(hbp) [524] [11:52] [cthoyt@wlan-241:~/dev/pypath/src]
$ python pypath/bel.py bel
:: Module `cairo` not available.
Some plotting functionalities won't be accessible.
:: Module `pygraphviz` not available.
You don't need it unless you want to export dot files.
:: Module `pysftp` not available.
Only downloading of a small number of resources
relies on this module.
Please install by PIP if it is necessary for you.
:: Module `bioservices` not available.
No module `cairo` available.
Some plotting functionalities won't be accessible.
:: Module `hcluster` not available.
=== d i s c l a i m e r ===
All data coming with this module
either as redistributed copy or downloaded using the
programmatic interfaces included in the present module
are available under public domain, are free to use at
least for academic research or education purposes.
Please be aware of the licences of all the datasets
you use in your analysis, and please give appropriate
credits for the original sources when you publish your
results. To find out more about data sources please
look at `pypath.descriptions` and
`pypath.data_formats.urls`.
> New session started,
session ID: 'dnzki'
logfile: './log/dnzki.log'
pypath version: 0.7.121
Downloading `` from www.uniprot.org -- 0.00B downloaded: : 1.34Mit [00:39, 12.2kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/582ab5c0b5fffa42fb3e8d1757901ea1-`.
:: Loading data from cache previously downloaded from www.uniprot.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/582ab5c0b5fffa42fb3e8d1757901ea1-`.
> TRIP
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 430kit [00:05, 37.7kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/fe747bcda0777e9f7cd8b1ab47db1538-show`.
could not find uniprot for Gơq/11
could not find uniprot for Ƣ-tubulin-5
could not find uniprot for ơ-actinin
could not find uniprot for ơ-actinin-1
could not find uniprot for ơ1-syntrophin
could not find uniprot for PLCƣ1
could not find uniprot for VAMP
could not find uniprot for Homer
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 125kit [00:01, 21.5kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/cb1a9773e75b45415423b000eb70a4a4-show`.
could not find uniprot for TRPC2
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/76731af40f25e153c424547e40373728-show`.
could not find uniprot for 14-3-3 protein Ƣ/ơ
could not find uniprot for 14-3-3 protein ƥ
could not find uniprot for 14-3-3 protein Ƨ
could not find uniprot for ATP synthase Ƣ
could not find uniprot for Gơq
could not find uniprot for Gz-ơ
could not find uniprot for NKAơ1
could not find uniprot for NKAơ2
could not find uniprot for NKAơ3
could not find uniprot for ơSNAP
could not find uniprot for PKCƢ
could not find uniprot for PLCƢ1
could not find uniprot for PLCƣ2
could not find uniprot for PLCƢ2
could not find uniprot for PLCƢ3
could not find uniprot for RyR
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/66325b3451fbe1d75a70d463396b725c-show`.
could not find uniprot for Gơi2
could not find uniprot for Ƣ-catenin
could not find uniprot for ƢV-spectrin
could not find uniprot for ơII-spectrin
could not find uniprot for SHANK
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/c5f2ffd31855a92f7e488289af6d958a-show`.
could not find uniprot for CaMKIIƢ
could not find uniprot for Gơi3
could not find uniprot for ƢII-spectrin
could not find uniprot for ƢIII-spectrin
could not find uniprot for ơ-actinin-4
could not find uniprot for ơ2-actin
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/ce6ceb6edff7641e5526d53c5a68f460-show`.
could not find uniprot for PKCơ
could not find uniprot for TRPC2
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/7f61ed4b9bf1b751d96529758c866ce5-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 383kit [00:03, 59.8kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/07a8b3ce8b01eb8c5b54e58fac2278f5-show`.
could not find uniprot for Actin
could not find uniprot for Akt
could not find uniprot for AMPKơ2
could not find uniprot for CaMKII
could not find uniprot for Catenin-ơ2
could not find uniprot for Catenin-Ƥ2
could not find uniprot for Ƣ-arrestin 2
could not find uniprot for Ƣ-tubulin-3
could not find uniprot for KPNƢ1
could not find uniprot for KvƢ2
could not find uniprot for ơ-tubulin-1A
could not find uniprot for ơ-tubulin-1B
could not find uniprot for ơENaC
could not find uniprot for PI3K-p85Ƣ
could not find uniprot for PI3K-p85ơ
could not find uniprot for PKARIIơ
could not find uniprot for PKC
could not find uniprot for PKCƥ
could not find uniprot for PPARơ
could not find uniprot for PRKD1/PKCƬ
could not find uniprot for Tubulin
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/788e78790c8b92e236360a36dfcc1256-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/7ead76a9f4f53bed612d584d81532e75-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/21482ce48ae07c59c560a6f88668cf17-show`.
could not find uniprot for ƣ-actin
could not find uniprot for Ƣ-actin
could not find uniprot for Ƣ-arrestin 1
could not find uniprot for ơ2-integrin
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 166kit [00:02, 22.6kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/227671676e74327da717392ec065629c-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/00bdaab72698946e2c53a3ba1e161996-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 82.8kit [00:01, 18.9kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/fecb73d49aba8341fc1db62417212ff8-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 100kit [00:01, 19.6kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/a358ff6a4e27f47cf3ee45365f6ac052-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/adf5d53c1038cdf2a3c0935761f240ab-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/d06c932e82cdc2a2073b1dcd1f3a4de6-show`.
could not find uniprot for 14-3-3ƣ
could not find uniprot for ƣENaC
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 57.0kit [00:01, 11.4kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/2d43a4d3fbf33eefd82daa86efe3622f-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 97.5kit [00:01, 19.2kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/4eda1e60f9b24541231a1253f943b8e0-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/2363983add5b88011be3eec09f638a05-show`.
could not find uniprot for PLCƤ1
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 99.7kit [00:01, 20.9kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/b1448c259747e453e680439cf5c5cb91-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 197kit [00:02, 35.3kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/cb9900b1b9f2cef7716d2c6f40942f89-show`.
could not find uniprot for NovelProtein/NP9
could not find uniprot for Unnamed protein (BAE)
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/69788e06e95a5311786f04508170199e-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/91bcafcd37e96d2c2a27763379b66f16-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/62a420224285648723fa67eb83a988b9-show`.
could not find uniprot for eIF2ơ
could not find uniprot for ƣ-adaptin
could not find uniprot for Ƣ-Trcp1
could not find uniprot for Ƣ-Trcp2
could not find uniprot for H2-D1
could not find uniprot for H2-K1
could not find uniprot for ơ-actinin-2
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 122kit [00:01, 16.9kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/80ba011a21cfecb35f405c1a1e49aecb-show`.
Downloading `show` from www.trpchannel.org -- 0.00B downloaded: : 87.2kit [00:02, 12.8kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/909a3c98fd81f2a635605bcc0c5a268c-show`.
:: Loading data from cache previously downloaded from www.trpchannel.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/adb2b5376d5b4e53192c2bef37d3c492-show`.
:: Loading 'uniprot-sec' to 'uniprot-pri' mapping table
Downloading `` from www.uniprot.org -- 0.00B downloaded: : 0.00it [00:00, ?it/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/15ff42ede8eb6a22b432a886075c2203-`.
Downloading `sec_ac.txt` from ftp.uniprot.org -- 29.32MB downloaded: 100%|█| 29.3M/29.3M [00:14<00:00, 1.25Mi Downloading `sec_ac.txt` from ftp.uniprot.org -- 29.32MB downloaded: 100%|█| 29.3M/29.3M [00:14<00:00, 1.25Mi Downloading `sec_ac.txt` from ftp.uniprot.org -- 29.32MB downloaded: 100%|█| 29.3M/29.3M [00:14<00:00, 1.25Mit/s]
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/.pypath/cache/49314fe217bf0f2a5544a2c4314b4adf-sec_ac.txt`.
Reading from file -- finished: : 0.00it [00:00, ?it/s]
:: Loading 'genesymbol' to 'trembl' mapping table
Downloading `` from www.uniprot.org -- 0.00B downloaded: : 2.03Mit [00:15, 130kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/ef6ae0ad05e8af48aff2d74a77bd4520-`.
Processing nodes -- finished: 100%|█████████████████████████████████████████| 370/370 [00:00<00:00, 420kit/s]
Processing edges -- finished: 100%|█████████████████████████████████████████| 370/370 [00:00<00:00, 241kit/s]
Processing attributes -- finished: 100%|███████████████████████████████████| 370/370 [00:00<00:00, 9.61kit/s]
> SPIKE
Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 0%| | 11.4k/3.89M [00:03<37:08, 1.74kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 0%| | 8.09k/3.89M [00:04<42:02, 1.54kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 0%| | 9.28k/3.89M [00:04<32:09, 2.01kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 1%| | 22.3k/3.89M [00:04<22:50, 2.82kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 1%| | 58.0k/3.89M [00:04<16:03, 3.98kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 2%| | 86.5k/3.89M [00:04<11:16, 5.62kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 2%| | 94.8k/3.89M [00:05<08:02, 7.86kit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 3%| | 116k/3.89M [00:05<05:56, 10.6kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 3%| | 130k/3.89M [00:05<04:20, 14.5kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 4%| | 148k/3.89M [00:05<03:11, 19.6kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 4%| | 170k/3.89M [00:05<02:22, 26.2kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 5%| | 191k/3.89M [00:06<01:47, 34.5kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 6%| | 218k/3.89M [00:06<01:21, 45.0kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 6%| | 247k/3.89M [00:06<01:03, 57.8kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 7%| | 278k/3.89M [00:06<00:49, 72.9kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 8%| | 309k/3.89M [00:06<00:40, 89.5kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 9%| | 341k/3.89M [00:06<00:33, 107kit/s] Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 27%|▎| 1.04M/3.89M [00:08<00:07, 381kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 29%|▎| 1.14M/3.89M [00:09<00:08, 308kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 31%|▎| 1.20M/3.89M [00:09<00:08, 334kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 33%|▎| 1.27M/3.89M [00:09<00:07, 356kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 35%|▎| 1.36M/3.89M [00:09<00:06, 387kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 37%|▎| 1.43M/3.89M [00:09<00:06, 404kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 37%|▎| 1.45M/3.89M [00:09<00:05, 423kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 40%|▍| 1.54M/3.89M [00:10<00:05, 407kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 42%|▍| 1.63M/3.89M [00:10<00:05, 395kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 44%|▍| 1.72M/3.89M [00:10<00:04, 442kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 46%|▍| 1.81M/3.89M [00:10<00:05, 392kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 48%|▍| 1.88M/3.89M [00:10<00:04, 442kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 49%|▍| 1.91M/3.89M [00:10<00:04, 462kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 51%|▌| 1.97M/3.89M [00:11<00:03, 481kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 53%|▌| 2.07M/3.89M [00:11<00:03, 540kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 54%|▌| 2.12M/3.89M [00:11<00:03, 557kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 58%|▌| 2.26M/3.89M [00:11<00:03, 485kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 60%|▌| 2.35M/3.89M [00:11<00:03, 468kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 65%|▋| 2.51M/3.89M [00:11<00:02, 535kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 68%|▋| 2.63M/3.89M [00:11<00:01, 641kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 69%|▋| 2.70M/3.89M [00:12<00:01, 660kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 72%|▋| 2.78M/3.89M [00:12<00:01, 681kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 74%|▋| 2.88M/3.89M [00:12<00:01, 727kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 77%|▊| 2.98M/3.89M [00:12<00:01, 734kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 80%|▊| 3.10M/3.89M [00:12<00:00, 810kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 82%|▊| 3.18M/3.89M [00:12<00:00, 833kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 84%|▊| 3.28M/3.89M [00:12<00:00, 852kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 87%|▊| 3.38M/3.89M [00:12<00:00, 856kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 91%|▉| 3.53M/3.89M [00:12<00:00, 931kit/s Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 98%|▉| 3.80M/3.89M [00:13<00:00, 1.10Mit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- busy: 100%|▉| 3.89M/3.89M [00:13<00:00, 1.18Mit/ Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- 3.89MB downloaded: 100%|█| 3.89M/3.89M [00:13<00 Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- 3.89MB downloaded: 100%|█| 3.89M/3.89M [00:13<00 Downloading `LatestSpikeDB.xml.zip` from www.cs.tau.ac.il -- 3.89MB downloaded: : 4.03Mit [00:13, 306kit/s]
:: Ready. Resulted `zip extracted data` of type dict of file objects.
:: Local file at `/Users/cthoyt/.pypath/cache/da5f2fa9bc0a975c375ed43448233ece-LatestSpikeDB.xml.zip`.
:: Loading 'genesymbol' to 'uniprot' mapping table
Downloading `` from www.uniprot.org -- 0.00B downloaded: : 277kit [00:10, 16.3kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/c4e5738ebca52db4a3ebc6b5b07757e9-`.
:: Loading 'genesymbol-syn' to 'uniprot' mapping table
Downloading `` from www.uniprot.org -- 0.00B downloaded: : 292kit [00:07, 32.8kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/8927495f7a090077145f56f74d2842c4-`.
Processing nodes -- finished: 100%|█████████████████████████████████████| 3.72k/3.72k [00:00<00:00, 623kit/s]
Processing edges -- finished: 100%|█████████████████████████████████████| 3.72k/3.72k [00:00<00:00, 243kit/s]
Processing attributes -- finished: 100%|███████████████████████████████| 3.72k/3.72k [00:00<00:00, 4.19kit/s]
> SignaLink3
Reading file -- finished: 100%|████████████████████████████████████████| 16.3M/16.3M [00:00<00:00, 40.6Mit/s]
:: Loading 'genesymbol' to 'swissprot' mapping table
:: Loading data from cache previously downloaded from www.uniprot.org
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/c4e5738ebca52db4a3ebc6b5b07757e9-`.
:: Loading 'genesymbol-syn' to 'swissprot' mapping table
Processing nodes -- finished: 100%|█████████████████████████████████████| 6.94k/6.94k [00:00<00:00, 645kit/s]
Processing edges -- finished: 100%|█████████████████████████████████████| 6.94k/6.94k [00:00<00:00, 175kit/s]
Processing attributes -- finished: 100%|███████████████████████████████| 6.94k/6.94k [00:01<00:00, 3.91kit/s]
> Guide2Pharma
Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 1%| | 53.8k/3.69M [00:00<00:33, 10 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 11%| | 411k/3.69M [00:00<00:21, 152 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 26%|▎| 947k/3.69M [00:00<00:12, 214 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 40%|▍| 1.49M/3.69M [00:00<00:07, 29 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 52%|▌| 1.90M/3.69M [00:00<00:04, 38 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 58%|▌| 2.14M/3.69M [00:00<00:02, 52 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 73%|▋| 2.69M/3.69M [00:01<00:01, 70 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 83%|▊| 3.08M/3.69M [00:01<00:00, 93 Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: 92%|▉| 3.39M/3.69M [00:01<00:00, 1. Downloading `interactions.csv` from www.guidetopharmacology.org -- busy: : 3.73Mit [00:01, 1.46Mit/s] Downloading `interactions.csv` from www.guidetopharmacology.org -- 3.69MB downloaded: 100%|█| 3.69M/3.69M [00 Downloading `interactions.csv` from www.guidetopharmacology.org -- 3.69MB downloaded: 100%|█| 3.69M/3.69M [00 Downloading `interactions.csv` from www.guidetopharmacology.org -- 3.69MB downloaded: : 4.00Mit [00:01, 2.85Mit/s]
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/.pypath/cache/61ddc6eb0ff8ef877c52f5d1a81b9db2-interactions.csv`.
Processing nodes -- finished: 100%|█████████████████████████████████████████| 291/291 [00:00<00:00, 335kit/s]
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> CA1
Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 0%| | 0.00/509k [00:00<?, Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 3%| | 14.5k/509k [00:01<01 Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 8%| | 40.0k/509k [00:01<00 Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 18%|▏| 89.2k/509k [00:01<00 Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 29%|▎| 147k/509k [00:01<00: Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 49%|▍| 249k/509k [00:01<00: Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: 78%|▊| 396k/509k [00:01<00: Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- busy: : 523kit [00:01, 54.4kit/s] Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- 508.71kB downloaded: 100%|█| 509k/ Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- 508.71kB downloaded: 100%|█| 509k/ Downloading `Maayan_SOM_External_Files.zip` from science.sciencemag.org -- 508.71kB downloaded: : 613kit [00:01, 320kit/s]
:: Ready. Resulted `zip extracted data` of type dict of unicode strings.
:: Local file at `/Users/cthoyt/.pypath/cache/a221dcf8846ad398634f9997a1011b9e-Maayan_SOM_External_Files.zip`.
Processing nodes -- finished: 100%|█████████████████████████████████████| 1.48k/1.48k [00:00<00:00, 581kit/s]
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Processing attributes -- finished: 100%|███████████████████████████████| 1.48k/1.48k [00:00<00:00, 4.87kit/s]
> ARN
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/dev/pypath/src/pypath/data/arn_curated.csv`.
Processing nodes -- finished: 100%|███████████████████████████████████████| 95.0/95.0 [00:00<00:00, 102kit/s]
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Processing attributes -- finished: 100%|█████████████████████████████████| 95.0/95.0 [00:00<00:00, 1.76kit/s]
> NRF2ome
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/dev/pypath/src/pypath/data/nrf2ome.csv`.
Processing nodes -- finished: 100%|█████████████████████████████████████████| 109/109 [00:00<00:00, 236kit/s]
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> Macrophage
Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com: initializing curl: 0.00it [00:00, ?it/s Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- busy: : 0.00it [00:00, ?it/s] Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- busy: 48%|▍| 588k/1.22M [00: Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- busy: : 1.74Mit [00:00, 708ki Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- 1.22MB downloaded: 100%|█| 1. Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- 1.22MB downloaded: 100%|█| 1. Downloading `12918_2010_452_MOESM2_ESM.XLS` from static-content.springer.com -- 1.22MB downloaded: : 1.43Mit [00:00, 2.06Mit/s]
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/.pypath/cache/e7b73bcce14b977a3e384518d40f3637-12918_2010_452_MOESM2_ESM.XLS`.
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Processing attributes -- finished: 100%|███████████████████████████████| 4.86k/4.86k [00:00<00:00, 12.4kit/s]
> DeathDomain
Downloading `show` from www.deathdomain.org -- busy: 0%| | 0.00/296 [00:01<?, ?it/s]
:: Error in `pypath.dataio.deathdomain_interactions()`. Skipping to next resource.
:: ("object of type 'NoneType' has no len()",)
File "/Users/cthoyt/dev/pypath/src/pypath/main.py", line 2284, in read_data_file
infile = inputFunc(**settings.inputArgs)
File "/Users/cthoyt/dev/pypath/src/pypath/dataio.py", line 8355, in deathdomain_interactions
soup = bs4.BeautifulSoup(html, 'lxml')
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/bs4/__init__.py", line 245, in __init__
elif len(markup) <= 256 and (
### ERROR ###### deathdomain_interactions: No such file or dataio function! :(
> PDZBase
Downloading `allinteractions` from abc.med.cornell.edu -- 433.27kB downloaded: 100%|█| 433k/433k [00:01<00:00 Downloading `allinteractions` from abc.med.cornell.edu -- 433.27kB downloaded: 100%|█| 433k/433k [00:01<00:00 Downloading `allinteractions` from abc.med.cornell.edu -- 433.27kB downloaded: : 443kit [00:01, 339kit/s]
:: Ready. Resulted `plain text` of type unicode string.
:: Local file at `/Users/cthoyt/.pypath/cache/d16213901cd27de19ef825068fd8faa6-allinteractions`.
Processing nodes -- finished: 100%|█████████████████████████████████████████| 125/125 [00:00<00:00, 278kit/s]
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> Signor
Downloading `download_entity.php` from signor.uniroma2.it -- 0.00B downloaded: : 8.67Mit [00:03, 2.02Mit/s]
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/.pypath/cache/a357fe979f74a823bf4a42150a6dcf33-download_entity.php`.
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Processing attributes -- finished: 100%|███████████████████████████████| 10.1k/10.1k [00:03<00:00, 3.33kit/s]
> HPMR
Downloading HPMR data -- finished: 100%|████████████████████████████████| 1.27k/1.27k [26:15<00:00, 1.04s/it]
Processing nodes -- finished: 100%|█████████████████████████████████████████| 579/579 [00:00<00:00, 491kit/s]
Processing edges -- finished: 100%|█████████████████████████████████████████| 579/579 [00:00<00:00, 213kit/s]
Processing attributes -- finished: 100%|███████████████████████████████████| 579/579 [00:00<00:00, 1.33kit/s]
> CellPhoneDB
Downloading `interactions_cellphonedb.csv` from www.cellphonedb.org -- 128.54kB downloaded: 100%|█| 129k/129k Downloading `interactions_cellphonedb.csv` from www.cellphonedb.org -- 128.54kB downloaded: 100%|█| 129k/129k Downloading `interactions_cellphonedb.csv` from www.cellphonedb.org -- 128.54kB downloaded: : 169kit [00:00, 335kit/s]
:: Ready. Resulted `plain text` of type file object.
:: Local file at `/Users/cthoyt/.pypath/cache/142eb923569634ee61ca1d56843de13a-interactions_cellphonedb.csv`.
Traceback (most recent call last):
File "pypath/bel.py", line 307, in <module>
main()
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 1134, in invoke
Command.invoke(self, ctx)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/Users/cthoyt/.virtualenvs/hbp/lib/python3.7/site-packages/click/decorators.py", line 17, in new_func
return f(get_current_context(), *args, **kwargs)
File "pypath/bel.py", line 291, in _main
resource = get_resource(resource_name)
File "pypath/bel.py", line 282, in get_resource
pa.init_network(data_formats.pathway)
File "/Users/cthoyt/dev/pypath/src/pypath/main.py", line 1665, in init_network
cache_files=cache_files)
File "/Users/cthoyt/dev/pypath/src/pypath/main.py", line 5816, in load_resources
reread=reread, redownload=redownload)
File "/Users/cthoyt/dev/pypath/src/pypath/main.py", line 5884, in load_resource
redownload=redownload)
File "/Users/cthoyt/dev/pypath/src/pypath/main.py", line 2371, in read_data_file
for line in infile: # XXX: here could be used enumerate for lnum
File "/Users/cthoyt/dev/pypath/src/pypath/dataio.py", line 5265, in cellphonedb_interactions
if uniprot1 in ligands and uniprot2 in receptors:
NameError: name 'ligands' is not defined