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abundance-dist.py incorrectly not supporting output to STDOUT #607

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mr-c opened this issue Sep 18, 2014 · 3 comments
Closed

abundance-dist.py incorrectly not supporting output to STDOUT #607

mr-c opened this issue Sep 18, 2014 · 3 comments

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@mr-c
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mr-c commented Sep 18, 2014

(env)mcrusoe@athyra:~/papers/2013-read-aligner/ecoli_rand_error$ abundance-dist.py reads.ht reads.fasta /dev/stdout | awk '{ print $2 }' 

|| This is the script 'abundance-dist.py' in khmer.
|| You are running khmer version 1.2-rc1-71-ged65dbc
|| You are also using screed version 0.7
||
|| If you use this script in a publication, please cite EACH of the following:
||
||   * MR Crusoe et al., 2014. doi: 10.6084/m9.figshare.979190
||   * Q Zhang et al., arXiv:1309.2975 [q-bio.GN]
||
|| Please see http://khmer.readthedocs.org/en/latest/citations.html for details.

ERROR: /dev/stdout exists; not squashing.
from
30
sizes:
to

Probably also abundance-dist-single.py. Squashing code should be updated to ignore /dev

@mr-c
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mr-c commented Sep 18, 2014

Diagnostic and status information is output to STDOUT instead of STDERR, which also defeats attempts to stream abundance information to another program.

@b-wyss
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b-wyss commented Sep 19, 2014

I'll work on this one.

@mr-c
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mr-c commented Dec 17, 2014

This was done in #626

@mr-c mr-c closed this as completed Dec 17, 2014
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