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``README.md`` does not say which versions of the PFAM database, HMMER tool, nor ``pfam_scan.pl `` script are used.
In particular, since they are not compatible, do you use HMMER 2 or 3? This in tur…
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The searchPfam function appears to be broken as a result of a URL change.
For example
```
searchPfam('PF00047')
```
Results in:
```
ValueError: failed to parse results XML, check URL: htt…
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I'm working on an institute-wide pipeline for JCVI and had some trouble running your tool.
Here's my version installed via pip:
```
viral_verify --version
viral_verify, version 0.1.1
```
…
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## Short description of the problem
Hello there,
anvi-setup-pfams fail with Config Error
```
anvi-setup-pfams --pfam-data-dir $SCRATCH/pfam
* No Pfam version specified. Using current release.
…
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This is tested on sparql.uniprot.org on virtuoso 7.2.1 and uniprot release 2015_08
``` sparql
PREFIX rdf:
PREFIX uniprot:
PREFIX taxon:
PREFIX rdfs:
PREFIX up:
PREFIX pfam:
SELECT (COUNT(?this)…
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Hi,
I found that I can extract some new GO terms from pfam database,
for example, in eggnog-mapper result table, TPR_8 can be found in PFAM column, and TPR_8 match go:0005515 in pfam metadatas,…
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Hi,
Sorry that I do not have time to make this properly, meditate and push useful changes to the code.
There are some issues in setupDB.py that do not allow it to work properly when downloading th…
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Yeast has
RNA polymerase I core factor complex (GO:0070860)
A RNA polymerase I-specific transcription factor complex that is required for the transcription of rDNA by RNA polymerase I. In yeast the …
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Dear developers,
We are trying to download VIBRANT (v 1.2.1) database and it's failed to open key file profile_names/VIBRANT_pfam-plasmid_profiles.txt.
```This script will download, extract subset…
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Dear team:
I use trinity & trinotate one year ago with load unipro & pfam, can report the annotation tab with full info of 2 db and gave the go annotation. But, one year passed, I want compare th…