Error

[dudimarcus]

The sequence below gave the following error:

query ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSYLAYADGKPVVICSTGIGGPSTSIAVEELAQ LGVNTFLRVGTTGAIQPHVNVGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHIGVTASSDTFY PGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMVSAVSIVVA AAKKLLA

Setting host to http://beta.cathdb.info/ Submitting sequence... POST /search/by_funfhmmer 202 Sequence submitted... got task id: de649055d6545dd54d0dc7203b2406b4 GET /search/by_funfhmmer/check/de649055d6545dd54d0dc7203b2406b4 200 status: running GET /search/by_funfhmmer/check/de649055d6545dd54d0dc7203b2406b4 200 status: running GET /search/by_funfhmmer/check/de649055d6545dd54d0dc7203b2406b4 200 status: running GET /search/by_funfhmmer/check/de649055d6545dd54d0dc7203b2406b4 200 status: running GET /search/by_funfhmmer/check/de649055d6545dd54d0dc7203b2406b4 200 status: done Retrieving scan results for task id: de649055d6545dd54d0dc7203b2406b4 GET /search/by_funfhmmer/results/de649055d6545dd54d0dc7203b2406b4?max_hits=50 200 HIT 3.40.50.1580/FF/5979 9.6e-138 Uridine phosphorylase HIT 3.40.50.1580/FF/2436 1.2e-43 Uridine phosphorylase HIT 3.40.50.1580/FF/4594 1.7e-34 Phosphorylase superfamily protein HIT 3.40.50.1580/FF/6092 2.7e-30 Purine nucleoside phosphorylase DeoD-type HIT 3.40.50.1580/FF/4309 4.6e-30 Purine or other phosphorylase family 1 HIT 3.40.50.1580/FF/3469 2.1e-23 Uridine phosphorylase HIT 3.40.50.1580/FF/6091 1.6e-15 Uridine phosphorylase 1, isoform CRA_a HIT 3.40.50.1580/FF/2937 5.2e-10 Uridine phosphorylase HIT 3.40.50.1580/FF/6120 2.9e-07 MTA/SAH nucleosidase HIT 3.40.50.1580/FF/5988 1.8e-04 Putative AMP nucleosidase Retrieving alignment [1] 3.40.50.1580/FF/5979 ... POST /search/by_sequence/align_hit 200 ! Error: id '1rxsj00' does not look like a CATH domain id at cath-tools-seqscan-master/script/../lib/Cath/Tools/Seqscan.pm line 210. Cath::Tools::Seqscan::get_domain_lookup_from_alignment('IO::String=GLOB(0x7f8243b51ce8)') called at cath-tools-seqscan-master/script/../lib/Cath/Tools/Seqscan.pm line 157 Cath::Tools::Seqscan::run('Cath::Tools::Seqscan=HASH(0x7f8243a1c0c0)') called at ../cath-tools-seqscan-master/script/cath-tools-seqscan.pl line 13

[sillitoe]

Thanks.

I was being too strict expecting only uppercase chain codes.

I've added a test to cover:

prove -l t/gh_006.t

I'll let you close the ticket if you're happy

[dudimarcus]

Great! works now.

[dudimarcus]

Something might have changed in the server as the error is back now:

Setting host to http://beta.cathdb.info/ Submitting sequence... POST /search/by_funfhmmer 202 Sequence submitted... got task id: d1ae65fae5b1cdda25d6e3687f56bd66 GET /search/by_funfhmmer/check/d1ae65fae5b1cdda25d6e3687f56bd66 200 status: done Retrieving scan results for task id: d1ae65fae5b1cdda25d6e3687f56bd66 GET /search/by_funfhmmer/results/d1ae65fae5b1cdda25d6e3687f56bd66?max_hits=5 200 HIT 1.10.565.10/FF/338 4.5e-195 Estrogen receptor alpha variant U1 HIT 1.10.565.10/FF/1898 9.4e-153 Estrogen receptor HIT 1.10.565.10/FF/5096 7.7e-115 Estrogen receptor beta 1 HIT 3.30.50.10/FF/4124 6.5e-39 Estrogen receptor beta 4 HIT 1.10.565.10/FF/5028 3.9e-30 Retinoic acid receptor RXR-beta Retrieving alignment [1] 1.10.565.10/FF/338 ... POST /search/by_sequence/align_hit 200 ! Error: id '1ereE00 ' does not look like a CATH domain id at cath/cath-tools-seqscan-master/script/../lib/Cath/Tools/Seqscan.pm line 220. Cath::Tools::Seqscan::get_domain_lookup_from_alignment('IO::String=GLOB(0x7ffe9902cfe0)') called at cath/cath-tools-seqscan-master/script/../lib/Cath/Tools/Seqscan.pm line 165 Cath::Tools::Seqscan::run('Cath::Tools::Seqscan=HASH(0x7ffe97796ac0)') called at ../cath-tools-seqscan-master/script/cath-tools-seqscan.pl line 13

[sillitoe]

This is me fixing #7 - 2 secs

[sillitoe]

Made some changes to the backend server to accomodate #7

3f6f2114f4493078903bc6104a45498edb65138d allows this code to work with those changes