Re: "med.bio" under Ubuntu-MATE 18.04 LTS
Hi,
just a short note: The metapackage is called med-bio (with a dash not a
dot ... just in case somebody might seek in the wrong direction).
On Mon, May 28, 2018 at 01:36:48AM +0100, Tony Travis wrote:
> On 27/05/18 23:13, Tony Travis wrote:
> > [...]
> >> File "/usr/share/metaphlan2/_metaphlan2.py", line 22
> >> print("Command: {}".format(' '.join(cmd)), end='\n\n')
> >> ^
> >> SyntaxError: invalid syntax
>
> Hi,
>
> The problem is that "_metaphlan2.py" uses Python3 syntax but the Debian
> "postinst" script runs "pycompile" on it, which defaults to Python2.
>
> Here is a patch, with the print function included from the future and
> function annotations removed.
Thanks for the patch - I'll upload it soon. Regarding the bug report:
If the issue can be verified on a Debian system it surely belongs to the
Debian BTS. In general we try hard to fix also bugs reported on Ubuntu
(if somebody points us to the issue).
I have a question to the patch below:
> --- _metaphlan2.py.orig 2018-02-07 10:43:00.000000000 +0000
> +++ _metaphlan2.py 2018-05-28 01:27:41.168280522 +0100
> @@ -3,7 +3,7 @@
> # This module defines the functions which run MetaPhlAn2 on
> # single and paired fastq data.
>
> -
> +from __future__ import print_function
OK, this fits the description of the patch and should solve the
issue.
> import subprocess as sb
> from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt
> from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt
> @@ -11,7 +11,6 @@
> import biom
> import os
>
> -
> def metaphlan2_helper(raw_data, nproc, input_type, output_file, verbose=True):
> cmd = ['metaphlan2.py', str(raw_data), '--input_type', str(input_type),
> '--biom', str(output_file), '--nproc', str(nproc)]
> @@ -24,8 +23,7 @@
> sb.run(cmd, check=True)
>
>
> -def profile_single_fastq(raw_data: SingleLanePerSampleSingleEndFastqDirFmt,
> - nproc: int=1) -> biom.Table:
> +def profile_single_fastq(raw_data, nproc=1):
> output_biom = None
Could you please comment on this chunk (and the similar one later)? In
how far is this related to the issue above?
Thanks a lot for your contribution
Andreas.
--
http://fam-tille.de
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