dbolser

[dbolser@ebi-cli-001 Solidi]$ ../virtualenv-1.5.2/virtualenv.py --no-site-packages myenv
New python executable in myenv/bin/python
Installing setuptools.....................
  Complete output from command /nfs/production/panda/ensemblg...ython -c "#!python
\"\"\"Bootstrap setuptoo...




" --always-copy -U setuptools:

dbolser

./python -E -tt -m test.regrtest -v test_anydbm 
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
Traceback (most recent call last):
  File "/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Lib/site.py", line 539, in <module>
    main()
  File "/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Lib/site.py", line 521, in main
    known_paths = addusersitepackages(known_paths)
  File "/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Lib/site.py", line 266, in addusersitepackages
    user_site = getusersitepackages()

dbolser

[dbolser@ebi6-063 Python-2.7.14]$ make
running build
running build_ext
building dbm using ndbm
building '_tkinter' extension
gcc -pthread -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINIT=1 -I/usr/X11/include -I. -IInclude -I./Include -I/usr/local/include -I/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Include -I/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14 -c /nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Modules/_tkinter.c -o build/temp.linux-x86_64-2.7/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Modules/_tkinter.o
gcc -pthread -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DWITH_APPINIT=1 -I/usr/X11/include -I. -IInclude -I./Include -I/usr/local/include -I/nfs/production/panda/ensemblgenomes/development/dbolser/Build/Python-2.7.14/Include -I/nfs/production/panda/ensemblgenomes/development/dbolser/Bu

dbolser

sudo apt-get update | pastebin
Hit:1 http://archive.canonical.com/ubuntu xenial InRelease
Ign:2 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages serena InRelease
Hit:3 http://archive.ubuntu.com/ubuntu xenial InRelease
Get:4 http://archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]
Hit:5 http://www.mirrorservice.org/sites/packages.linuxmint.com/packages serena Release
Get:6 http://archive.ubuntu.com/ubuntu xenial-backports InRelease [102 kB]
Get:7 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Ign:8 https://download.docker.com/linux/ubuntu serena InRelease
Ign:9 https://download.docker.com/linux/ubuntu serena Release

dbolser

### Keybase proof

I hereby claim:

  * I am dbolser on github.
  * I am danbolser (https://keybase.io/danbolser) on keybase.
  * I have a public key whose fingerprint is C6E4 C97A 53DE F36B 560D  8A7B E61C AC74 4189 AE09

To claim this, I am signing this object:

dbolser

### Keybase proof

I hereby claim:

  * I am danbolser on github.
  * I am danbolser (https://keybase.io/danbolser) on keybase.
  * I have a public key whose fingerprint is C6E4 C97A 53DE F36B 560D  8A7B E61C AC74 4189 AE09

To claim this, I am signing this object:

dbolser

SYNOPSIS
       bgzip [-cdhB] [-b virtualOffset] [-s size] [file]

       tabix  [-0lf]  [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol]
       [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]]

DESCRIPTION
       Tabix indexes a TAB-delimited genome position file in.tab.bgz and  cre‐
       ates  an  index file in.tab.bgz.tbi when region is absent from the com‐

dbolser

Program: tabix (TAB-delimited file InderXer)
Version: 0.2.5 (r1005)

Usage:   tabix <in.tab.bgz> [region1 [region2 [...]]]

Options: -p STR     preset: gff, bed, sam, vcf, psltbl [gff]
         -s INT     sequence name column [1]
         -b INT     start column [4]
         -e INT     end column; can be identical to '-b' [5]
         -S INT     skip first INT lines [0]

dbolser

21:13 < dbolser_> On another issue... I'm usign LWP::Simple to grab this: 
                  https://letstalkbitcoin.com/api/v1/forum/threads, which is 
                  "Content-Type:application/json", however, when I decode_json 
                  (using JSON), I get the error: malformed JSON string, neither 
                  array, object, number, string or atom, at character offset 0 
                  (before "\x{ef}\x{bb}\x{bf}{"...") at ./get_and_load_data.plx 
                  line 24
21:14 < dngor> Maybe it's compressed.
21:14 < mauke> no, UTF-8 BOM
21:14 < mauke> a.k.a. malformed JSON

dbolser

diff --git a/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm b/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
index ceec266..739fd31 100644
--- a/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
+++ b/modules/Bio/EnsEMBL/EGPipeline/Xref/UniProtLoader.pm
@@ -196,6 +196,10 @@ sub add_uniprot_xrefs {
 
 sub store_uniprot_xrefs {
   my ( $self, $ddba, $tid, $uniprots, $gene_id, $gene_attribs ) = @_;
+
+  my $n = 0;