Repository 'tmhmm_and_signalp'
hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/tmhmm_and_signalp

Changeset 12:6753a9261390 (2013-04-03)
Previous changeset 11:99b82a2b1272 (2013-04-03) Next changeset 13:dc958c2a963a (2013-04-23)
Commit message:
Uploaded v0.2.1 which removes some stray test files accidentally included in the previous update.
removed:
test-data/four_human_proteins.blast2go.tabular
test-data/four_human_proteins.blastp_nr.top2.tabular
test-data/four_human_proteins.blastp_nr.top3.tabular
test-data/four_human_proteins.blastp_nr.top4.xml
test-data/four_human_proteins.predictnls.tabular
b
diff -r 99b82a2b1272 -r 6753a9261390 test-data/four_human_proteins.blast2go.tabular
--- a/test-data/four_human_proteins.blast2go.tabular Wed Apr 03 10:49:10 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,96 +0,0 @@
-sp|Q9BS26|ERP44_HUMAN GO:0005789 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0006457 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0005788 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0009100 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0045454 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0005515 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0005793 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0006986 endoplasmic reticulum resident protein 44
-sp|Q9BS26|ERP44_HUMAN GO:0003756 endoplasmic reticulum resident protein 44
-sp|Q9NSY1|BMP2K_HUMAN GO:0006468 bmp-2-inducible protein kinase
-sp|Q9NSY1|BMP2K_HUMAN GO:0004674 bmp-2-inducible protein kinase
-sp|Q9NSY1|BMP2K_HUMAN GO:0005730 bmp-2-inducible protein kinase
-sp|Q9NSY1|BMP2K_HUMAN GO:0030500 bmp-2-inducible protein kinase
-sp|Q9NSY1|BMP2K_HUMAN GO:0005524 bmp-2-inducible protein kinase
-sp|Q9NSY1|BMP2K_HUMAN GO:0019208 bmp-2-inducible protein kinase
-sp|P06213|INSR_HUMAN GO:0032148 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005525 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045995 insulin receptor
-sp|P06213|INSR_HUMAN GO:0023014 insulin receptor
-sp|P06213|INSR_HUMAN GO:0031995 insulin receptor
-sp|P06213|INSR_HUMAN GO:0043548 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005901 insulin receptor
-sp|P06213|INSR_HUMAN GO:0008284 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045429 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005625 insulin receptor
-sp|P06213|INSR_HUMAN GO:0009749 insulin receptor
-sp|P06213|INSR_HUMAN GO:0018108 insulin receptor
-sp|P06213|INSR_HUMAN GO:0051384 insulin receptor
-sp|P06213|INSR_HUMAN GO:0043423 insulin receptor
-sp|P06213|INSR_HUMAN GO:0046326 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005829 insulin receptor
-sp|P06213|INSR_HUMAN GO:0042169 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045725 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045821 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045471 insulin receptor
-sp|P06213|INSR_HUMAN GO:0043410 insulin receptor
-sp|P06213|INSR_HUMAN GO:0001933 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005792 insulin receptor
-sp|P06213|INSR_HUMAN GO:0031994 insulin receptor
-sp|P06213|INSR_HUMAN GO:0042593 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005159 insulin receptor
-sp|P06213|INSR_HUMAN GO:0004716 insulin receptor
-sp|P06213|INSR_HUMAN GO:0033574 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045740 insulin receptor
-sp|P06213|INSR_HUMAN GO:0043559 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045444 insulin receptor
-sp|P06213|INSR_HUMAN GO:0010310 insulin receptor
-sp|P06213|INSR_HUMAN GO:0010042 insulin receptor
-sp|P06213|INSR_HUMAN GO:0043560 insulin receptor
-sp|P06213|INSR_HUMAN GO:0010629 insulin receptor
-sp|P06213|INSR_HUMAN GO:0048639 insulin receptor
-sp|P06213|INSR_HUMAN GO:0032403 insulin receptor
-sp|P06213|INSR_HUMAN GO:0051290 insulin receptor
-sp|P06213|INSR_HUMAN GO:0014823 insulin receptor
-sp|P06213|INSR_HUMAN GO:0010008 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005009 insulin receptor
-sp|P06213|INSR_HUMAN GO:0003007 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005524 insulin receptor
-sp|P06213|INSR_HUMAN GO:0030335 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045202 insulin receptor
-sp|P06213|INSR_HUMAN GO:0030238 insulin receptor
-sp|P06213|INSR_HUMAN GO:0007186 insulin receptor
-sp|P06213|INSR_HUMAN GO:0019087 insulin receptor
-sp|P06213|INSR_HUMAN GO:0046777 insulin receptor
-sp|P06213|INSR_HUMAN GO:0019903 insulin receptor
-sp|P06213|INSR_HUMAN GO:0010560 insulin receptor
-sp|P06213|INSR_HUMAN GO:0051425 insulin receptor
-sp|P06213|INSR_HUMAN GO:0033280 insulin receptor
-sp|P06213|INSR_HUMAN GO:0071363 insulin receptor
-sp|P06213|INSR_HUMAN GO:0051897 insulin receptor
-sp|P06213|INSR_HUMAN GO:0032355 insulin receptor
-sp|P06213|INSR_HUMAN GO:0000187 insulin receptor
-sp|P06213|INSR_HUMAN GO:0045840 insulin receptor
-sp|P06213|INSR_HUMAN GO:0032410 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005634 insulin receptor
-sp|P06213|INSR_HUMAN GO:0005899 insulin receptor
-sp|P06213|INSR_HUMAN GO:0034612 insulin receptor
-sp|P06213|INSR_HUMAN GO:0031405 insulin receptor
-sp|P06213|INSR_HUMAN GO:0060267 insulin receptor
-sp|P06213|INSR_HUMAN GO:0031017 insulin receptor
-sp|P06213|INSR_HUMAN GO:0008286 insulin receptor
-sp|P06213|INSR_HUMAN GO:0006355 insulin receptor
-sp|P08100|OPSD_HUMAN GO:0016056 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0071482 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0006468 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0009586 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0046872 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0004930 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0018298 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0060342 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0042622 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0005515 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0060041 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0009881 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0005794 rhodopsin
-sp|P08100|OPSD_HUMAN GO:0005887 rhodopsin
b
diff -r 99b82a2b1272 -r 6753a9261390 test-data/four_human_proteins.blastp_nr.top2.tabular
--- a/test-data/four_human_proteins.blastp_nr.top2.tabular Wed Apr 03 10:49:10 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,5 +0,0 @@
-#Query BLAST hit 1 BLAST hit 2
-sp|Q9BS26|ERP44_HUMAN gi|52487191|ref|NP_055866.1| endoplasmic reticulum resident protein 44 precursor [Homo sapiens] >gi|332832471|ref|XP_003312248.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan troglodytes] >gi|395740740|ref|XP_002820091.2| PREDICTED: endoplasmic reticulum resident protein 44 [Pongo abelii] >gi|397499932|ref|XP_003820684.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan paniscus] >gi|31077035|sp|Q9BS26.1|ERP44_HUMAN RecName: Full=Endoplasmic reticulum resident protein 44; Short=ER protein 44; Short=ERp44; AltName: Full=Thioredoxin domain-containing protein 4; Flags: Precursor >gi|13529224|gb|AAH05374.1| Endoplasmic reticulum protein 44 [Homo sapiens] >gi|18857865|emb|CAC87611.1| ERp44 protein [Homo sapiens] >gi|168267418|dbj|BAG09765.1| thioredoxin domain-containing protein 4 [synthetic construct] >gi|193786731|dbj|BAG52054.1| unnamed protein product [Homo sapiens] >gi|410223880|gb|JAA09159.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410253060|gb|JAA14497.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410293858|gb|JAA25529.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410329535|gb|JAA33714.1| endoplasmic reticulum protein 44 [Pan troglodytes] gi|3043670|dbj|BAA25499.1| KIAA0573 protein [Homo sapiens]
-sp|Q9NSY1|BMP2K_HUMAN gi|38787935|ref|NP_942595.1| BMP-2-inducible protein kinase isoform a [Homo sapiens] >gi|34222653|sp|Q9NSY1.2|BMP2K_HUMAN RecName: Full=BMP-2-inducible protein kinase; Short=BIKe gi|332819458|ref|XP_526576.3| PREDICTED: BMP-2-inducible protein kinase [Pan troglodytes]
-sp|P06213|INSR_HUMAN gi|119395736|ref|NP_000199.2| insulin receptor isoform Long preproprotein [Homo sapiens] >gi|308153655|sp|P06213.4|INSR_HUMAN RecName: Full=Insulin receptor; Short=IR; AltName: CD_antigen=CD220; Contains: RecName: Full=Insulin receptor subunit alpha; Contains: RecName: Full=Insulin receptor subunit beta; Flags: Precursor gi|386830|gb|AAA59452.1| insulin receptor [Homo sapiens]
-sp|P08100|OPSD_HUMAN gi|4506527|ref|NP_000530.1| rhodopsin [Homo sapiens] >gi|114589117|ref|XP_516740.2| PREDICTED: rhodopsin [Pan troglodytes] >gi|297670049|ref|XP_002813191.1| PREDICTED: rhodopsin [Pongo abelii] >gi|332231791|ref|XP_003265078.1| PREDICTED: rhodopsin [Nomascus leucogenys] >gi|397518622|ref|XP_003829483.1| PREDICTED: rhodopsin [Pan paniscus] >gi|426342073|ref|XP_004036340.1| PREDICTED: rhodopsin [Gorilla gorilla gorilla] >gi|129207|sp|P08100.1|OPSD_HUMAN RecName: Full=Rhodopsin; AltName: Full=Opsin-2 >gi|1236137|gb|AAC31763.1| rhodopsin [Homo sapiens] >gi|21928611|dbj|BAC05894.1| seven transmembrane helix receptor [Homo sapiens] >gi|31873264|emb|CAD97623.1| hypothetical protein [Homo sapiens] >gi|85567017|gb|AAI12107.1| Rhodopsin [Homo sapiens] >gi|85567192|gb|AAI12105.1| Rhodopsin [Homo sapiens] >gi|108752084|gb|AAI11452.1| RHO protein [synthetic construct] >gi|117644328|emb|CAL37658.1| hypothetical protein [synthetic construct] >gi|119599650|gb|EAW79244.1| rhodopsin (opsin 2, rod pigment) (retinitis pigmentosa 4, autosomal dominant) [Homo sapiens] >gi|208967306|dbj|BAG73667.1| rhodopsin [synthetic construct] gi|403268285|ref|XP_003926208.1| PREDICTED: rhodopsin [Saimiri boliviensis boliviensis]
b
diff -r 99b82a2b1272 -r 6753a9261390 test-data/four_human_proteins.blastp_nr.top3.tabular
--- a/test-data/four_human_proteins.blastp_nr.top3.tabular Wed Apr 03 10:49:10 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,5 +0,0 @@
-#Query BLAST hit 1 BLAST hit 2 BLAST hit 3
-sp|Q9BS26|ERP44_HUMAN gi|52487191|ref|NP_055866.1| endoplasmic reticulum resident protein 44 precursor [Homo sapiens] >gi|332832471|ref|XP_003312248.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan troglodytes] >gi|395740740|ref|XP_002820091.2| PREDICTED: endoplasmic reticulum resident protein 44 [Pongo abelii] >gi|397499932|ref|XP_003820684.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan paniscus] >gi|31077035|sp|Q9BS26.1|ERP44_HUMAN RecName: Full=Endoplasmic reticulum resident protein 44; Short=ER protein 44; Short=ERp44; AltName: Full=Thioredoxin domain-containing protein 4; Flags: Precursor >gi|13529224|gb|AAH05374.1| Endoplasmic reticulum protein 44 [Homo sapiens] >gi|18857865|emb|CAC87611.1| ERp44 protein [Homo sapiens] >gi|168267418|dbj|BAG09765.1| thioredoxin domain-containing protein 4 [synthetic construct] >gi|193786731|dbj|BAG52054.1| unnamed protein product [Homo sapiens] >gi|410223880|gb|JAA09159.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410253060|gb|JAA14497.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410293858|gb|JAA25529.1| endoplasmic reticulum protein 44 [Pan troglodytes] >gi|410329535|gb|JAA33714.1| endoplasmic reticulum protein 44 [Pan troglodytes] gi|3043670|dbj|BAA25499.1| KIAA0573 protein [Homo sapiens] gi|37183214|gb|AAQ89407.1| TXNDC4 [Homo sapiens]
-sp|Q9NSY1|BMP2K_HUMAN gi|38787935|ref|NP_942595.1| BMP-2-inducible protein kinase isoform a [Homo sapiens] >gi|34222653|sp|Q9NSY1.2|BMP2K_HUMAN RecName: Full=BMP-2-inducible protein kinase; Short=BIKe gi|332819458|ref|XP_526576.3| PREDICTED: BMP-2-inducible protein kinase [Pan troglodytes] gi|119626236|gb|EAX05831.1| BMP2 inducible kinase, isoform CRA_c [Homo sapiens]
-sp|P06213|INSR_HUMAN gi|119395736|ref|NP_000199.2| insulin receptor isoform Long preproprotein [Homo sapiens] >gi|308153655|sp|P06213.4|INSR_HUMAN RecName: Full=Insulin receptor; Short=IR; AltName: CD_antigen=CD220; Contains: RecName: Full=Insulin receptor subunit alpha; Contains: RecName: Full=Insulin receptor subunit beta; Flags: Precursor gi|386830|gb|AAA59452.1| insulin receptor [Homo sapiens] gi|410220302|gb|JAA07370.1| insulin receptor [Pan troglodytes] >gi|410250978|gb|JAA13456.1| insulin receptor [Pan troglodytes] >gi|410291630|gb|JAA24415.1| insulin receptor [Pan troglodytes] >gi|410335477|gb|JAA36685.1| insulin receptor [Pan troglodytes]
-sp|P08100|OPSD_HUMAN gi|4506527|ref|NP_000530.1| rhodopsin [Homo sapiens] >gi|114589117|ref|XP_516740.2| PREDICTED: rhodopsin [Pan troglodytes] >gi|297670049|ref|XP_002813191.1| PREDICTED: rhodopsin [Pongo abelii] >gi|332231791|ref|XP_003265078.1| PREDICTED: rhodopsin [Nomascus leucogenys] >gi|397518622|ref|XP_003829483.1| PREDICTED: rhodopsin [Pan paniscus] >gi|426342073|ref|XP_004036340.1| PREDICTED: rhodopsin [Gorilla gorilla gorilla] >gi|129207|sp|P08100.1|OPSD_HUMAN RecName: Full=Rhodopsin; AltName: Full=Opsin-2 >gi|1236137|gb|AAC31763.1| rhodopsin [Homo sapiens] >gi|21928611|dbj|BAC05894.1| seven transmembrane helix receptor [Homo sapiens] >gi|31873264|emb|CAD97623.1| hypothetical protein [Homo sapiens] >gi|85567017|gb|AAI12107.1| Rhodopsin [Homo sapiens] >gi|85567192|gb|AAI12105.1| Rhodopsin [Homo sapiens] >gi|108752084|gb|AAI11452.1| RHO protein [synthetic construct] >gi|117644328|emb|CAL37658.1| hypothetical protein [synthetic construct] >gi|119599650|gb|EAW79244.1| rhodopsin (opsin 2, rod pigment) (retinitis pigmentosa 4, autosomal dominant) [Homo sapiens] >gi|208967306|dbj|BAG73667.1| rhodopsin [synthetic construct] gi|403268285|ref|XP_003926208.1| PREDICTED: rhodopsin [Saimiri boliviensis boliviensis] gi|109098032|ref|XP_001094250.1| PREDICTED: rhodopsin [Macaca mulatta] >gi|402887068|ref|XP_003906927.1| PREDICTED: rhodopsin [Papio anubis] >gi|355564526|gb|EHH21026.1| hypothetical protein EGK_04000 [Macaca mulatta] >gi|355786368|gb|EHH66551.1| hypothetical protein EGM_03566 [Macaca fascicularis]
b
diff -r 99b82a2b1272 -r 6753a9261390 test-data/four_human_proteins.blastp_nr.top4.xml
--- a/test-data/four_human_proteins.blastp_nr.top4.xml Wed Apr 03 10:49:10 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
b'@@ -1,546 +0,0 @@\n-<?xml version="1.0"?>\n-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n-<BlastOutput>\n-  <BlastOutput_program>blastp</BlastOutput_program>\n-  <BlastOutput_version>BLASTP 2.2.26+</BlastOutput_version>\n-  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n-  <BlastOutput_db>/var/local/blast/ncbi/nr</BlastOutput_db>\n-  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n-  <BlastOutput_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</BlastOutput_query-def>\n-  <BlastOutput_query-len>406</BlastOutput_query-len>\n-  <BlastOutput_param>\n-    <Parameters>\n-      <Parameters_matrix>BLOSUM62</Parameters_matrix>\n-      <Parameters_expect>0.001</Parameters_expect>\n-      <Parameters_gap-open>11</Parameters_gap-open>\n-      <Parameters_gap-extend>1</Parameters_gap-extend>\n-      <Parameters_filter>F</Parameters_filter>\n-    </Parameters>\n-  </BlastOutput_param>\n-  <BlastOutput_iterations>\n-    <Iteration>\n-      <Iteration_iter-num>1</Iteration_iter-num>\n-      <Iteration_query-ID>Query_1</Iteration_query-ID>\n-      <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n-      <Iteration_query-len>406</Iteration_query-len>\n-      <Iteration_hits>\n-        <Hit>\n-          <Hit_num>1</Hit_num>\n-          <Hit_id>gi|52487191|ref|NP_055866.1|</Hit_id>\n-          <Hit_def>endoplasmic reticulum resident protein 44 precursor [Homo sapiens] &gt;gi|332832471|ref|XP_003312248.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan troglodytes] &gt;gi|395740740|ref|XP_002820091.2| PREDICTED: endoplasmic reticulum resident protein 44 [Pongo abelii] &gt;gi|397499932|ref|XP_003820684.1| PREDICTED: endoplasmic reticulum resident protein 44 [Pan paniscus] &gt;gi|31077035|sp|Q9BS26.1|ERP44_HUMAN RecName: Full=Endoplasmic reticulum resident protein 44; Short=ER protein 44; Short=ERp44; AltName: Full=Thioredoxin domain-containing protein 4; Flags: Precursor &gt;gi|13529224|gb|AAH05374.1| Endoplasmic reticulum protein 44 [Homo sapiens] &gt;gi|18857865|emb|CAC87611.1| ERp44 protein [Homo sapiens] &gt;gi|168267418|dbj|BAG09765.1| thioredoxin domain-containing protein 4 [synthetic construct] &gt;gi|193786731|dbj|BAG52054.1| unnamed protein product [Homo sapiens] &gt;gi|410223880|gb|JAA09159.1| endoplasmic reticulum protein 44 [Pan troglodytes] &gt;gi|410253060|gb|JAA14497.1| endoplasmic reticulum protein 44 [Pan troglodytes] &gt;gi|410293858|gb|JAA25529.1| endoplasmic reticulum protein 44 [Pan troglodytes] &gt;gi|410329535|gb|JAA33714.1| endoplasmic reticulum protein 44 [Pan troglodytes]</Hit_def>\n-          <Hit_accession>NP_055866</Hit_accession>\n-          <Hit_len>406</Hit_len>\n-          <Hit_hsps>\n-            <Hsp>\n-              <Hsp_num>1</Hsp_num>\n-              <Hsp_bit-score>847.04</Hsp_bit-score>\n-              <Hsp_score>2187</Hsp_score>\n-              <Hsp_evalue>0</Hsp_evalue>\n-              <Hsp_query-from>1</Hsp_query-from>\n-              <Hsp_query-to>406</Hsp_query-to>\n-              <Hsp_hit-from>1</Hsp_hit-from>\n-              <Hsp_hit-to>406</Hsp_hit-to>\n-              <Hsp_query-frame>0</Hsp_query-frame>\n-              <Hsp_hit-frame>0</Hsp_hit-frame>\n-              <Hsp_identity>406</Hsp_identity>\n-              <Hsp_positive>406</Hsp_positive>\n-              <Hsp_gaps>0</Hsp_gaps>\n-              <Hsp_align-len>406</Hsp_align-len>\n-              <Hsp_qseq>MHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRFSQMLHPIFEEASDVIKEEFPNENQVVFARVDCDQHSDIAQRYRISKYPTLKLFRNGMMMKREYRGQRSVKALADYIRQQKSDPIQEIRDLAEITTLDRSKRNIIGYFEQKDSDNYRVFERVANILHDDCA'..b'AEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>\n-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq>\n-              <Hsp_midline>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCN EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA+IYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_midline>\n-            </Hsp>\n-          </Hit_hsps>\n-        </Hit>\n-        <Hit>\n-          <Hit_num>4</Hit_num>\n-          <Hit_id>gi|3024288|sp|Q28886.1|OPSD_MACFA</Hit_id>\n-          <Hit_def>RecName: Full=Rhodopsin &gt;gi|21466156|gb|AAB33079.2| opsin [Macaca fascicularis]</Hit_def>\n-          <Hit_accession>Q28886</Hit_accession>\n-          <Hit_len>348</Hit_len>\n-          <Hit_hsps>\n-            <Hsp>\n-              <Hsp_num>1</Hsp_num>\n-              <Hsp_bit-score>705.286</Hsp_bit-score>\n-              <Hsp_score>1819</Hsp_score>\n-              <Hsp_evalue>0</Hsp_evalue>\n-              <Hsp_query-from>1</Hsp_query-from>\n-              <Hsp_query-to>348</Hsp_query-to>\n-              <Hsp_hit-from>1</Hsp_hit-from>\n-              <Hsp_hit-to>348</Hsp_hit-to>\n-              <Hsp_query-frame>0</Hsp_query-frame>\n-              <Hsp_hit-frame>0</Hsp_hit-frame>\n-              <Hsp_identity>341</Hsp_identity>\n-              <Hsp_positive>344</Hsp_positive>\n-              <Hsp_gaps>0</Hsp_gaps>\n-              <Hsp_align-len>348</Hsp_align-len>\n-              <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_qseq>\n-              <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNAEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLFGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTVKEARAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSASIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_hseq>\n-              <Hsp_midline>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCN EGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMI+IFFCYGQLVFTVKEA AQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSA+IYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA</Hsp_midline>\n-            </Hsp>\n-          </Hit_hsps>\n-        </Hit>\n-      </Iteration_hits>\n-      <Iteration_stat>\n-        <Statistics>\n-          <Statistics_db-num>23216691</Statistics_db-num>\n-          <Statistics_db-len>7978792554</Statistics_db-len>\n-          <Statistics_hsp-len>143</Statistics_hsp-len>\n-          <Statistics_eff-space>955055176905</Statistics_eff-space>\n-          <Statistics_kappa>0.041</Statistics_kappa>\n-          <Statistics_lambda>0.267</Statistics_lambda>\n-          <Statistics_entropy>0.14</Statistics_entropy>\n-        </Statistics>\n-      </Iteration_stat>\n-    </Iteration>\n-  </BlastOutput_iterations>\n-</BlastOutput>\n\\ No newline at end of file\n'
b
diff -r 99b82a2b1272 -r 6753a9261390 test-data/four_human_proteins.predictnls.tabular
--- a/test-data/four_human_proteins.predictnls.tabular Wed Apr 03 10:49:10 2013 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
[
@@ -1,2 +0,0 @@
-#ID NLS start NLS seq NLS pattern Type ProtCount %NucProt ProtList ProtLoci
-sp|P06213|INSR_HUMAN 758 SRKRRS [STQM]RKRR[STQM] Potential 1 100 mklp_human nuc