cannot find the file :

gtftk get_example -d mini_real | gtftk peak_anno -m gene_biotype -p ENCFF112BHN_H3K4me3_K562_sub.bed -c hg38.genome -D
 -n  -if example_pa_02.png
 |-- 15:57-ERROR : Unable to load file: ENCFF112BHN_H3K4me3_K562_sub.bed.

[dputhier]

gtftk get_example -d mini_real -f '*'

[dputhier]

Just try to make them pass without taking care of sphinx embedding.

[qferre]

What ? gtftk get_example -d mini_real -f '*' did not work either.

[dputhier]

@qferre I mean the first objective is to make it work inside or outside Sphinx doc.

[dputhier]

@dputhier sorry part of your reply was masked. Can understand why get_example is not working. What is the output ?

[qferre]

Okay, here is the error :

|-- 11:20-ERROR-peak_anno : Less than 2 remaining regions in one of the BED files. This is likely due to them being all in regions marked in the excl
usion file.

I know the cause : the program exits if at any point there are less than 2 regions in a BED file. I will change it so that it returns "-1" in the result file.

[qferre]

Partially fixed. There is just a problem now on the fitting of a negative binomial for such regions. Working on it.

[qferre]

There was a small, stupid error : when trying to fit a negative binomial, if the range was too small (<2) it would make an empty count table at some point (I'll spare you the details). Should have been fixed now, can you try again ?

[qferre]

@dputhier : Bump. Forgot to tag you in my previous answer. Can you try again when you've got some time ? Thanks.

[dputhier]

I have fixed the help files (annotation.rst). The outputs of peak_anno which are in pdf format are enclosed in html frames and can be downloaded, if required, by the user. The only problem is that the computation is rather time consuming. It may lead to some problem when we will compile the help files on readthedocs (there is a walltime). Maybe we will need to ask for additional computation time on readthedoc server... Fixed in 17a3675cd3706ede58c427fae66d8b1d7859ce80

[qferre]

When you say "time consuming", how much do you mean ? Minutes ? Hours ? Worst case, maybe we can replace the "mini_real" files with "simple" ones ?