| Next changeset 1:3175a61346e8 (2021-03-29) |
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Commit message:
"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87" |
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added:
macros.xml spring_cross.xml test-data/cross/pdb.ffdata test-data/cross/pdb.ffindex test-data/cross/reference.tabular test-data/ffindex_indices.loc test-data/map/chains.tabular test-data/map/mapped.reference.tabular test-data/mcc/biogrid_fret.txt test-data/mcc/human_hv1h2.png test-data/mcc/human_hv1h2.txt test-data/minz/NP_000282.1.hhr test-data/minz/NP_000290.2.hhr test-data/minz/NP_000548.2.hhr test-data/minz/NP_000836.2.hhr test-data/minz/pdb70_random.txt test-data/minz/pdb70_result.0.txt test-data/minz/pdb70_result.1.txt test-data/model/ACE2_HUMAN.hhr test-data/model/SPIKE_SARS2.hhr test-data/model/crossreference.txt test-data/model/hhr.ffdata test-data/model/hhr.ffindex test-data/model/log.txt test-data/model/pairs.txt test-data/model/pdb_structures.ffdata test-data/model/pdb_structures.ffindex test-data/model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb tool-data/ffindex_indices.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r dbbcc7cd889f macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,89 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">springsuite</requirement> + <yield /> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="ffindex_single_inputs"> + <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." /> + <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." /> + </xml> + + <xml name="ffindex_single_inputs_hhr"> + <param name="ffdata" type="data" format="ffdata" label="HHR Database" help="Database Data file." /> + <param name="ffindex" type="data" format="ffindex" label="HHR Database Index" help="Database Index file." /> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1021/ci300579r</citation> + </citations> + </xml> + <xml name="logfile"> + <param name="logfile" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log file" /> + </xml> + + <xml name="pdb_source"> + <conditional name="pdb_source"> + <param name="pdb_source_selector" type="select" label="Custom or built-in PDB" help="Built-ins have been indexed using ffindex"> + <option value="indexed" selected="true">Use a built-in index</option> + <option value="history">Use a PDB index from history</option> + </param> + <when value="indexed"> + <param name="pdb" type="select" label="Select PDB database" help=""> + <options from_data_table="ffindex_indices"> + <filter type="sort_by" column="0" /> + <filter type="static_value" column="3" value="pdb" /> + <validator type="no_options" message="No indices are available" /> + </options> + </param> + </when> + <when value="history"> + <expand macro="ffindex_single_inputs" /> + </when> + </conditional> + </xml> + <xml name="hhr_source"> + <conditional name="hhr_source"> + <param name="hhr_source_selector" type="select" label="Custom or built-in HHR index" help="Built-ins have been indexed using ffindex"> + <option value="indexed" selected="true">Use a built-in index</option> + <option value="history">Use a HHR index from history</option> + </param> + <when value="indexed"> + <param name="hhr" type="select" label="Select HHR database" help=""> + <options from_data_table="ffindex_indices"> + <filter type="sort_by" column="0" /> + <filter type="static_value" column="3" value="hhr" /> + <validator type="no_options" message="No indices are available" /> + </options> + </param> + </when> + <when value="history"> + <expand macro="ffindex_single_inputs_hhr" /> + </when> + </conditional> + </xml> + + <token name="@pdb_source@"> + #if $pdb_source.pdb_source_selector == 'indexed': + -d '${pdb_source.pdb.fields.path}.ffdata' + -i '${pdb_source.pdb.fields.path}.ffindex' + #else + -d '$pdb_source.ffdata' + -i '$pdb_source.ffindex' + #end if + </token> + <token name="@hhr_source@"> + #if $hhr_source.hhr_source_selector == 'indexed': + -dh '${hhr_source.hhr.fields.path}.ffdata' + -ih '${hhr_source.hhr.fields.path}.ffindex' + #else + -dh '$hhr_source.ffdata' + -ih '$hhr_source.ffindex' + #end if + </token> +</macros> |
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| diff -r 000000000000 -r dbbcc7cd889f spring_cross.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spring_cross.xml Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,51 @@ +<tool id="spring_cross" name="SPRING Cross" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>reference builder</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + spring_cross.py + @pdb_source@ + -o '$output' + -g '$log' + ]]></command> + <inputs> + <expand macro="pdb_source" /> + <expand macro="logfile" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="SPRING Cross Reference" /> + <data format="txt" name="log" label="SPRING Cross Log"> + <filter>logfile</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <conditional name="pdb_source"> + <param name="pdb_source_selector" value="history" /> + <param name="ffindex" value="cross/pdb.ffindex" /> + <param name="ffdata" value="cross/pdb.ffdata" /> + </conditional> + <param name="logfile" value="false" /> + <output name="output" file="cross/reference.tabular" /> + </test> + <test expect_num_outputs="2"> + <conditional name="pdb_source"> + <param name="pdb_source_selector" value="indexed" /> + <param name="pdb" value="pdb01_cross" /> + </conditional> + <param name="logfile" value="true" /> + <output name="output" file="cross/reference.tabular" /> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database. +This reference is required as input for the SPRING min-Z calculator. + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/cross/pdb.ffdata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cross/pdb.ffdata Tue Mar 23 13:55:42 2021 +0000 |
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| b'@@ -0,0 +1,107645 @@\n+HEADER VIRAL PROTEIN 25-FEB-20 6VYB \n+TITLE SARS-COV-2 SPIKE ECTODOMAIN STRUCTURE (OPEN STATE) \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: SPIKE GLYCOPROTEIN; \n+COMPND 3 CHAIN: A, B, C; \n+COMPND 4 FRAGMENT: ECTODOMAIN; \n+COMPND 5 SYNONYM: S GLYCOPROTEIN,E2,PEPLOMER PROTEIN; \n+COMPND 6 ENGINEERED: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS \n+SOURCE 3 2; \n+SOURCE 4 ORGANISM_COMMON: 2019-NCOV; \n+SOURCE 5 ORGANISM_TAXID: 2697049; \n+SOURCE 6 GENE: S, 2; \n+SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; \n+SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; \n+SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606 \n+KEYWDS CORONAVIRUS, SARS-COV-2, SARS-COV, SPIKE GLYCOPROTEIN, FUSION \n+KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR \n+KEYWDS 3 INFECTIOUS DISEASE, SSGCID, VIRAL PROTEIN \n+EXPDTA ELECTRON MICROSCOPY \n+AUTHOR A.C.WALLS,Y.J.PARK,M.A.TORTORICI,A.WALL,SEATTLE STRUCTURAL GENOMICS \n+AUTHOR 2 CENTER FOR INFECTIOUS DISEASE (SSGCID),A.T.MCGUIRE,D.VEESLER \n+REVDAT 6 29-JUL-20 6VYB 1 COMPND REMARK HETNAM LINK \n+REVDAT 6 2 1 SITE ATOM \n+REVDAT 5 06-MAY-20 6VYB 1 COMPND SOURCE DBREF SEQADV \n+REVDAT 4 29-APR-20 6VYB 1 JRNL \n+REVDAT 3 01-APR-20 6VYB 1 COMPND \n+REVDAT 2 25-MAR-20 6VYB 1 JRNL \n+REVDAT 1 11-MAR-20 6VYB 0 \n+JRNL AUTH A.C.WALLS,Y.J.PARK,M.A.TORTORICI,A.WALL,A.T.MCGUIRE, \n+JRNL AUTH 2 D.VEESLER \n+JRNL TITL STRUCTURE, FUNCTION, AND ANTIGENICITY OF THE SARS-COV-2 \n+JRNL TITL 2 SPIKE GLYCOPROTEIN. \n+JRNL REF CELL V. 181 281 2020 \n+JRNL REFN ISSN 1097-4172 \n+JRNL PMID 32155444 \n+JRNL DOI 10.1016/J.CELL.2020.02.058 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 3.20 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 SOFTWARE PACKAGES : LEGINON, RELION, RELION \n+REMARK 3 RECONSTRUCTION SCHEMA : NULL \n+REMARK 3 \n+REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT \n+REMARK 3 PDB ENTRY : NULL \n+REMARK 3 REFINEMENT SPACE : NULL \n+REMARK 3 REFINEMENT PROTOCOL '..b' \n+CONECT 1816 8594 \n+CONECT 1857 8594 \n+CONECT 1889 8594 \n+CONECT 3297 8595 \n+CONECT 4527 8595 \n+CONECT 4550 8595 \n+CONECT 4556 8595 \n+CONECT 8283 8606 \n+CONECT 8290 8630 \n+CONECT 8594 1771 1816 1857 1889 \n+CONECT 8595 3297 4527 4550 4556 \n+CONECT 8596 8597 8598 8599 8600 \n+CONECT 8597 8596 \n+CONECT 8598 8596 \n+CONECT 8599 8596 \n+CONECT 8600 8596 8601 8605 \n+CONECT 8601 8600 8602 8603 8604 \n+CONECT 8602 8601 \n+CONECT 8603 8601 \n+CONECT 8604 8601 \n+CONECT 8605 8600 \n+CONECT 8606 8283 \n+CONECT 8607 8612 8620 \n+CONECT 8608 8610 8618 8620 \n+CONECT 8609 8613 8616 \n+CONECT 8610 8608 8615 8625 \n+CONECT 8611 8614 8620 8624 \n+CONECT 8612 8607 \n+CONECT 8613 8609 8624 8627 \n+CONECT 8614 8611 \n+CONECT 8615 8610 8623 \n+CONECT 8616 8609 8630 \n+CONECT 8617 8622 8623 \n+CONECT 8618 8608 8621 \n+CONECT 8619 8630 \n+CONECT 8620 8607 8608 8611 8627 \n+CONECT 8621 8618 8625 \n+CONECT 8622 8617 8625 8626 \n+CONECT 8623 8615 8617 \n+CONECT 8624 8611 8613 8628 \n+CONECT 8625 8610 8621 8622 \n+CONECT 8626 8622 \n+CONECT 8627 8613 8620 \n+CONECT 8628 8624 \n+CONECT 8629 8630 \n+CONECT 8630 8290 8616 8619 8629 \n+MASTER 498 0 6 55 31 0 8 6 8630 5 47 103 \n+END \n' |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/cross/pdb.ffindex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cross/pdb.ffindex Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,11 @@ +6vyb.pdb 0 2088828 +6vyo.pdb 2088829 758727 +6w37.pdb 2847557 66582 +6w4h.pdb 2914140 675378 +6w9c.pdb 3589519 1250964 +6w9q.pdb 4840484 182574 +6wey.pdb 5023059 436995 +6wji.pdb 5460055 983583 +6wlc.pdb 6443639 1054296 +7bqy.pdb 7497936 448173 +7bv2.pdb 7946110 773145 |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/cross/reference.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cross/reference.tabular Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,44 @@ +6VYB_A 6VYB_B +6VYB_A 6VYB_C +6VYB_B 6VYB_A +6VYB_B 6VYB_C +6VYB_C 6VYB_A +6VYB_C 6VYB_B +6VYO_A 6VYO_B +6VYO_A 6VYO_D +6VYO_B 6VYO_A +6VYO_B 6VYO_C +6VYO_C 6VYO_B +6VYO_C 6VYO_D +6VYO_D 6VYO_A +6VYO_D 6VYO_C +6W4H_A 6W4H_B +6W4H_B 6W4H_A +6W9C_A 6W9C_B +6W9C_A 6W9C_C +6W9C_B 6W9C_A +6W9C_B 6W9C_C +6W9C_C 6W9C_A +6W9C_C 6W9C_B +6WJI_A 6WJI_B +6WJI_B 6WJI_A +6WJI_B 6WJI_D +6WJI_B 6WJI_E +6WJI_C 6WJI_D +6WJI_C 6WJI_E +6WJI_D 6WJI_B +6WJI_D 6WJI_C +6WJI_E 6WJI_B +6WJI_E 6WJI_C +6WJI_E 6WJI_F +6WJI_F 6WJI_E +6WLC_A 6WLC_B +6WLC_B 6WLC_A +7BQY_A 7BQY_C +7BQY_C 7BQY_A +7BV2_A 7BV2_B +7BV2_A 7BV2_C +7BV2_B 7BV2_A +7BV2_B 7BV2_C +7BV2_C 7BV2_A +7BV2_C 7BV2_B |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/ffindex_indices.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ffindex_indices.loc Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,5 @@ +##ffindex indices +#unique_id display name path type +pdb01_model PDB 2021-03-17-model ${__HERE__}/model/pdb_structures pdb +pdb01_cross PDB 2021-03-17-cross ${__HERE__}/cross/pdb pdb +hhr_model HHR model - cross ${__HERE__}/model/hhr hhr |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/map/chains.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map/chains.tabular Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,16 @@ +6VYB_A +6VYB_B +6VYB_C +6VYO_A +6W4H_A +6W4H_B +6W9C_A +6W9Q_A +6W37_A +6WEY_A +6WJI_A +6WLC_A +7BQY_A +7BQY_C +7BV2_A +7BV2_B \ No newline at end of file |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/map/mapped.reference.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map/mapped.reference.tabular Tue Mar 23 13:55:42 2021 +0000 |
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| @@ -0,0 +1,20 @@ +6VYB_A 6VYB_B 6VYB_A 6VYB_B +6VYB_A 6VYB_C 6VYB_A 6VYB_C +6VYB_B 6VYB_A 6VYB_B 6VYB_A +6VYB_B 6VYB_C 6VYB_B 6VYB_C +6VYB_C 6VYB_A 6VYB_C 6VYB_A +6VYB_C 6VYB_B 6VYB_C 6VYB_B +6W4H_A 6W4H_B 6W4H_A 6W4H_B +6W4H_B 6W4H_A 6W4H_B 6W4H_A +6W9C_A 6W9C_A 6W9C_A 6W9C_B +6W9C_A 6W9C_A 6W9C_A 6W9C_C +6W9C_A 6W9C_A 6W9C_B 6W9C_A +6W9C_A 6W9C_A 6W9C_B 6W9C_C +6W9C_A 6W9C_A 6W9C_C 6W9C_A +6W9C_A 6W9C_A 6W9C_C 6W9C_B +6WLC_A 6WLC_A 6WLC_A 6WLC_B +6WLC_A 6WLC_A 6WLC_B 6WLC_A +7BQY_A 7BQY_C 7BQY_A 7BQY_C +7BQY_C 7BQY_A 7BQY_C 7BQY_A +7BV2_A 7BV2_B 7BV2_A 7BV2_B +7BV2_B 7BV2_A 7BV2_B 7BV2_A |
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| diff -r 000000000000 -r dbbcc7cd889f test-data/mcc/biogrid_fret.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcc/biogrid_fret.txt Tue Mar 23 13:55:42 2021 +0000 |
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| b'@@ -0,0 +1,3458 @@\n+140012\t852276\t850450\t32692\t31060\tYBL007C\tYCR088W\tSLA1\tABP1\tcytoskeletal protein-binding protein SLA1|L000001912\tL000000013\tFRET\tphysical\tWarren DT (2002)\tPUBMED:11950888\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP32790\t-\tNP_009546\tP15891\t-\tNP_010012\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+143270\t855828\t856499\t35915\t36532\tYPL248C\tYHR099W\tGAL4\tTRA1\tGAL81|galactose-responsive transcription factor GAL4|L000000661\thistone acetyltransferase TRA1|L000003945\tFRET\tphysical\tBhaumik SR (2004)\tPUBMED:14871930\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP04386\t-\tNP_015076\tP38811\t-\tNP_011967\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145346\t853385\t853808\t33693\t34076\tYJL061W\tYKL057C\tNUP82\tNUP120\tHRB187|linker nucleoporin NUP82|L000002941\tRAT2|L000003138\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP40368\t-\tNP_012474\tP35729\t-\tNP_012866\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145347\t853808\t853385\t34076\t33693\tYKL057C\tYJL061W\tNUP120\tNUP82\tRAT2|L000003138\tHRB187|linker nucleoporin NUP82|L000002941\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP35729\t-\tNP_012866\tP40368\t-\tNP_012474\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145348\t853385\t855066\t33693\t35221\tYJL061W\tYMR047C\tNUP82\tNUP116\tHRB187|linker nucleoporin NUP82|L000002941\tNSP116|FG-nucleoporin NUP116|L000001293\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP40368\t-\tNP_012474\tQ02630\t-\tNP_013762\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145349\t855066\t853385\t35221\t33693\tYMR047C\tYJL061W\tNUP116\tNUP82\tNSP116|FG-nucleoporin NUP116|L000001293\tHRB187|linker nucleoporin NUP82|L000002941\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tQ02630\t-\tNP_013762\tP40368\t-\tNP_012474\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145350\t855184\t850552\t35328\t31150\tYMR153W\tYFR002W\tNUP53\tNIC96\tFG-nucleoporin NUP53\tlinker nucleoporin NIC96|L000001250\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tQ03790\t-\tNP_013873\tP34077\t-\tNP_116657\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145351\t850552\t855184\t31150\t35328\tYFR002W\tYMR153W\tNIC96\tNUP53\tlinker nucleoporin NIC96|L000001250\tFG-nucleoporin NUP53\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP34077\t-\tNP_116657\tQ03790\t-\tNP_013873\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145352\t854265\t854868\t34496\t35040\tYOR098C\tYML103C\tNUP1\tNUP188\tFG-nucleoporin NUP1|L000001288\tL000003099\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP20676\t-\tNP_014741\tP52593\t-\tNP_013604\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145353\t854868\t854265\t35040\t34496\tYML103C\tYOR098C\tNUP188\tNUP1\tL000003099\tFG-nucleoporin NUP1|L000001288\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP52593\t-\tNP_013604\tP20676\t-\tNP_014741\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145354\t854868\t853957\t35040\t34213\tYML103C\tYKR082W\tNUP188\tNUP133\tL000003099\tRAT3|L000002620\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP52593\t-\tNP_013604\tP36161\t-\tNP_013008\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145355\t853957\t854868\t34213\t35040\tYKR082W\tYML103C\tNUP133\tNUP188\tRAT3|L000002620\tL000003099\tFRET\tphysical\tDamelin M (2002)\tPUBMED:12496130\t559292\t559292\tLow Throughput\t-\t-\t-\t-\tBIOGRID\tP36161\t-\tNP_013008\tP52593\t-\tNP_013604\t-\t-\t-\t-\t-\t-\tSaccharomyces cerevisiae (S288c)\tSaccharomyces cerevisiae (S288c)\n+145356\t854868\t855066\t35040\t3'..b'hila melanogaster\n+2870679\t38611\t39332\t64077\t64693\tDmel_CG10642\tDmel_CG7293\tKlp64D\tKlp68D\tCG10642|DmKlp64D|DmelCG10642|KIF 3A|KIF3A|KLP4|KLP64Ddm|Klp 64D\tCG7293|DmKlp68D|DmelCG7293|KIF 3B|KIF3B|KLP-5|KLP5|KLP68Ddm|KLP[[64D/68D]]\tFRET\tphysical\tAhmed Z (2019)\tPUBMED:31420166\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\t-\tQ9VRK9\tNP_523934\tP46867\tM9PF68\tNP_524029|NP_001261726\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2870680\t38611\t39332\t64077\t64693\tDmel_CG10642\tDmel_CG7293\tKlp64D\tKlp68D\tCG10642|DmKlp64D|DmelCG10642|KIF 3A|KIF3A|KLP4|KLP64Ddm|Klp 64D\tCG7293|DmKlp68D|DmelCG7293|KIF 3B|KIF3B|KLP-5|KLP5|KLP68Ddm|KLP[[64D/68D]]\tFRET\tphysical\tAhmed Z (2020)\tPUBMED:31784087\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\t-\tQ9VRK9\tNP_523934\tP46867\tM9PF68\tNP_524029|NP_001261726\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2870745\t39018\t39018\t64423\t64423\tDmel_CG43782\tDmel_CG43782\torb2\torb2\tCG43113|CG43782|CG5735|DmelCG43782|Dmel_CG43113|Dmel_CG5735|Dmel_CG5741|anon-WO0140519.222\tCG43113|CG43782|CG5735|DmelCG43782|Dmel_CG43113|Dmel_CG5735|Dmel_CG5741|anon-WO0140519.222\tFRET\tphysical\tNil Z (2019)\tPUBMED:31491385\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\tQ9VSR3\tA4V1P2\tNP_648266|NP_729427|NP_729429|NP_729428|NP_001261608\tQ9VSR3\tA4V1P2\tNP_648266|NP_729427|NP_729429|NP_729428|NP_001261608\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2870798\t39409\t53554\t64761\t72787\tDmel_CG10698\tDmel_CG1487\tCrzR\tkrz\tCG10698|Crz-R|DCR|DGRHRII|DmelCG10698|GRH-RII|GRHRII|GRHRII_Dro|anon-WO0170980.196|anon-WO0170980.197\t0952/14|CG1487|DmelCG1487|Kurz|l(3)S095214\tFRET\tphysical\tChai F (2019)\tPUBMED:31325455\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\t-\tM9PF00|Q9VTW7\tNP_001261755|NP_648571\t-\tQ9V393\tNP_524988|NP_001247400\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2870884\t39748\t39748\t65059\t65059\tDmel_CG5830\tDmel_CG5830\tCG5830\tCG5830\tDmelCG5830\tDmelCG5830\tFRET\tphysical\tNil Z (2019)\tPUBMED:31491385\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\t-\tQ9VUX0|M9PFN0\tNP_001261912|NP_648825\t-\tQ9VUX0|M9PFN0\tNP_001261912|NP_648825\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2871052\t40616\t40616\t65830\t65830\tDmel_CG2530\tDmel_CG2530\tcorto\tcorto\t7128|CG2530|CP-1|Ccf|DmelCG2530|anon-WO02059370.59|l(3)07128|l(3)neo31|l(3)neo32\t7128|CG2530|CP-1|Ccf|DmelCG2530|anon-WO02059370.59|l(3)07128|l(3)neo31|l(3)neo32\tFRET\tphysical\tNil Z (2019)\tPUBMED:31491385\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\tP41046\t-\tNP_001287166|NP_524231|NP_001246921|NP_001246923|NP_001246922\tP41046\t-\tNP_001287166|NP_524231|NP_001246921|NP_001246923|NP_001246922\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2871859\t43767\t41565\t68605\t66658\tDmel_CG2125\tDmel_CG6054\tci\tSu(fu)\tCG2125|CID|Ce|Ci/GLI|Ci155|Ci[D]|DmelCG2125|Gli|Siah|ci-D|l(4)102ABc|l(4)13|l(4)17\tCG6054|DmelCG6054|SUFU|dSufu\tFRET\tphysical\tHan Y (2019)\tPUBMED:31279575\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\tP19538\tH9XVL6|H5V858|H9XVL7\tNP_524617|NP_001245402|NP_001245401\t-\tQ9VG38\tNP_536750\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2871874\t43832\t37007\t68658\t62693\tDmel_CG11081\tDmel_CG6446\tPlexA\tSema-1b\tBcDNA:GM05237|CG11081|D-Plex A|DPlexA|DmelCG11081|Plex1|PlexA1|lincRNA.927|plex|plex A\tBcDNA:GH03186|CG6446|D-semaIII|DmelCG6446|Sema 1b|Sema III|Sema1b|sema-III\tFRET\tphysical\tRozbesky D (2020)\tPUBMED:32500924\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\t-\tQ0KIF1|Q9V491|H9XVP3\tNP_524637|NP_726627|NP_726628|NP_001245428\t-\tQ7KK54\tNP_001163178|NP_611244|NP_995879\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n+2871937\t44353\t38218\t68999\t63751\tDmel_CG18247\tDmel_CG2086\tshark\tdrpr\tCG18247|DmelCG18247|Dtk7|SYK/SHARK|Syk|Tk7|l(2)W4|l(2R)W4\tBcDNA:GH03529|CG18172|CG2086|CT41022|CT6730|DmelCG2086\tFRET\tphysical\tWilliamson AP (2018)\tPUBMED:30139739\t7227\t7227\tLow Throughput\t-\t-\t-\t-\tFLYBASE\tQ24145\t-\tNP_524743\t-\tQ9W0A1|Q9W0A0|M9PDW5|M9PGU6|M9NEX8|M9PBI3\tNP_001246549|NP_728660|NP_001261276|NP_001261277|NP_001261275|NP_477450\t-\t-\t-\t-\t-\t-\tDrosophila melanogaster\tDrosophila melanogaster\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/mcc/human_hv1h2.png |
| b |
| Binary file test-data/mcc/human_hv1h2.png has changed |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/mcc/human_hv1h2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mcc/human_hv1h2.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,20796 @@\n+sp|P04601|NEF_HV1H2\tsp|Q96CW1|AP2M1_HUMAN\t495.9\t3TB8_A\t5FPI_A\t6OWT_N\t6QH5_N\n+sp|P04601|NEF_HV1H2\tsp|Q9BXS5|AP1M1_HUMAN\t474.5\t3TB8_A\t4P6Z_M\t4EN2_B\t6CRI_M\n+sp|P04601|NEF_HV1H2\tsp|Q9Y6Q5|AP1M2_HUMAN\t442.4\t3TB8_A\t4P6Z_M\t4EN2_B\t6CRI_M\n+sp|P69723|VIF_HV1H2\tsp|Q13951|PEBB_HUMAN\t412.1\t4N9F_b\t6P59_C\t4N9F_b\t6P59_A\n+sp|P04601|NEF_HV1H2\tsp|P53677|AP3M2_HUMAN\t406.8\t3TB8_A\t2XA7_M\t6OWT_N\t6QH5_N\n+sp|P04601|NEF_HV1H2\tsp|Q9Y2T2|AP3M1_HUMAN\t404.8\t3TB8_A\t6QH5_N\t6OWT_N\t6QH5_N\n+sp|P04601|NEF_HV1H2\tsp|O00189|AP4M1_HUMAN\t353.7\t3TB8_A\t2XA7_M\t6OWT_N\t6QH5_N\n+sp|P69723|VIF_HV1H2\tsp|Q13616|CUL1_HUMAN\t328.9\t4N9F_b\t1LDJ_A\t4N9F_b\t4JGH_D\n+sp|P69723|VIF_HV1H2\tsp|Q13620|CUL4B_HUMAN\t295.0\t4N9F_b\t2HYE_C\t4N9F_b\t4JGH_D\n+sp|P69726|VPR_HV1H2\tsp|P13051|UNG_HUMAN\t291.6\t1ESX_A\t3FCI_A\t5JK7_F\t3FCI_A\n+sp|P69726|VPR_HV1H2\tsp|Q10570|CPSF1_HUMAN\t291.6\t1ESX_A\t6F9N_A\t5JK7_F\t5JK7_B\n+sp|P69726|VPR_HV1H2\tsp|Q15393|SF3B3_HUMAN\t291.6\t1ESX_A\t6FF7_v\t5JK7_F\t5JK7_B\n+sp|P69726|VPR_HV1H2\tsp|Q16531|DDB1_HUMAN\t291.6\t1ESX_A\t5JK7_B\t5JK7_F\t5JK7_B\n+sp|P69723|VIF_HV1H2\tsp|Q9NRW3|ABC3C_HUMAN\t286.5\t4N9F_b\t5CQH_A\t6NIL_F\t5HX4_A\n+sp|P69723|VIF_HV1H2\tsp|Q93034|CUL5_HUMAN\t286.1\t4N9F_b\t6V9I_C\t4N9F_b\t4JGH_D\n+sp|P69723|VIF_HV1H2\tsp|Q13619|CUL4A_HUMAN\t281.7\t4N9F_b\t2HYE_C\t4N9F_b\t4JGH_D\n+sp|P69723|VIF_HV1H2\tsp|Q13618|CUL3_HUMAN\t278.9\t4N9F_b\t2HYE_C\t4N9F_b\t4JGH_D\n+sp|P69723|VIF_HV1H2\tsp|Q8IUX4|ABC3F_HUMAN\t275.2\t4N9F_b\t6P3X_B\t6NIL_F\t5HX4_A\n+sp|P04608|TAT_HV1H2\tsp|A0A0B4J2F2|SIK1B_HUMAN\t264.2\t3MI9_C\t3FE3_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O00444|PLK4_HUMAN\t264.2\t3MI9_C\t6N45_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O14965|AURKA_HUMAN\t264.2\t3MI9_C\t4DEE_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O15264|MK13_HUMAN\t264.2\t3MI9_C\t3COI_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O76039|CDKL5_HUMAN\t264.2\t3MI9_C\t4BGQ_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O95747|OXSR1_HUMAN\t264.2\t3MI9_C\t5DBX_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|O96017|CHK2_HUMAN\t264.2\t3MI9_C\t3I6U_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P06493|CDK1_HUMAN\t264.2\t3MI9_C\t6GU2_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P11801|KPSH1_HUMAN\t264.2\t3MI9_C\t4B99_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P20794|MAK_HUMAN\t264.2\t3MI9_C\t6O9L_8\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P21127|CD11B_HUMAN\t264.2\t3MI9_C\t6O9L_8\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P24941|CDK2_HUMAN\t264.2\t3MI9_C\t1FVV_C\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P42685|FRK_HUMAN\t264.2\t3MI9_C\t1AD5_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P50613|CDK7_HUMAN\t264.2\t3MI9_C\t6O9L_8\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P50750|CDK9_HUMAN\t264.2\t3MI9_C\t3MI9_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P53350|PLK1_HUMAN\t264.2\t3MI9_C\t3FC2_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P53778|MK12_HUMAN\t264.2\t3MI9_C\t1CM8_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P54646|AAPK2_HUMAN\t264.2\t3MI9_C\t5ISO_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|P57059|SIK1_HUMAN\t264.2\t3MI9_C\t3FE3_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00526|CDK3_HUMAN\t264.2\t3MI9_C\t6Q4G_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00532|CDKL1_HUMAN\t264.2\t3MI9_C\t4AGU_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00534|CDK6_HUMAN\t264.2\t3MI9_C\t1BLX_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00535|CDK5_HUMAN\t264.2\t3MI9_C\t1UNL_B\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00536|CDK16_HUMAN\t264.2\t3MI9_C\t3MTL_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q00537|CDK17_HUMAN\t264.2\t3MI9_C\t3MTL_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q12851|M4K2_HUMAN\t264.2\t3MI9_C\t5J5T_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q13554|KCC2B_HUMAN\t264.2\t3MI9_C\t5U6Y_C\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q13555|KCC2G_HUMAN\t264.2\t3MI9_C\t5U6Y_C\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q13557|KCC2D_HUMAN\t264.2\t3MI9_C\t5U6Y_C\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q14004|CDK13_HUMAN\t264.2\t3MI9_C\t5EFQ_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q14012|KCC1A_HUMAN\t264.2\t3MI9_C\t6QP5_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q15131|CDK10_HUMAN\t264.2\t3MI9_C\t4B99_A\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q16539|MK14_HUMAN\t264.2\t3MI9_C\t4LOP_C\t3MI9_C\t3MI9_A\n+sp|P04608|TAT_HV1H2\tsp|Q5MAI5|CDKL4_HUMAN\t264.2\t3MI9_C\t4AGU_B\t3MI9_C\t3MI9'..b'\t3J70_P\n+sp|P04585|POL_HV1H2\ttr|A0A075B6Z9|A0A075B6Z9_HUMAN\t14.4\t1L6N_A\t5U64_B\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\ttr|A0A075B6Z9|A0A075B6Z9_HUMAN\t14.4\t1L6N_A\t5U64_B\t2XT1_A\t6FPV_A\n+tr|A0A0J9YWJ2|A0A0J9YWJ2_HUMAN\tsp|P04585|POL_HV1H2\t14.4\t2DL1_A\t1L6N_A\t6BK8_D\t6BK8_O\n+tr|A0A0J9YWJ2|A0A0J9YWJ2_HUMAN\tsp|P04591|GAG_HV1H2\t14.4\t2DL1_A\t1L6N_A\t6BK8_D\t6BK8_O\n+tr|A0A075B6U7|A0A075B6U7_HUMAN\tsp|P04578|ENV_HV1H2\t14.3\t5OVW_L\t6PWU_E\t6VN0_G\t6MTJ_B\n+tr|A0A075B6Y0|A0A075B6Y0_HUMAN\tsp|P04578|ENV_HV1H2\t14.3\t6GKD_B\t6PWU_E\t6NIJ_H\t3J70_P\n+tr|A0A075B6W2|A0A075B6W2_HUMAN\tsp|P04578|ENV_HV1H2\t14.2\t6GKD_B\t6PWU_E\t6VN0_I\t6MTJ_B\n+tr|A0A0A0MT92|A0A0A0MT92_HUMAN\tsp|P04578|ENV_HV1H2\t14.1\t5VM4_B\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B6X3|A0A075B6X3_HUMAN\tsp|P04578|ENV_HV1H2\t14.1\t6GJS_B\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B6Z2|A0A075B6Z2_HUMAN\tsp|P04578|ENV_HV1H2\t14.1\t6GKD_B\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04585|POL_HV1H2\ttr|A0N4Z8|A0N4Z8_HUMAN\t14.0\t1L6N_A\t4HGM_A\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\ttr|A0N4Z8|A0N4Z8_HUMAN\t14.0\t1L6N_A\t4HGM_A\t2XT1_A\t6FPV_A\n+tr|A0A075B6V6|A0A075B6V6_HUMAN\tsp|P04578|ENV_HV1H2\t14.0\t3ZHK_A\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B6Y8|A0A075B6Y8_HUMAN\tsp|P04578|ENV_HV1H2\t14.0\t3ZHK_A\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04585|POL_HV1H2\ttr|A0A087WU04|A0A087WU04_HUMAN\t13.9\t1L6N_A\t6GJS_B\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\ttr|A0A087WU04|A0A087WU04_HUMAN\t13.9\t1L6N_A\t6GJS_B\t2XT1_A\t6FPV_A\n+sp|A0A0A0MTA4|TJB25_HUMAN\tsp|P04578|ENV_HV1H2\t13.9\t3ZHK_A\t6PWU_E\t6VN0_I\t6MTJ_B\n+tr|A0A075B6V9|A0A075B6V9_HUMAN\tsp|P04578|ENV_HV1H2\t13.9\t1ZMY_A\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B6X9|A0A075B6X9_HUMAN\tsp|P04578|ENV_HV1H2\t13.9\t5FOJ_A\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04585|POL_HV1H2\tsp|A0A0A0MT94|TJB22_HUMAN\t13.8\t1L6N_A\t6TYL_J\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\tsp|A0A0A0MT94|TJB22_HUMAN\t13.8\t1L6N_A\t6TYL_J\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\tsp|A0A0C5B5G6|MOTSC_HUMAN\t13.8\t1L6N_A\t5AOQ_M\t6SW9_8\t5JB3_Y\n+tr|A0A075B6U9|A0A075B6U9_HUMAN\tsp|P04578|ENV_HV1H2\t13.8\t5FOJ_A\t6PWU_E\t6VN0_I\t6MTJ_B\n+sp|P04585|POL_HV1H2\tsp|A0A0A0MT89|KJ01_HUMAN\t13.7\t1L6N_A\t4HGM_A\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\tsp|A0A0A0MT89|KJ01_HUMAN\t13.7\t1L6N_A\t4HGM_A\t2XT1_A\t6FPV_A\n+sp|A0A0J9YXG5|TJB14_HUMAN\tsp|P04578|ENV_HV1H2\t13.6\t6VI4_D\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B702|A0A075B702_HUMAN\tsp|P04578|ENV_HV1H2\t13.6\t1ZMY_A\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04585|POL_HV1H2\tsp|A0A0A0MT70|TJB26_HUMAN\t13.5\t1L6N_A\t3ZHK_A\t2XT1_A\t6FPV_A\n+sp|P04585|POL_HV1H2\ttr|A0A0A0MTA1|A0A0A0MTA1_HUMAN\t13.5\t1L6N_A\t5VM4_B\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\tsp|A0A0A0MT70|TJB26_HUMAN\t13.5\t1L6N_A\t3ZHK_A\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\ttr|A0A0A0MTA1|A0A0A0MTA1_HUMAN\t13.5\t1L6N_A\t5VM4_B\t2XT1_A\t6FPV_A\n+sp|A0A0A0MT87|TJB24_HUMAN\tsp|P04578|ENV_HV1H2\t13.5\t5OVW_L\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A075B6Z4|A0A075B6Z4_HUMAN\tsp|P04578|ENV_HV1H2\t13.5\t5NGV_H\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04585|POL_HV1H2\ttr|A0A0A0MT85|A0A0A0MT85_HUMAN\t13.4\t1L6N_A\t3GKZ_A\t2XT1_A\t6FPV_A\n+sp|P04591|GAG_HV1H2\ttr|A0A0A0MT85|A0A0A0MT85_HUMAN\t13.4\t1L6N_A\t3GKZ_A\t2XT1_A\t6FPV_A\n+sp|A0A0A0MT70|TJB26_HUMAN\tsp|P04578|ENV_HV1H2\t13.4\t3ZHK_A\t6PWU_E\t6VPX_K\t3J70_P\n+sp|P04601|NEF_HV1H2\ttr|A0A0A0MT93|A0A0A0MT93_HUMAN\t13.3\t3TB8_A\t6APO_A\t4ORZ_B\t5MZV_D\n+tr|A0A075B6V0|A0A075B6V0_HUMAN\tsp|P04578|ENV_HV1H2\t13.3\t5UJR_A\t6PWU_E\t6VPX_K\t3J70_P\n+tr|A0A0A0MTA3|A0A0A0MTA3_HUMAN\tsp|P04578|ENV_HV1H2\t13.2\t4KV5_E\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|A0A0A0MT94|TJB22_HUMAN\tsp|P04578|ENV_HV1H2\t13.1\t6TYL_J\t6PWU_E\t6NIJ_H\t3J70_P\n+tr|A0A075B6W8|A0A075B6W8_HUMAN\tsp|P04578|ENV_HV1H2\t13.1\t6GJS_B\t6PWU_E\t6VN0_I\t6MTJ_B\n+sp|P04578|ENV_HV1H2\tsp|A0A0A0MT89|KJ01_HUMAN\t13.0\t6PWU_E\t4HGM_A\t6DCQ_D\t6VPX_P\n+tr|A0A0A0MT85|A0A0A0MT85_HUMAN\tsp|P04578|ENV_HV1H2\t12.5\t3GKZ_A\t6PWU_E\t6NIJ_H\t3J70_P\n+sp|P04608|TAT_HV1H2\ttr|A0A0J9YWD0|A0A0J9YWD0_HUMAN\t12.3\t3MI9_C\t3C5T_B\t6N4Y_C\t4NBX_B\n+sp|A0A0J9YXM7|TJB15_HUMAN\tsp|P04578|ENV_HV1H2\t12.1\t6GKD_B\t6PWU_E\t6VO0_I\t4TVP_G\n+tr|A0A0A0MT96|A0A0A0MT96_HUMAN\tsp|P04578|ENV_HV1H2\t11.7\t2I24_N\t6PWU_E\t6VO0_I\t4TVP_G\n+tr|A0A0A0MTA1|A0A0A0MTA1_HUMAN\tsp|P04578|ENV_HV1H2\t11.7\t5VM4_B\t6PWU_E\t6VO0_G\t4TVP_G\n+tr|A0A0A0MT69|A0A0A0MT69_HUMAN\tsp|P04578|ENV_HV1H2\t11.3\t4HGM_A\t6PWU_E\t6VO0_I\t4TVP_G\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/NP_000282.1.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/NP_000282.1.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,1458 @@\n+Query NP_000282.1\n+Match_columns 417\n+No_of_seqs 604 out of 4515\n+Neff 6.98956\n+Searched_HMMs 787\n+Date Fri Jul 24 20:35:21 2020\n+Command /home/guerler/hh-suite/build/bin/hhblits -i /home/guerler/human/fasta/NP_00/NP_000282.1.fasta -d /home/guerler/pdb70/pdb70 -o /home/guerler/human/hhr/NP_00/NP_000282.1.hhr \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 2WZB_A PHOSPHOGLYCERATE KINASE 100.0 9E-114 7E-118 875.1 0.0 415 3-417 2-416 (416)\n+ 2 1HDI_A PHOSPHOGLYCERATE KINASE 100.0 4E-113 3E-117 868.7 0.0 412 6-417 2-413 (413)\n+ 3 6Y3A_A Phosphoglycerate kinase 100.0 3E-112 2E-116 865.4 0.0 414 2-416 9-423 (424)\n+ 4 3UWD_A Phosphoglycerate kinase 100.0 7E-112 6E-116 855.6 0.0 391 4-416 1-393 (394)\n+ 5 1QPG_A 3-PHOSPHOGLYCERATE KINA 100.0 7E-112 6E-116 861.3 0.0 413 2-416 1-413 (415)\n+ 6 3PGK_A PHOSPHOGLYCERATE KINASE 100.0 8E-112 7E-116 861.3 0.0 413 2-416 2-414 (416)\n+ 7 3Q3V_A Phosphoglycerate kinase 100.0 3E-111 3E-115 852.3 0.0 392 2-416 3-399 (403)\n+ 8 1PHP_A 3-PHOSPHOGLYCERATE KINA 100.0 1E-110 9E-115 847.6 0.0 387 8-416 5-393 (394)\n+ 9 1VPE_A PHOSPHOGLYCERATE KINASE 100.0 1E-110 1E-114 848.4 0.0 392 6-416 2-395 (398)\n+ 10 4FEY_A Phosphoglycerate kinase 100.0 6E-110 5E-114 842.0 0.0 388 2-416 2-391 (395)\n+ 11 1V6S_B Phosphoglycerate kinase 100.0 1E-109 1E-113 838.8 0.0 386 7-416 2-390 (390)\n+ 12 3ZLB_A PHOSPHOGLYCERATE KINASE 100.0 2E-109 1E-113 840.0 0.0 394 4-416 1-397 (398)\n+ 13 4EHJ_A Phosphoglycerate kinase 100.0 2E-109 2E-113 837.1 0.0 386 4-416 1-388 (392)\n+ 14 16PK_A 3-PHOSPHOGLYCERATE KINA 100.0 4E-109 4E-113 840.3 0.0 395 6-416 2-414 (415)\n+ 15 3OZ7_B Phosphoglycerate kinase 100.0 4E-109 4E-113 840.5 0.0 413 3-416 4-417 (417)\n+ 16 4DG5_A Phosphoglycerate kinase 100.0 5E-109 4E-113 836.1 0.0 392 5-416 9-402 (403)\n+ 17 6HXE_A Phosphoglycerate kinase 100.0 4E-108 4E-112 826.1 0.0 381 4-416 1-383 (387)\n+ 18 4NG4_B Phosphoglycerate kinase 100.0 5E-108 4E-112 830.0 0.0 389 1-416 9-399 (404)\n+ 19 4NG4_C Phosphoglycerate kinase 100.0 5E-108 4E-112 830.0 0.0 389 1-416 9-399 (404)\n+ 20 6I06_A Phosphoglycerate kinase 100.0 1E-107 9E-112 823.4 0.0 381 4-416 1-383 (387)\n+ 21 2CUN_A Phosphoglycerate kinase 100.0 3E-105 3E-109 811.0 0.0 387 8-416 3-400 (410)\n+ 22 1FW8_A PHOSPHOGLYCERATE KINASE 100.0 8.8E-90 7.6E-94 698.3 0.0 342 74-416 2-343 (416)\n+ 23 1FW8_A PHOSPHOGLYCERATE KINASE 99.3 3.2E-16 2.7E-20 156.7 0.0 68 3-70 347-414 (416)\n+ 24 2Q33_B D-MONELLIN CHAIN A, D-M 34.3 5.9 0.00042 24.6 0.0 11 310-320 2-12 (48)\n+\n+No 1\n+>2WZB_A PHOSPHOGLYCERATE KINASE 1 (E.C.2.7.2.3); HEREDITARY HEMOLYTIC ANEMIA, TRANSFERASE, PHOSPHOPROTEIN; HET: ADP, 3PG; 1.47A {HOMO SAPIENS}\n+Probab=100.00 E-value=8.6e-114 Score=875.06 Aligned_cols=415 Identities=100% Similarity=1.449 Sum_probs=363.4 Template_Neff=6.400\n+\n+Q NP_000282.1 3 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVA 82 (417)\n+Q Consensus 3 ~~~~~~i~~~~l~gK~VlvRvD~NVPl~~~~i~d~~RI~~~lpTI~~Ll~~gak~vil~SHlGRP~g~~~~~~~Sl~~va 82 (417)\n+ +..|++++|.|++|||||||+|+|||+++++|.|++||++++|||+||+++||++|||+||+|||+++..++.+||+||+\n+T Consensus 2 ~~~~~~l~~~~l~gK~vlvR~D~NVPl~~~~i~dd~RI~~~lpTI~~Ll~~gak~vil~sHlGrP~g~~~~~~~Sl~pv~ 81 (416)\n+T 2WZB_A 2 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVA 81 (416)\n+T ss_dssp CTTBCBGGGCCCTTCEEEEECCCCCCEETTEESCCHHHHHHHHHHHHHHHTTCSEEEEECCCSCCTTSCCHHHHCSHHHH\n+T ss_pred CcccccccccccCCCEEEEEeEccccccCCccCCChHHHHHHHHHHHHHHCCCCEEEEEeeCCCCCCCCCCcccChHHHH\n+Confidence 457888988899999999999'..b'CSCSTTTHHHHHHHHTTCSE\n+T ss_pred HHhhCCeEeecccccCCccccCcccCCCchhhhcHHHHHHHHHHHHHhhCCCCCEEEEEcCCCHHHHHHHHHHHHHhcCE\n+Confidence 99999999999999999999999999976589999999999999999999999999999999999999999999999999\n+\n+\n+Q NP_000282.1 234 MIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMG 313 (417)\n+Q Consensus 234 iligG~~a~tfl~a~~g~~ig~s~~e~~~~~~a~~il~~a~~~~~~i~lP~D~~v~~~~~~~~~~~~~~~~~~i~~~~~~ 313 (417)\n+ |++||+|||+||+|++++++|+|++|++..+.|++++++|+.++++|+||+|++|.+.+..+.....+...+.+|++|++\n+T Consensus 161 IligG~~a~tfL~a~~~~~iG~S~~e~~~~~~a~~il~~a~~~~~ki~LP~D~vv~~~~~~~~~~~~~~~~~~i~~~~~i 240 (416)\n+T 1FW8_A 161 IIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQG 240 (416)\n+T ss_dssp EEEEGGGHHHHHHHHSCCCCCSCCCCHHHHHHHHHHHHHHHHHTCEEECCSEEEEESSSSTTCCEEEEETTTCCCTTCEE\n+T ss_pred EEeCchHHHHHHHHhCCCccCccccchhhhhHHHHHHHHHHHcCCeEEeeeeEEEeccccCCCCCceeeccCCCCCCCcc\n+Confidence 99999999999999755689999999988999999999988999999999999998865322211111122378899999\n+\n+\n+Q NP_000282.1 314 LDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVS 393 (417)\n+Q Consensus 314 ~DIGp~Ti~~~~~~I~~aktI~WnGp~G~~E~~~f~~GT~~l~~al~~~~~~~~~~ivGGGdT~~~~~~~g~~~~~~~vS 393 (417)\n+ +||||+|++.|.+.|++|||||||||||+||.++|++||+++++++++++.+++++|+|||||+++++++|+.++++|||\n+T Consensus 241 lDIGp~Ti~~~~~~I~~aktI~wnGP~G~~E~~~f~~GT~~i~~ai~~~~~~~a~~ivGGGdT~~~~~~~g~~~~~s~vS 320 (416)\n+T 1FW8_A 241 LDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVS 320 (416)\n+T ss_dssp EEECHHHHHHHHHHHHHCSEEEEESCSSCTTSGGGCHHHHHHHHHHHHHHHTTCEEEECTTHHHHHHHHTTCGGGSSEEC\n+T ss_pred cccCHHHHHHHHHHHHcCCEEEEcCCCCcccccccChHHHHHHHHHHHHhcCCCeEEEechhHHHHHHHhCCCCCceEEe\n+Confidence 99999999999999999999999999999998889999999999997632236899999999999998889878899999\n+\n+\n+Q NP_000282.1 394 TGGGASLELLEGKVLPGVDALSN 416 (417)\n+Q Consensus 394 tgGgA~Le~L~G~~LPgl~aL~~ 416 (417)\n+ |||||+||||+|+.||||++|++\n+T Consensus 321 TGGGA~Le~L~Gk~LPgieaL~~ 343 (416)\n+T 1FW8_A 321 TGGGASLELLEGKELPGVAFLSE 343 (416)\n+T ss_dssp SCSHHHHHHHTTCCCHHHHTSCS\n+T ss_pred cCchHHHHHHcCCCCCceeehhh\n+Confidence 99999999999999999999985\n+\n+\n+No 23\n+>1FW8_A PHOSPHOGLYCERATE KINASE (E.C.2.7.2.3); phosphotransferase, kinase, phosphoglycerate kinase, glycolysis; HET: GOL; 2.3A {Saccharomyces cerevisiae} SCOP: c.86.1.1\n+Probab=99.28 E-value=3.2e-16 Score=156.69 Aligned_cols=68 Identities=57% Similarity=0.940 Sum_probs=61.4 Template_Neff=6.400\n+\n+Q NP_000282.1 3 LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV 70 (417)\n+Q Consensus 3 ~~~~~~i~~~~l~gK~VlvRvD~NVPl~~~~i~d~~RI~~~lpTI~~Ll~~gak~vil~SHlGRP~g~ 70 (417)\n+ ++.++++++.+++|||||||+|+|||+++++|.|++||++++|||+||+++||++||++||+|||+++\n+T Consensus 347 ~~~~~~~~~~~~~~k~vl~R~D~nvp~~~~~i~d~~Ri~~~~~ti~~l~~~~~~~vii~sH~grp~~~ 414 (416)\n+T 1FW8_A 347 LSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGE 414 (416)\n+T ss_dssp SSCSCBGGGSCCTTCEEEEECCCCCCBSSSSBSCTHHHHHHHHHHHHHHHTCCSEEEEECCCSCCCSS\n+T ss_pred ccccccccccccCCCEEEEEeecCCCCCCCCcCCCHHHHhHHHHHHHHHHcCCCEEEEeeccCCCCCC\n+Confidence 45567777788999999999999999988899999999999999999999998449999999999875\n+\n+\n+No 24\n+>2Q33_B D-MONELLIN CHAIN A, D-MONELLIN CHAIN; ALPHA/BETA, ALL-D PROTEIN, DE NOVO; 1.8A {N/A}\n+Probab=34.33 E-value=5.9 Score=24.60 Aligned_cols=11 Identities=36% Similarity=0.761 Sum_probs=9.2 Template_Neff=1.000\n+\n+Q NP_000282.1 310 GWMGLDCGPES 320 (417)\n+Q Consensus 310 ~~~~~DIGp~T 320 (417)\n+ .|.++||||-|\n+T Consensus 2 eweiidigpft 12 (48)\n+T 2Q33_B 2 EWEIIDIGPFT 12 (48)\n+Confidence 58899999955\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/NP_000290.2.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/NP_000290.2.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b"@@ -0,0 +1,17574 @@\n+Query NP_000290.2\n+Match_columns 747\n+No_of_seqs 3849 out of 40250\n+Neff 6.23432\n+Searched_HMMs 998\n+Date Fri Jul 24 20:45:58 2020\n+Command /home/guerler/hh-suite/build/bin/hhblits -i /home/guerler/human/fasta/NP_00/NP_000290.2.fasta -d /home/guerler/pdb70/pdb70 -o /home/guerler/human/hhr/NP_00/NP_000290.2.hhr \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 1XM9_A plakophilin 1 Plakophi 99.7 6.3E-22 7.3E-26 206.9 0.0 453 246-719 3-455 (457)\n+ 2 3L6X_A Catenin delta-1, E-cadh 99.4 1.1E-17 1.2E-21 185.5 0.0 438 245-729 48-492 (584)\n+ 3 5D5K_C Importin subunit alpha- 98.6 1.1E-11 1.4E-15 126.2 0.0 369 243-713 11-386 (466)\n+ 4 3NMZ_A APC variant protein, Rh 98.6 1.3E-11 1.4E-15 129.0 0.0 381 238-715 25-452 (458)\n+ 5 4UAF_B Importin alpha 1 import 98.5 1.3E-11 1.6E-15 125.7 0.0 369 243-713 11-386 (466)\n+ 6 4U5L_A deltaIBB-importin-alpha 98.5 1.7E-11 2E-15 123.0 0.0 360 246-712 49-425 (426)\n+ 7 6SA7_B DARPin-Armadillo fusion 98.5 2.5E-11 2.9E-15 127.0 0.0 136 244-380 172-309 (510)\n+ 8 4RV1_D Engineered Protein OR49 98.5 2.7E-11 3.2E-15 120.8 0.0 362 247-715 4-369 (420)\n+ 9 6S9O_F designed Armadillo repe 98.5 2.8E-11 3.3E-15 117.9 0.0 167 545-724 170-338 (344)\n+ 10 5MFD_C YIIIM''6AII, Capsid dec 98.5 3E-11 3.5E-15 116.2 0.0 318 246-712 5-326 (328)\n+ 11 4MZ6_E Deoxyuridine 5'-triphos 98.5 3.5E-11 4E-15 125.0 0.0 368 244-713 56-430 (509)\n+ 12 5UMZ_B Importin subunit alpha- 98.5 3.5E-11 4E-15 125.0 0.0 368 244-713 56-430 (509)\n+ 13 2JDQ_A IMPORTIN ALPHA-1 SUBUNI 98.4 3.6E-11 4.2E-15 122.1 0.0 367 244-716 19-393 (450)\n+ 14 4E4V_A Importin subunit alpha- 98.4 3.6E-11 4.2E-15 124.3 0.0 364 246-716 76-456 (485)\n+ 15 4B18_A IMPORTIN SUBUNIT ALPHA- 98.4 4E-11 4.7E-15 121.6 0.0 368 244-717 16-391 (447)\n+ 16 4XZR_B Heh1-NLS, Kap60; karyop 98.4 4.3E-11 5E-15 119.8 0.0 363 248-717 4-375 (423)\n+ 17 5XZX_A Importin subunit alpha- 98.4 4.3E-11 5.1E-15 119.5 0.0 133 247-380 4-140 (416)\n+ 18 1JDH_A BETA-CATENIN, hTcf-4; B 98.4 4.4E-11 5.2E-15 123.9 0.0 378 245-726 101-502 (529)\n+ 19 3IFQ_A plakoglobin, E-cadherin 98.4 4.5E-11 5.3E-15 124.5 0.0 381 246-726 104-503 (553)\n+ 20 4UAD_A Importin alpha import a 98.4 6E-11 7E-15 121.8 0.0 372 246-723 68-456 (479)\n+ 21 5ZHX_D Rap1 GTPase-GDP dissoci 98.4 6.3E-11 7.5E-15 120.9 0.0 407 246-727 19-458 (487)\n+ 22 1EE4_A KARYOPHERIN ALPHA; ARM 98.4 8.2E-11 9.6E-15 117.7 0.0 364 247-717 3-375 (423)\n+ 23 1EE4_B KARYOPHERIN ALPHA; ARM 98.4 8.2E-11 9.6E-15 117.7 0.0 364 247-717 3-375 (423)\n+ 24 4EV8_A Catenin beta-1; mouse c 98.3 9.8E-11 1.2E-14 121.5 0.0 382 246-727 103-504 (538)\n+ 25 4RXH_B Importin subunit alpha, 98.3 1.1E-10 1.2E-14 121.7 0.0 365 246-716 72-457 (495)\n+ 26 4BQK_A IMPORTIN SUBUNIT ALPHA- 98.3 1.2E-10 1.3E-14 118.5 0.0 366 246-716 46-427 (456)\n+ 27 6BW9_A Importin subunit alpha- 98.3 1.3E-10 1.5E-14 118.5 0.0 366 246-717 53-428 (459)\n+ 28 1WA5_B GTP-BINDING NUCLEAR PRO 98.3 1.9E-10 2.2E-14 121.4 0.0 134 245-379 173-308 (530)\n+ 29 5XGC_A Rap1 GTPase-GDP dissoci 98.3 2E-10 2.3E-14 117.7 0.0 409 246-729 35-476 (503)\n+ 30 4BPL_A IMPORTIN SUBUNIT ALPHA- 98.2 2.4E-10 2.9E-14 115.9 0.0 367 246-717 44-426 (454)\n+ 31 4B8J_A IMPORTIN SUBUNIT ALPHA- 98.2 2.6E-10 2.9E-14 120.0 0.0 367 246-717 118-500 (528)\n+ 32 5T94_B Guanine nucleotide exch 98.2 2.9E-10 3.3E-14 120.5 0.0 364 246-716 131-513 (542)\n+ 33 4TNM_A Importin-alpha3 / MOS6; 98.2 3.2E-10 3.7E-14 119.6 0.0 369 246-719 119-504 (531)\n+ 34 5TBK_C Importin subunit alpha- 98.2 3.4E-10 3.8E-14 119.3 0.0 366 245-716 71-443 (521)\n+ 35 5TBK_D Importin subunit alpha- 98.2 3.4E-10 3.8E-14 119.3 0.0 366 245-716 71-443"..b'CCHHHHHHHHHHHHHHHHH\n+Confidence 1234555555564 45677888888888877653\n+\n+\n+No 498\n+>2QK1_A Protein STU2; stu2, Stu2p, XMAP215, Dis1, TOG; 1.7A {Saccharomyces cerevisiae}\n+Probab=67.88 E-value=0.42 Score=40.93 Aligned_cols=116 Identities=3% Similarity=-0.016 Sum_probs=68.4 Template_Neff=12.900\n+\n+Q NP_000290.2 244 GLTIPKAVQYLSSQDEKYQAIGAYYIQHTCFQDESAKQQVYQLGGICKLVDLLRSPNQNVQQAAAGALRNLVFRSTTN-- 321 (747)\n+Q Consensus 244 ~~iL~~Ll~lL~ssd~eVr~sAL~aLsnLs~~~~~~~~~li~~~IL~~Ll~lL~s~d~eVr~~AL~aLs~La~~~~~~-- 321 (747)\n+ ..+++.+...+.+.+..++..++.++..+...............+++.+...+.+.++.++..++.++..++...... \n+T Consensus 103 ~~~~~~l~~~l~~~~~~v~~~a~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~vr~~~~~~l~~~~~~~~~~~~ 182 (249)\n+T 2QK1_A 103 SLVFTPLLDRTKEKKPSVIEAIRKALLTICKYYDPLASSGRNEDMLKDILEHMKHKTPQIRMECTQLFNASMKEEKDGYS 182 (249)\n+T ss_dssp HHHHHHHHHGGGCCCHHHHHHHHHHHHHHHHHSCTTCTTCTTHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHCCSCSH\n+T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhChhcccCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhccccch\n+Confidence 345556666666666777888888888776543210000111245566666666667778888888888776543310 \n+\n+\n+Q NP_000290.2 322 -KLETRRQNGIREAVSLLRRTGNAEIQKQLTGLLWNLSST 360 (747)\n+Q Consensus 322 -~~~ll~~~IL~~Ll~lL~ss~d~eVr~~AL~aLsnLas~ 360 (747)\n+ ........+++.+...+. +.++.++..++.++..+...\n+T Consensus 183 ~~~~~~~~~~~~~l~~~l~-~~~~~vr~~a~~~l~~l~~~ 221 (249)\n+T 2QK1_A 183 TLQRYLKDEVVPIVIQIVN-DTQPAIRTIGFESFAILIKI 221 (249)\n+T ss_dssp HHHHHCCCCCHHHHHHHHT-CSSHHHHHHHHHHHHHHHHH\n+T ss_pred hhhHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHH\n+Confidence 000111235555666665 55677888888888877653\n+\n+\n+No 499\n+>4D4Z_A DEOXYHYPUSINE HYDROXYLASE (E.C.1.14.99.29); OXIDOREDUCTASE, EIF-5A, HYPUSINE; HET: B3P, GOL; 1.7A {HOMO SAPIENS}\n+Probab=67.63 E-value=0.43 Score=42.31 Aligned_cols=60 Identities=10% Similarity=0.123 Sum_probs=34.5 Template_Neff=12.700\n+\n+Q NP_000290.2 547 DAIRTYLNLMGKSK--KDATLEACAGALQNLTASKGLMSSGMSQLIGLKEKGLPQIARLLQSGNSDVVRSGASLLSNMS 623 (747)\n+Q Consensus 547 G~I~~LL~LL~ss~--d~eVr~~AL~aL~nLs~~s~~~s~~~~~~llie~giI~~Ll~LL~s~d~eVr~~AL~aLsnLa 623 (747)\n+ ..++.|...+. +. ++.++..++.+|..+... ..++.+...+.+.++.++..++.+|..+.\n+T Consensus 74 ~~~~~l~~~l~-~~~~~~~vr~~a~~~l~~~~~~----------------~~~~~l~~~l~~~~~~v~~~a~~~l~~~~ 135 (294)\n+T 4D4Z_A 74 RAIPMLVDVLQ-DTRQEPMVRHEAGEALGAIGDP----------------EVLEILKQYSSDPVIEVAETCQLAVRRLE 135 (294)\n+T ss_dssp GGHHHHHHHHH-CTTSCHHHHHHHHHHHHHHCCG----------------GGHHHHHHHTTCSSHHHHHHHHHHHHHHH\n+T ss_pred chHHHHHHHhh-CCCCCHHHHHHHHHHHHHhCCH----------------HHHHHHHHHccCCCchHHHHHHHHHHHHH\n+Confidence 34556666666 34 566777777776655421 12334455555556666666666666553\n+\n+\n+No 500\n+>4D50_A DEOXYHYPUSINE HYDROXYLASE (E.C.1.14.99.29); OXIDOREDUCTASE; HET: GAI; 1.7A {HOMO SAPIENS}\n+Probab=67.63 E-value=0.43 Score=42.31 Aligned_cols=60 Identities=10% Similarity=0.123 Sum_probs=34.5 Template_Neff=12.700\n+\n+Q NP_000290.2 547 DAIRTYLNLMGKSK--KDATLEACAGALQNLTASKGLMSSGMSQLIGLKEKGLPQIARLLQSGNSDVVRSGASLLSNMS 623 (747)\n+Q Consensus 547 G~I~~LL~LL~ss~--d~eVr~~AL~aL~nLs~~s~~~s~~~~~~llie~giI~~Ll~LL~s~d~eVr~~AL~aLsnLa 623 (747)\n+ ..++.|...+. +. ++.++..++.+|..+... ..++.+...+.+.++.++..++.+|..+.\n+T Consensus 74 ~~~~~l~~~l~-~~~~~~~vr~~a~~~l~~~~~~----------------~~~~~l~~~l~~~~~~v~~~a~~~l~~~~ 135 (294)\n+T 4D50_A 74 RAIPMLVDVLQ-DTRQEPMVRHEAGEALGAIGDP----------------EVLEILKQYSSDPVIEVAETCQLAVRRLE 135 (294)\n+T ss_dssp GGHHHHHHHHH-CTTSCHHHHHHHHHHHHHHCCG----------------GGHHHHHHHTTCSSHHHHHHHHHHHHHHH\n+T ss_pred chHHHHHHHhh-CCCCCHHHHHHHHHHHHHhCCH----------------HHHHHHHHHccCCCchHHHHHHHHHHHHH\n+Confidence 34556666666 34 566777777776655421 12334455555556666666666666553\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/NP_000548.2.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/NP_000548.2.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,1626 @@\n+Query NP_000548.2\n+Match_columns 501\n+No_of_seqs 1691 out of 7065\n+Neff 7.55495\n+Searched_HMMs 400\n+Date Sat Jul 25 00:10:29 2020\n+Command /home/guerler/hh-suite/build/bin/hhblits -i /home/guerler/human/fasta/NP_00/NP_000548.2.fasta -d /home/guerler/pdb70/pdb70 -o /home/guerler/human/hhr/NP_00/NP_000548.2.hhr \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 5FFO_H Integrin alpha-V, Integ 100.0 2.3E-42 2.1E-46 353.3 0.0 315 143-501 24-363 (363)\n+ 2 3RJR_C Transforming growth fac 100.0 3.4E-42 3.1E-46 351.8 0.0 315 143-501 24-363 (363)\n+ 3 5VQF_C Transforming growth fac 100.0 3.4E-42 3.2E-46 351.8 0.0 315 143-501 24-363 (363)\n+ 4 5NTU_A Growth/differentiation 100.0 9.5E-42 8.8E-46 343.8 0.0 309 142-501 17-335 (335)\n+ 5 5HLY_A Inhibin beta A chain; G 100.0 3E-39 2.7E-43 332.7 0.0 307 142-501 40-383 (383)\n+ 6 6SF3_B Serine/threonine-protei 99.8 1.5E-26 1.3E-30 194.7 0.0 105 397-501 4-108 (108)\n+ 7 4MPL_A Growth/differentiation 99.8 2.3E-26 2E-30 196.3 0.0 106 396-501 10-116 (116)\n+ 8 6Z3J_B Growth/differentiation 99.8 2.6E-26 2.3E-30 196.2 0.0 107 395-501 11-117 (117)\n+ 9 5I05_A Growth/differentiation 99.8 4E-26 3.5E-30 192.9 0.0 106 396-501 4-110 (110)\n+ 10 4N1D_A Bone morphogenetic prot 99.8 4.5E-26 3.9E-30 194.5 0.0 106 396-501 11-116 (116)\n+ 11 2QCQ_B Bone morphogenetic prot 99.8 5.7E-26 5E-30 191.9 0.0 105 397-501 5-110 (110)\n+ 12 1LXI_A BONE MORPHOGENETIC PROT 99.8 9E-26 7.8E-30 198.7 0.0 111 391-501 29-139 (139)\n+ 13 6OMN_G Bone morphogenetic prot 99.8 9.8E-26 8.7E-30 189.8 0.0 105 396-501 4-108 (108)\n+ 14 2R53_A Bone morphogenetic prot 99.8 9.9E-26 8.7E-30 192.3 0.0 106 396-501 11-116 (116)\n+ 15 2R53_B Bone morphogenetic prot 99.8 9.9E-26 8.7E-30 192.3 0.0 106 396-501 11-116 (116)\n+ 16 1REU_A bone morphogenetic prot 99.8 1.1E-25 1E-29 187.7 0.0 102 399-501 2-103 (103)\n+ 17 1M4U_L Bone Morphogenetic Prot 99.8 1.2E-25 1.1E-29 197.8 0.0 111 391-501 29-139 (139)\n+ 18 2H62_B Bone morphogenetic prot 99.8 2.1E-25 1.9E-29 189.6 0.0 105 396-501 10-114 (114)\n+ 19 6Q2J_B Growth/differentiation 99.8 3.8E-25 3.2E-29 193.7 0.0 102 396-501 34-135 (135)\n+ 20 1KTZ_A TRANSFORMING GROWTH FAC 99.8 7.5E-25 6.6E-29 185.6 0.0 102 395-501 10-112 (112)\n+ 21 5TY4_B TGF-beta receptor type- 99.8 9.9E-25 8.8E-29 179.9 0.0 96 400-500 1-97 (97)\n+ 22 5VT2_B Growth/differentiation 99.8 1.1E-24 9.5E-29 184.6 0.0 102 396-501 11-112 (112)\n+ 23 5VZ3_A Growth/differentiation 99.8 1.1E-24 9.5E-29 184.6 0.0 102 396-501 11-112 (112)\n+ 24 2ARP_A Inhibin beta A chain, F 99.8 1.3E-24 1.2E-28 184.9 0.0 105 397-501 8-116 (116)\n+ 25 2ARV_A Inhibin beta A chain; h 99.8 1.3E-24 1.2E-28 184.9 0.0 105 397-501 8-116 (116)\n+ 26 2P6A_B Activin A, Follistatin 99.8 1.3E-24 1.2E-28 184.9 0.0 105 397-501 8-116 (116)\n+ 27 2TGI_A TRANSFORMING GROWTH FAC 99.8 1.5E-24 1.3E-28 183.7 0.0 101 396-501 11-112 (112)\n+ 28 3HH2_B Growth/differentiation 99.8 2.4E-24 2.1E-28 181.5 0.0 99 396-501 11-109 (109)\n+ 29 5F3B_C RK35 Chimeric antibody 99.8 2.4E-24 2.1E-28 181.5 0.0 99 396-501 11-109 (109)\n+ 30 3KFD_D Transforming growth fac 99.8 3.7E-24 3.2E-28 181.3 0.0 102 395-501 10-112 (112)\n+ 31 5E4G_A Growth/differentiation 99.8 1.2E-23 1.1E-27 177.0 0.0 99 396-501 11-109 (109)\n+ 32 5NMZ_B Neurturin; cystine knot 99.7 2.2E-22 1.9E-26 167.0 0.0 93 397-501 4-101 (101)\n+ 33 5NMZ_C Neurturin; cystine knot 99.7 2.2E-22 1.9E-26 167.0 0.0 93 397-501 4-101 (101)\n+ 34 2GH0_C artemin, GDNF family re 99.7 2.9E-22 2.6E-26 166.0 0.0 95 398-501 2-100 (101)\n+ 35 5MR4_B Neurturin, GDNF family 99.7 4.4E-22 3.9E-26 165.4 0.0 94 396-501 4-102 (1'..b'piens}\n+Probab=57.82 E-value=1.2 Score=34.98 Aligned_cols=72 Identities=21% Similarity=0.280 Sum_probs=38.3 Template_Neff=7.700\n+\n+Q NP_000548.2 422 LEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR 501 (501)\n+Q Consensus 422 ~~~~a~yC~G~C~~~~~~~~~~~~h~~i~~~~~~~~~~~~~~pCC~P~~~~~l~ily~d~~~~~~~~~~~~mvv~~CgC~ 501 (501)\n+ ..+..++|.|.|....... ........ ........-.||.|.++....+...=.++..+. ..-.++.+|.|.\n+T Consensus 37 ~~v~~~~C~G~C~S~~~~~----p~~~~~~~--~~~~~~~~C~CC~p~~~~~~~v~l~C~~g~~~~--~~~~~i~~C~C~ 108 (122)\n+T 5BPU_A 37 KMVLLARCEGHCSQASRSE----PLVSFSTV--LKQPFRSSCHCCRPQTSKLKALRLRCSGGMRLT--ATYRYILSCHCE 108 (122)\n+T ss_pred CcEeceeeeccccceeecC----CCcccCCC--CCCcceeeeecCcCeEeEEEEEEEECCCCCeEE--EEEEEEEeceee\n+Confidence 6678899999998753200 00000000 000012345899999988766533323332222 333478899994\n+\n+\n+No 58\n+>5BQ8_C Norrin; Wnt signalling pathway, Norrie disease; HET: MLY; 2.0A {Homo sapiens}\n+Probab=53.96 E-value=1.5 Score=34.27 Aligned_cols=93 Identities=19% Similarity=0.268 Sum_probs=46.5 Template_Neff=7.800\n+\n+Q NP_000548.2 398 ARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISIL 477 (501)\n+Q Consensus 398 ~~Cc~~~l~V~F~dlGW~~wIiaP~~~~a~yC~G~C~~~~~~~~~~~~h~~i~~~~~~~~~~~~~~pCC~P~~~~~l~il 477 (501)\n+ ..|....+...+..=.. .- .. ..+..++|.|.|....... ........ ........-.||.|.++....|.\n+T Consensus 16 ~~C~~~~~~~~i~~~~~-gC-~s-~~v~~~~C~G~C~S~~~~~----p~~~~~~~--~~~~~~~~C~CC~p~~~~~~~V~ 86 (122)\n+T 5BQ8_C 16 RRCMRHHYVDSISHPLY-KC-SS-KMVLLARCEGHCSQASRSE----PLVSFSTV--LKQPFRSSCHCCRPQTSKLKALR 86 (122)\n+T ss_dssp TSSEEEEEEEEECCSSS-CB-CC-EEEEEEEEEECCSSCEEEE----ECCEETTB--CCCSEEEECEEEEEEEEEEEEEE\n+T ss_pred CCeEEEeeEEEEEcCCC-Cc-ee-ceeEeeeEEEecccceecC----CccccCCC--CCCCceeEceecCCeEeEEEEEE\n+Confidence 45666555444432100 11 22 6678899999998753200 00000000 00001234589999998876653\n+\n+\n+Q NP_000548.2 478 FIDSANNVVYKQYEDMVVESCGCR 501 (501)\n+Q Consensus 478 y~d~~~~~~~~~~~~mvv~~CgC~ 501 (501)\n+ ..=.++..+ ...-+++.+|.|.\n+T Consensus 87 l~C~~g~~~--~~~~~~i~~C~C~ 108 (122)\n+T 5BQ8_C 87 LRCSGGMRL--TATYRYILSCHCE 108 (122)\n+T ss_dssp EEETTTEEE--EEEEEEEEEEEEE\n+T ss_pred EECCCCceE--EEEEEEEEeceee\n+Confidence 332333322 2334578999994\n+\n+\n+No 59\n+>5BQE_A Frizzled-4; Wnt signalling pathway, Norrie disease; HET: MLY, NAG, PG0; 2.3A {Homo sapiens}\n+Probab=53.96 E-value=1.5 Score=34.27 Aligned_cols=93 Identities=19% Similarity=0.268 Sum_probs=46.5 Template_Neff=7.800\n+\n+Q NP_000548.2 398 ARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISIL 477 (501)\n+Q Consensus 398 ~~Cc~~~l~V~F~dlGW~~wIiaP~~~~a~yC~G~C~~~~~~~~~~~~h~~i~~~~~~~~~~~~~~pCC~P~~~~~l~il 477 (501)\n+ ..|....+...+..=.. .- .. ..+..++|.|.|....... ........ ........-.||.|.++....|.\n+T Consensus 16 ~~C~~~~~~~~i~~~~~-gC-~s-~~v~~~~C~G~C~S~~~~~----p~~~~~~~--~~~~~~~~C~CC~p~~~~~~~V~ 86 (122)\n+T 5BQE_A 16 RRCMRHHYVDSISHPLY-KC-SS-KMVLLARCEGHCSQASRSE----PLVSFSTV--LKQPFRSSCHCCRPQTSKLKALR 86 (122)\n+T ss_dssp TSSEEEEEEEEECCSSS-CB-CC-EEEEEEEEEECCSSCEEEE----ECCBCSSS--CSSCEEEECEEEEEEEEEEEEEE\n+T ss_pred CCeEEEeeEEEEEcCCC-Cc-ee-ceeEeeeEEEecccceecC----CccccCCC--CCCCceeEceecCCeEeEEEEEE\n+Confidence 45666555444432100 11 22 6678899999998753200 00000000 00001234589999998876653\n+\n+\n+Q NP_000548.2 478 FIDSANNVVYKQYEDMVVESCGCR 501 (501)\n+Q Consensus 478 y~d~~~~~~~~~~~~mvv~~CgC~ 501 (501)\n+ ..=.++..+ ...-+++.+|.|.\n+T Consensus 87 l~C~~g~~~--~~~~~~i~~C~C~ 108 (122)\n+T 5BQE_A 87 LRCSGGMRL--TATYRYILSCHCE 108 (122)\n+T ss_dssp EEBSSSCEE--EEEEEEEEEEEEE\n+T ss_pred EECCCCceE--EEEEEEEEeceee\n+Confidence 332333322 2334578999994\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/NP_000836.2.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/NP_000836.2.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,19542 @@\n+Query NP_000836.2\n+Match_columns 908\n+No_of_seqs 3628 out of 54127\n+Neff 10.7604\n+Searched_HMMs 7012\n+Date Sun Jul 26 14:02:06 2020\n+Command /home/guerler/hh-suite/build/bin/hhblits -i /home/guerler/human/fasta/NP_00/NP_000836.2.fasta -d /home/guerler/pdb70/pdb70 -o /home/guerler/human/hhr/NP_00/NP_000836.2.hhr \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 6N4X_A Metabotropic glutamate 100.0 2.5E-77 1.8E-81 724.0 0.0 801 35-855 30-845 (877)\n+ 2 6N52_B Metabotropic glutamate 100.0 1.2E-76 8.4E-81 718.1 0.0 803 34-856 29-846 (871)\n+ 3 6N51_B Metabotropic glutamate 100.0 6.7E-76 4.8E-80 706.5 0.0 786 37-842 4-804 (804)\n+ 4 6W2Y_A Gamma-aminobutyric acid 100.0 3.8E-66 2.8E-70 620.7 0.0 685 36-853 22-734 (829)\n+ 5 6W2X_B Gamma-aminobutyric acid 100.0 8.6E-65 6.2E-69 611.4 0.0 678 36-852 13-725 (908)\n+ 6 6UO8_A Gamma-aminobutyric acid 100.0 9.3E-65 6.7E-69 605.5 0.0 682 42-856 3-712 (762)\n+ 7 6UO8_B Gamma-aminobutyric acid 100.0 2.2E-64 1.6E-68 602.9 0.0 675 39-852 9-718 (779)\n+ 8 7C7Q_A Gamma-aminobutyric acid 100.0 3.4E-62 2.5E-66 592.4 0.0 685 40-855 166-876 (879)\n+ 9 2E4U_A Metabotropic glutamate 100.0 1.2E-43 8.6E-48 406.8 0.0 535 40-584 9-553 (555)\n+ 10 2E4X_B Metabotropic glutamate 100.0 1.2E-43 8.6E-48 406.8 0.0 535 40-584 9-553 (555)\n+ 11 6N50_A Metabotropic glutamate 100.0 4.1E-43 3E-47 405.6 0.0 536 36-576 42-589 (596)\n+ 12 6N4Y_C Metabotropic glutamate 100.0 4.4E-43 3.2E-47 405.3 0.0 536 36-576 42-589 (596)\n+ 13 5K5S_B Extracellular calcium-s 100.0 1.3E-42 9.6E-47 402.9 0.0 534 39-580 25-609 (615)\n+ 14 5KZQ_A Metabotropic glutamate 100.0 1.7E-42 1.2E-46 398.2 0.0 529 38-580 24-564 (570)\n+ 15 5K5T_A Extracellular calcium-s 100.0 2.4E-42 1.8E-46 400.9 0.0 534 39-580 25-609 (615)\n+ 16 6FFH_A Metabotropic glutamate 100.0 9.6E-38 6.9E-42 309.0 0.0 266 573-852 4-431 (444)\n+ 17 6FFI_A Metabotropic glutamate 100.0 9.6E-38 6.9E-42 309.0 0.0 266 573-852 4-431 (444)\n+ 18 4OR2_B Chimera of Soluble cyto 100.0 1.8E-37 1.3E-41 330.2 0.0 271 570-854 108-380 (389)\n+ 19 6BT5_B Metabotropic glutamate 99.9 2.3E-27 1.7E-31 265.1 0.0 468 40-507 4-471 (479)\n+ 20 6BSZ_A Metabotropic glutamate 99.9 3.3E-27 2.4E-31 263.8 0.0 468 40-507 4-471 (479)\n+ 21 3KS9_B Metabotropic glutamate 99.8 1.4E-26 1E-30 259.8 0.0 465 37-506 9-489 (496)\n+ 22 4XAR_A Metabotropic glutamate 99.8 1.6E-26 1.2E-30 260.6 0.0 462 37-506 32-503 (517)\n+ 23 6B7H_A Metabotropic glutamate 99.8 1.6E-26 1.2E-30 260.6 0.0 462 37-506 32-503 (517)\n+ 24 1EWK_B METABOTROPIC GLUTAMATE 99.8 1.8E-26 1.3E-30 258.4 0.0 464 38-506 5-484 (490)\n+ 25 1EWT_A METABOTROPIC GLUTAMATE 99.8 1.8E-26 1.3E-30 258.4 0.0 464 38-506 5-484 (490)\n+ 26 5C5C_A Metabotropic glutamate 99.8 2E-26 1.4E-30 257.7 0.0 468 38-505 9-480 (481)\n+ 27 3SM9_A Metabotropic glutamate 99.8 2.4E-26 1.7E-30 256.8 0.0 459 40-506 8-476 (479)\n+ 28 4XAQ_A Metabotropic glutamate 99.8 9.3E-26 6.8E-30 253.4 0.0 453 40-506 28-491 (503)\n+ 29 5CNI_A Metabotropic glutamate 99.8 9.3E-26 6.8E-30 253.4 0.0 453 40-506 28-491 (503)\n+ 30 5CNJ_A Metabotropic glutamate 99.8 1.1E-25 7.8E-30 252.8 0.0 454 39-506 27-491 (503)\n+ 31 5FBK_A Extracellular calcium-s 99.8 3.8E-25 2.8E-29 252.0 0.0 460 40-507 53-560 (568)\n+ 32 5FBK_B Extracellular calcium-s 99.8 4.7E-25 3.4E-29 251.3 0.0 460 40-507 53-560 (568)\n+ 33 1DP4_A ATRIAL NATRIURETIC PEPT 99.8 2.8E-24 2E-28 236.6 0.0 369 44-494 1-397 (435)\n+ 34 1DP4_C ATRIAL NATRIURETIC PEPT 99.8 2.8E-24 2E-28 236.6 0.0 369 44-494 1-397 (435)\n+ 35 5X2M_A Taste receptor, type 1, 99.8 4.3E-24 3.1E-28 237.0 0.0 419 35-494 4-43'..b'10 (331)\n+T ss_dssp -CTTHHHHHHHHHHHHHH\n+T ss_pred chhHHHHHHHHHHHHHHH\n+Confidence 456787776665544443\n+\n+\n+No 467\n+>5DHG_B Nociceptin receptor-Cytochrome b562 Chimera; Nociceptin/orphanin FQ peptide receptor, NOP; HET: DGV, OLA, OLC; 3.0A {Escherichia coli}\n+Probab=23.42 E-value=12 Score=36.65 Aligned_cols=34 Identities=18% Similarity=0.097 Sum_probs=17.4 Template_Neff=12.100\n+\n+Q NP_000836.2 644 DTIICSFRRVFLGLGMCFSYAALLTK-TNRIHRIF 677 (908)\n+Q Consensus 644 ~~~~C~~~~~~~~~gf~l~~~~l~~K-~~ri~~if 677 (908)\n+ ....|.+..++..+++...+-.++.- ..|...+.\n+T Consensus 193 ~~~~c~~~~~~~~~~~~~s~~~~~~iai~R~~~i~ 227 (424)\n+T 5DHG_B 193 GNALCKTVIAIDYYNMFTSTFTLTAMSVDRYVAIC 227 (424)\n+T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh\n+Confidence 35678877776655544433333332 33444443\n+\n+\n+No 468\n+>5DHH_B GPCR-BRIL Chimera; Nociceptin/orphanin FQ peptide receptor, NOP; HET: OLA, OLC, DGW; 3.004A {Homo sapiens}\n+Probab=23.42 E-value=12 Score=36.65 Aligned_cols=34 Identities=18% Similarity=0.097 Sum_probs=17.4 Template_Neff=12.100\n+\n+Q NP_000836.2 644 DTIICSFRRVFLGLGMCFSYAALLTK-TNRIHRIF 677 (908)\n+Q Consensus 644 ~~~~C~~~~~~~~~gf~l~~~~l~~K-~~ri~~if 677 (908)\n+ ....|.+..++..+++...+-.++.- ..|...+.\n+T Consensus 193 ~~~~c~~~~~~~~~~~~~s~~~~~~iai~R~~~i~ 227 (424)\n+T 5DHH_B 193 GNALCKTVIAIDYYNMFTSTFTLTAMSVDRYVAIC 227 (424)\n+T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh\n+Confidence 35678877776655544433333332 33444443\n+\n+\n+No 469\n+>4DKL_A Mu-type opioid receptor, lysozyme chimera; G-protein coupled receptor, 7 transmembrane; HET: SO4, CLR, MPG, BF0, 1PE; 2.8A {Mus musculus, Enterobacteria phage T4}\n+Probab=20.35 E-value=15 Score=36.47 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=10.1 Template_Neff=11.900\n+\n+Q NP_000836.2 644 DTIICSFRRVFLGLGMC 660 (908)\n+Q Consensus 644 ~~~~C~~~~~~~~~gf~ 660 (908)\n+ ....|.+..++..+++.\n+T Consensus 85 ~~~~C~~~~~~~~~~~~ 101 (464)\n+T 4DKL_A 85 GNILCKIVISIDYYNMF 101 (464)\n+T ss_dssp CSHHHHHHHHHHHHHHH\n+T ss_pred cchHHHHHHHHHHHHHH\n+Confidence 35678777766554433\n+\n+\n+No 470\n+>5NX2_A Glucagon-like peptide 1 receptor, truncated; 7TM, GPCR, signalling protein, membrane; HET: SOG, 9DQ, 9DZ, 9DT, 9DW, 9DK, NAG; 3.7A {Homo sapiens}\n+Probab=20.13 E-value=16 Score=36.14 Aligned_cols=33 Identities=15% Similarity=0.316 Sum_probs=19.8 Template_Neff=10.600\n+\n+Q NP_000836.2 645 TIICSFRRVFLGLGMCFSYAALLTKTNRIHRIF 677 (908)\n+Q Consensus 645 ~~~C~~~~~~~~~gf~l~~~~l~~K~~ri~~if 677 (908)\n+ +..|.+..++........+.-+++-.+-+++..\n+T Consensus 204 ~~~C~~~~~~~~~~~las~~w~~~~~~~~~~~i 236 (422)\n+T 5NX2_A 204 SLSCRLVFLFMQYCVAANYYWLLVEGVYLYTLL 236 (422)\n+T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC\n+T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 478888777766665555555555554444443\n+\n+\n+No 471\n+>6LN2_A Glucagon-like peptide 1 receptor,Rubredoxin,Glucagon-like peptide; Full length Human GLP1 receptor; HET: 97Y, NAG; 3.2A {Homo sapiens}\n+Probab=20.07 E-value=16 Score=36.87 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=21.7 Template_Neff=8.200\n+\n+Q NP_000836.2 644 DTIICSFRRVFLGLGMCFSYAALLTKTNRIHRIFE 678 (908)\n+Q Consensus 644 ~~~~C~~~~~~~~~gf~l~~~~l~~K~~ri~~if~ 678 (908)\n+ ....|.+..++....+...+.-+++-.+-+++.+.\n+T Consensus 199 ~~~~C~~~~~l~~y~~las~~W~~~~a~~l~~~i~ 233 (469)\n+T 6LN2_A 199 DSLACRLVFLLCQYCVAANYYWLLVEGVYLYTLLA 233 (469)\n+T ss_dssp HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 35778888777766666666666555555444443\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/pdb70_random.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/pdb70_random.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +6W4H_B 1XM9_A +6YZ1_B 3L6X_A +6SPB_2 5D5K_C +3UWD_A 3NMZ_A +5FFO_H 6N4X_A +3RJR_C 6N52_B +5VQF_C 6N51_B +5NTU_A 6W2Y_A +2WZB_A 2WZB_A +1HDI_A 1HDI_A +6Y3A_A 6Y3A_A +3UWD_A 3UWD_A +5FFO_H 5FFO_H +3RJR_C 3RJR_C +5VQF_C 5VQF_C +5NTU_A 5NTU_A +1XM9_A 6W4H_B +3L6X_A 6YZ1_B +5D5K_C 6SPB_2 +3NMZ_A 3UWD_A +6N4X_A 5FFO_H +6N52_B 3RJR_C +6N51_B 5VQF_C +6W2Y_A 5NTU_A \ No newline at end of file |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/pdb70_result.0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/pdb70_result.0.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,4 @@ +NP_000282.1.hhr NP_000282.1.hhr 875.1 2WZB_A 2WZB_A 2WZB_A 2WZB_A +NP_000548.2.hhr NP_000548.2.hhr 353.3 5FFO_H 5FFO_H 5FFO_H 5FFO_H +NP_000548.2.hhr NP_000836.2.hhr 353.3 5FFO_H 6N4X_A 5FFO_H 6N4X_A +NP_000282.1.hhr NP_000290.2.hhr 86.5 2WZB_A 1XM9_A 3UWD_A 3NMZ_A |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/minz/pdb70_result.1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minz/pdb70_result.1.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +NP_000282.1.hhr NP_000282.1.hhr 875.1 2WZB_A 2WZB_A 2WZB_A 2WZB_A +NP_000282.1.hhr NP_000290.2.hhr 86.5 2WZB_A 1XM9_A 3UWD_A 3NMZ_A |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/ACE2_HUMAN.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/ACE2_HUMAN.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,3879 @@\n+Query sp|Q9BYF1|ACE2_HUMAN Angiotensin-converting enzyme 2 OS=Homo sapiens (Human) OX=9606 GN=ACE2 PE=1 SV=2\n+Match_columns 805\n+No_of_seqs 1 out of 1\n+Neff 1\n+Searched_HMMs 82491\n+Date Sat Oct 10 23:55:36 2020\n+Command hhsearch -e 0.001 -i /galaxy-repl/main/files/046/047/dataset_46047478.dat -d hhdb -o /galaxy-repl/main/files/046/091/dataset_46091622.dat \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 6M18_B Sodium-dependent neutra 100.0 4E-194 5E-199 1504.8 0.0 804 2-805 3-814 (814)\n+ 2 1R42_A angiotensin I convertin 100.0 3.4E-78 4.2E-83 582.0 0.0 615 1-615 1-615 (615)\n+ 3 6LZG_A Angiotensin-converting 100.0 5.4E-74 6.6E-79 545.9 0.0 597 19-615 1-597 (597)\n+ 4 3D0I_B Crystal structure of sp 100.0 1.2E-73 1.5E-78 545.2 0.0 596 20-615 2-597 (597)\n+ 5 5AMB_A ANGIOTENSIN-CONVERTING 100.0 1.2E-69 1.5E-74 524.2 0.0 595 20-625 12-614 (629)\n+ 6 6H5W_A Angiotensin-converting 100.0 4.4E-61 5.4E-66 455.7 0.0 579 22-613 5-588 (591)\n+ 7 6S1Y_A Angiotensin-converting 100.0 4.6E-59 5.5E-64 450.3 0.0 579 21-610 11-600 (621)\n+ 8 4CA5_A ANGIOTENSIN-CONVERTING 100.0 3.9E-58 4.7E-63 435.5 0.0 578 22-612 5-587 (589)\n+ 9 5A2R_A ANGIOTENSIN-CONVERTING 100.0 2.8E-56 3.4E-61 425.1 0.0 579 22-611 5-594 (598)\n+ 10 4ASR_A ANGIOTENSIN-CONVERTING 100.0 2.9E-56 3.5E-61 426.4 0.0 578 22-611 6-595 (598)\n+ 11 4CA7_A ANGIOTENSIN-CONVERTING 100.0 3.2E-56 3.9E-61 426.0 0.0 578 22-611 6-595 (598)\n+ 12 2C6F_A ANGIOTENSIN-CONVERTING 100.0 2.3E-52 2.7E-57 400.7 0.0 579 22-611 14-599 (612)\n+ 13 5GIV_E Carboxypeptidase; M32 c 100.0 4.3E-52 5.2E-57 399.6 0.0 474 19-597 3-502 (503)\n+ 14 5GIV_F Carboxypeptidase; M32 c 100.0 4.3E-52 5.2E-57 399.6 0.0 474 19-597 3-502 (503)\n+ 15 3HQ2_B Bacillus subtilis M32 c 100.0 1.1E-47 1.3E-52 361.2 0.0 473 22-597 3-500 (501)\n+ 16 1K9X_B m32 carboxypeptidase; H 100.0 1.1E-46 1.3E-51 357.8 0.0 470 20-593 4-499 (499)\n+ 17 1KA2_A M32 carboxypeptidase; H 100.0 1.1E-46 1.3E-51 357.8 0.0 470 20-593 4-499 (499)\n+ 18 5E3X_A Thermostable carboxypep 100.0 2.4E-46 2.9E-51 356.7 0.0 456 27-597 2-486 (489)\n+ 19 3HOA_A Thermostable carboxypep 100.0 1.1E-45 1.3E-50 356.9 0.0 468 22-594 3-507 (509)\n+ 20 3DWC_B Metallocarboxypeptidase 100.0 2E-44 2.4E-49 343.9 0.0 459 23-593 3-501 (505)\n+ 21 5WVU_C Thermostable carboxypep 100.0 8.4E-44 1E-48 344.0 0.0 469 22-595 3-508 (510)\n+ 22 3SKS_A Putative Oligoendopepti 100.0 1.7E-38 2.1E-43 300.7 0.0 506 22-600 36-564 (567)\n+ 23 3AHN_A Oligopeptidase; HYDROLA 100.0 2.6E-38 3.2E-43 299.3 0.0 505 22-601 33-562 (564)\n+ 24 2QR4_A Peptidase M3B, oligoend 100.0 2E-33 2.4E-38 267.6 0.0 506 23-603 34-578 (587)\n+ 25 2O36_A Thimet oligopeptidase ( 99.9 5E-30 6.1E-35 254.5 0.0 518 26-588 47-660 (674)\n+ 26 3CE2_A Crystal structure of pu 99.9 1.1E-29 1.4E-34 244.3 0.0 507 23-601 67-609 (618)\n+ 27 2O3E_A Neurolysin (E.C.3.4.24. 99.9 9.4E-29 1.1E-33 246.4 0.0 515 31-588 68-676 (678)\n+ 28 5LV0_A Neurolysin, mitochondri 99.9 6.2E-28 7.6E-33 240.2 0.0 504 41-589 83-682 (686)\n+ 29 1S4B_P Thimet oligopeptidase ( 99.9 1.6E-27 2E-32 236.8 0.0 516 26-588 47-660 (674)\n+ 30 5L44_A K-26 dipeptidyl carboxy 99.8 4.9E-23 6E-28 205.4 0.0 512 28-589 76-681 (683)\n+ 31 5L43_B K-26 dipeptidyl carboxy 99.8 4.9E-23 6E-28 205.4 0.0 512 28-589 76-681 (683)\n+ 32 1Y79_1 Peptidyl-Dipeptidase Dc 99.4 4.5E-17 5.4E-22 163.2 0.0 501 41-588 70-676 (680)\n+ 33 4KA7_A Oligopeptidase A, short 99.4 5.8E-17 7.1E-22 163.7 0.0 407 144-589 239-706 (714)\n+ 34 2KNC_B Integrin alpha-IIb, Int 92.7 0.036 4.4E-07 45.3 0.0 31 733-763 2-32 (79)\n+ 35 2L8S_A Integrin alpha-1; Integ 87.6 0.29 '..b'l~~~~~~~~l~i~v~V~~l~~~~~~rYR~~~ 50 (296)\n+T 6KOE_F 11 GPVAEQQSDLILLSIGFMLFIVGVVFVLFTIILVKYRDRK 50 (296)\n+T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHchhcC\n+Confidence 4444333333444444444443333444444556655554\n+\n+\n+No 97\n+>6KOB_B AA3-600 quinol oxidase subunit I; Menaquinol oxidase, Complex, Proton pumping; HET: MQ7, HEA; 3.6A {Bacillus subtilis}\n+Probab=22.61 E-value=76 Score=33.75 Aligned_cols=40 Identities=20% Similarity=0.404 Sum_probs=15.7 Template_Neff=6.100\n+\n+Q sp|Q9BYF1|ACE2 732 GPPNQPPVSIWLIVFGVVMGVIVVGIVILIFTGIRDRKKK 771 (805)\n+Q Consensus 732 gppnqppvsiwlivfgvvmgvivvgiviliftgirdrkkk 771 (805)\n+ ||..+.-..++++.+++.+.|+++.++++++..+|-|+++\n+T Consensus 11 gp~a~~~~~l~~~~~~~~l~i~v~V~~l~~~~~~rYR~~~ 50 (296)\n+T 6KOB_B 11 GPVAEQQSDLILLSIGFMLFIVGVVFVLFTIILVKYRDRK 50 (296)\n+T ss_dssp -----CTTHHHHHHHHHHHHHHHHHHHHTTTSSSSSSCCC\n+T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHchhcC\n+Confidence 4444333333444444444443333444444556655554\n+\n+\n+No 98\n+>1Q90_G Apocytochrome f, Cytochrome b6, Cytochrome; MEMBRANE PROTEIN COMPLEX, PHOTOSYNTHESIS, ELECTRON; HET: LFA, CLA, BCR, SQD, LMG, HEM, TDS; 3.1A {Chlamydomonas reinhardtii} SCOP: f.23.26.1\n+Probab=22.36 E-value=78 Score=26.34 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=22.3 Template_Neff=2.400\n+\n+Q sp|Q9BYF1|ACE2 744 IVFGVVMGVIVVGIVILIFTGIRDRKKKN 772 (805)\n+Q Consensus 744 ivfgvvmgvivvgiviliftgirdrkkkn 772 (805)\n+ +.+|+|.|.|.|.++-|.++....-++.+\n+T Consensus 5 lL~GIVlGli~iTlaGLfv~AY~QyrRg~ 33 (37)\n+T 1Q90_G 5 LLCGIVLGLVPVTIAGLFVTAYLQYLRGD 33 (37)\n+T ss_pred hHHHHHHHhHHHHHHHHHHHHHHHHHhcc\n+Confidence 57899999999998888888765544433\n+\n+\n+No 99\n+>2GSM_B Cytochrome c oxidase subunit 1; transmembrane protein complex, OXIDOREDUCTASE; HET: TRD, DMU, HEA; 2.0A {Rhodobacter sphaeroides} SCOP: f.17.2.1, b.6.1.2\n+Probab=21.90 E-value=80 Score=31.85 Aligned_cols=6 Identities=67% Similarity=1.121 Sum_probs=2.5 Template_Neff=7.600\n+\n+Q sp|Q9BYF1|ACE2 721 SLEFLG 726 (805)\n+Q Consensus 721 sleflg 726 (805)\n+ ||++.|\n+T Consensus 4 ~~~~~~ 9 (262)\n+T 2GSM_B 4 SLEIIG 9 (262)\n+T ss_dssp -CCEEE\n+T ss_pred ccccCC\n+Confidence 455544\n+\n+\n+No 100\n+>3HB3_B Cytochrome c oxidase subunit 1-beta; Electron transfer, Proton transfer, Proton; HET: HEA, LDA, LMT; 2.25A {Paracoccus denitrificans}\n+Probab=21.53 E-value=83 Score=32.92 Aligned_cols=47 Identities=15% Similarity=0.280 Sum_probs=18.3 Template_Neff=6.900\n+\n+Q sp|Q9BYF1|ACE2 725 LGIQPTLGPPNQPPVSIWLIVFGVVMGVIVVGIV-ILIFTGIRDRKKKN 772 (805)\n+Q Consensus 725 lgiqptlgppnqppvsiwlivfgvvmgvivvgiv-iliftgirdrkkkn 772 (805)\n+ ++.|+..+|-.+.-...+-+++++. .+|++++. ++++.-+|-|++++\n+T Consensus 47 ~~~~~~aS~~a~~i~~L~~~~~~i~-~~Ifv~V~~ll~~~i~ryr~~~~ 94 (298)\n+T 3HB3_B 47 MNFQPASSPLAHDQQWLDHFVLYII-TAVTIFVCLLLLICIVRFNRRAN 94 (298)\n+T ss_dssp CSCSCCCSHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHSBTTTS\n+T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHccccCC\n+Confidence 3444444444443333333333332 22222222 23333355555443\n+\n+\n+No 101\n+>5X5V_A GD; herpes simplex virus, pseudorabies virus; 1.5A {Suid herpesvirus 1}\n+Probab=20.11 E-value=93 Score=35.59 Aligned_cols=28 Identities=32% Similarity=0.647 Sum_probs=0.0 Template_Neff=3.400\n+\n+Q sp|Q9BYF1|ACE2 742 WLIVFGVVMGVIVVGIVILIFTGIRDRK 769 (805)\n+Q Consensus 742 wlivfgvvmgvivvgiviliftgirdrk 769 (805)\n+ ..+-.|+.||.|+||+.+.||..+|..|\n+T Consensus 355 v~vgvg~~~~~~~~~~~~~~~~~~~~~~ 382 (402)\n+T 5X5V_A 355 VIVGTGTAMGALLVGVCVYIFFRLRGAK 382 (402)\n+T ss_dssp ----------------------------\n+T ss_pred eehhHHHHHHHHHHHHHHHHHHHccccc\n+Confidence 3456799999999999999998877654\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/SPIKE_SARS2.hhr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/SPIKE_SARS2.hhr Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,5096 @@\n+Query sp|P0DTC2|SPIKE_SARS2 Spike glycoprotein OS=Severe acute respiratory syndrome coronavirus 2 OX=2697049 GN=S PE=1 SV=1\n+Match_columns 1273\n+No_of_seqs 1 out of 1\n+Neff 1\n+Searched_HMMs 82491\n+Date Thu Nov 12 20:44:30 2020\n+Command hhsearch -e 0.001 -i /galaxy-repl/main/files/047/416/dataset_47416633.dat -d hhdb -o /galaxy-repl/main/files/047/416/dataset_47416669.dat \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 6X29_A Spike glycoprotein; Tri 100.0 3E-269 4E-274 2251.1 0.0 1198 16-1213 1-1198(1273)\n+ 2 6CS2_B Spike glycoprotein,Enve 100.0 3E-221 4E-226 1857.5 0.0 1161 31-1213 22-1182(1215)\n+ 3 6Q04_B Spike glycoprotein; Cor 100.0 2E-204 2E-209 1723.9 0.0 1150 31-1224 65-1321(1359)\n+ 4 5I08_C Spike glycoprotein; cor 100.0 2E-199 2E-204 1685.1 0.0 1142 30-1223 29-1293(1299)\n+ 5 5X5F_B S protein; MERS-CoV, sp 100.0 6E-198 7E-203 1670.1 0.0 1163 14-1220 12-1286(1323)\n+ 6 6VSJ_A Spike glycoprotein, Car 100.0 2E-195 3E-200 1649.5 0.0 1145 9-1204 22-1267(1275)\n+ 7 6VSJ_C Spike glycoprotein, Car 100.0 2E-195 3E-200 1649.5 0.0 1145 9-1204 22-1267(1275)\n+ 8 6OHW_A Spike surface glycoprot 100.0 7E-190 9E-195 1602.1 0.0 1144 2-1204 13-1299(1322)\n+ 9 6NZK_A Spike surface glycoprot 100.0 7E-190 9E-195 1602.1 0.0 1144 2-1204 13-1299(1322)\n+ 10 6M15_A Spike glycoprotein; VIR 100.0 6E-154 7E-159 1294.0 0.0 832 273-1215 216-1070(1118)\n+ 11 6M15_B Spike glycoprotein; VIR 100.0 6E-154 7E-159 1294.0 0.0 832 273-1215 216-1070(1118)\n+ 12 6JX7_A Feline Infectious Perit 100.0 2E-132 2E-137 1149.2 0.0 664 525-1216 674-1394(1468)\n+ 13 5SZS_A Spike glycoprotein; cor 100.0 7E-131 9E-136 1128.9 0.0 662 505-1215 575-1283(1325)\n+ 14 6IXB_B Spike glycoprotein; Alp 100.0 8E-129 1E-133 1101.7 0.0 647 518-1214 426-1116(1116)\n+ 15 6CV0_A Spike protein; infectio 100.0 3E-125 3E-130 1068.9 0.0 651 524-1212 399-1074(1105)\n+ 16 6VV5_C Spike glycoprotein; gly 100.0 2E-124 2E-129 1078.6 0.0 641 521-1213 614-1309(1356)\n+ 17 6M3W_B Spike glycoprotein,Spik 100.0 2E-124 2E-129 1000.4 0.0 491 706-1196 1-491 (491)\n+ 18 6U7K_C Spike glycoprotein; PED 100.0 1E-122 1E-127 1065.5 0.0 641 521-1213 629-1324(1399)\n+ 19 6BFU_C Spike protein; coronavi 100.0 4E-119 4E-124 1017.5 0.0 746 267-1148 240-1022(1024)\n+ 20 6B3O_B Spike glycoprotein; Cor 100.0 7E-117 9E-122 954.9 0.0 497 703-1203 45-560 (605)\n+ 21 6PZ8_A S protein, G2 heavy cha 100.0 8E-112 1E-116 897.4 0.0 445 694-1140 12-470 (472)\n+ 22 6PZ8_F S protein, G2 heavy cha 100.0 3.1E-74 3.8E-79 636.3 0.0 621 14-676 12-724 (726)\n+ 23 7BZ5_A Spike protein S1, Heavy 100.0 3.5E-52 4.2E-57 416.5 0.0 225 319-543 1-225 (229)\n+ 24 6YZ5_E Spike glycoprotein, Nan 100.0 3.5E-51 4.3E-56 405.6 0.0 205 330-534 1-205 (210)\n+ 25 6YLA_E SARS-CoV-2 RBD, Heavy C 100.0 3.8E-51 4.6E-56 406.0 0.0 207 328-534 2-208 (213)\n+ 26 6ZFO_A SARS-CoV-2 RBD, Nanobod 100.0 2.3E-47 2.8E-52 375.2 0.0 194 333-526 1-194 (194)\n+ 27 2GHV_C Spike glycoprotein; SAR 100.0 3.9E-37 4.7E-42 305.0 0.0 197 330-527 4-200 (203)\n+ 28 1WYY_A E2 Glycoprotein; membra 100.0 2.3E-36 2.8E-41 288.5 0.0 99 903-1001 3-101 (149)\n+ 29 1WYY_B E2 Glycoprotein; membra 100.0 2.3E-36 2.8E-41 288.5 0.0 99 903-1001 3-101 (149)\n+ 30 5X4S_A Spike glycoprotein; SAR 100.0 1.1E-34 1.4E-39 298.0 0.0 261 30-307 21-281 (285)\n+ 31 5KWB_A Spike glycoprotein; Cor 100.0 1.2E-33 1.4E-38 297.9 0.0 271 316-592 1-370 (371)\n+ 32 6LXT_F Spike protein S2; 2019- 99.9 2.8E-28 3.4E-33 230.5 0.0 112 910-1021 1-113 (132)\n+ 33 6LXT_C 2019-nCoV S2 subunit; 2 99.9 2.8E-28 3.4E-33 230.5 0.0 112 910-1021 1-113 (132)\n+ 34 6C6Z_A Spike protein, CDC2-C2 99.9 6.9E-26 8.3E-31 228.8 0.0 148 319-472 1-148 (231)\n+ 35 5XGR_H Spi'..b'sp TTCHHHHHHHHHHHHHHHHHHHHHHHGGGTCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTC\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 4555666666666666555555554432222 23445666666666666666666666666665543\n+\n+\n+No 128\n+>6W08_B NSP15 endoribnuclease; Tripartite pore forming toxin, Cytotoxin; HET: EDO; 1.75A {Vibrio cholerae O1 biovar El Tor str. N16961}\n+Probab=20.88 E-value=87 Score=32.75 Aligned_cols=55 Identities=15% Similarity=0.317 Sum_probs=27.7 Template_Neff=9.500\n+\n+Q sp|P0DTC2|SPIK 1139 DPLQPELDSFKEELDKYFKNHTSPDVDLGD--------ISGINASVVNIQKEIDRLNEVAKNL 1193 (1273)\n+Q Consensus 1139 dplqpeldsfkeeldkyfknhtspdvdlgd--------isginasvvniqkeidrlnevaknl 1193 (1273)\n+ +.++.+++.|+..|..+...-..-.-++.. ..+.++.+..++++|++|++-.+.+\n+T Consensus 122 ~~~~~~~~~~~~~l~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~L~~~I~~l~~~i~~~ 184 (359)\n+T 6W08_B 122 QSLTSNIKRYDEGLNAWARQVEDAHNTLQQTIAQIQQEEVSIQAEIIATNAQIDLMKQQIAAF 184 (359)\n+T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHH\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 456666667777666554442222222322 1334445556666666665544433\n+\n+\n+No 129\n+>3OGI_C Putative ESAT-6-like protein 6, Putative; Structural Genomics, PSI-2, Protein Structure; HET: MSE; 2.549A {Mycobacterium tuberculosis}\n+Probab=20.43 E-value=90 Score=26.79 Aligned_cols=66 Identities=14% Similarity=0.137 Sum_probs=31.7 Template_Neff=9.500\n+\n+Q sp|P0DTC2|SPIK 921 KLIANQFNSAIGKIQDSLSSTASALGKLQDV-VNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDK 986 (1273)\n+Q Consensus 921 klianqfnsaigkiqdslsstasalgklqdv-vnqnaqalntlvkqlssnfgaissvlndilsrldk 986 (1273)\n+ .-.++.+....+.|++.++.....+..|.+. ....+++......++...+..+...|+++-..|+.\n+T Consensus 11 ~~~a~~l~~~~~~l~~~~~~l~~~~~~l~~~W~G~a~~af~~~~~~~~~~~~~~~~~l~~~~~~l~~ 77 (101)\n+T 3OGI_C 11 DAHGAMIRAQAGLLEAEHQAIVRDVLAAGDFWGGAGSVACQEFITQLGRNFQVIYEQANAHGQKVQA 77 (101)\n+T ss_dssp --CHHHHHHHHHHHHHHHHHHHHHHHHTGGGTTCTTSHHHHHHHHHHHHHHHHHTTCC---------\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 3455666666666666666555555555332 22345555566666666666666666666555544\n+\n+\n+No 130\n+>5HJ3_L Envelope glycoprotein, KZ52 Antibody Fragment; Ebola virus, EOV, Ebolavirus, GP; HET: MAN, NAG, BMA; 3.3A {Ebola virus sp.}\n+Probab=20.10 E-value=93 Score=31.85 Aligned_cols=35 Identities=17% Similarity=0.174 Sum_probs=23.0 Template_Neff=5.300\n+\n+Q sp|P0DTC2|SPIK 930 AIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVK 964 (1273)\n+Q Consensus 930 aigkiqdslsstasalgklqdvvnqnaqalntlvk 964 (1273)\n+ .+....++++.....+..+..+|-||..||.-|.-\n+T Consensus 60 ~~n~t~~al~~L~~~l~sl~~vvLQNR~aLD~Lla 94 (136)\n+T 5HJ3_L 60 LANETTQALQLFLRATTELRTFSILNRKAIDFLLQ 94 (136)\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH\n+Confidence 33444455555555566677888999999887653\n+\n+\n+No 131\n+>6RX1_A Syncytin-1; HUMAN PLACENTAL PROTEIN, MEMBRANE FUSION; 2.1A {Homo sapiens}\n+Probab=20.03 E-value=93 Score=30.99 Aligned_cols=53 Identities=26% Similarity=0.386 Sum_probs=30.7 Template_Neff=5.000\n+\n+Q sp|P0DTC2|SPIK 908 GIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVK 964 (1273)\n+Q Consensus 908 gigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvk 964 (1273)\n+ |.|+++.-+. .+..+....+....++++.....+..+..+|-||..||.-|.-\n+T Consensus 12 ~~~~~~~~l~----~L~~~l~~~~n~t~~al~~L~~~l~sl~~vvLQNR~aLD~Ll~ 64 (108)\n+T 6RX1_A 12 FQSTSTQFYY----KLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTA 64 (108)\n+T ss_dssp ------CHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTG\n+T ss_pred ccchhhHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHH\n+Confidence 5555553222 2333444445556666777777777788899999999887653\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/crossreference.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/crossreference.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,33 @@ +1R42_A 1R42_A 2AJF_A 2AJF_B +1R42_A 6CS2_B 2AJF_A 2AJF_E +1R42_A 6CS2_B 2AJF_A 2AJF_F +1R42_A 1R42_A 2AJF_B 2AJF_A +1R42_A 6CS2_B 2AJF_B 2AJF_E +1R42_A 6CS2_B 2AJF_B 2AJF_F +6CS2_B 1R42_A 2AJF_E 2AJF_A +6CS2_B 1R42_A 2AJF_E 2AJF_B +6CS2_B 6CS2_B 2AJF_E 2AJF_F +6CS2_B 1R42_A 2AJF_F 2AJF_A +6CS2_B 1R42_A 2AJF_F 2AJF_B +6CS2_B 6CS2_B 2AJF_F 2AJF_E +6CS2_B 6CS2_B 6CS2_A 6CS2_B +6CS2_B 6CS2_B 6CS2_A 6CS2_C +6CS2_B 6LZG_A 6CS2_A 6CS2_D +6CS2_B 6CS2_B 6CS2_B 6CS2_A +6CS2_B 6CS2_B 6CS2_B 6CS2_C +6CS2_B 6LZG_A 6CS2_B 6CS2_D +6CS2_B 6CS2_B 6CS2_C 6CS2_A +6CS2_B 6CS2_B 6CS2_C 6CS2_B +6CS2_B 6LZG_A 6CS2_C 6CS2_D +6LZG_A 6CS2_B 6CS2_D 6CS2_A +6LZG_A 6CS2_B 6CS2_D 6CS2_B +6LZG_A 6CS2_B 6CS2_D 6CS2_C +6LZG_A 6YLA_E 6LZG_A 6LZG_B +6YLA_E 6LZG_A 6LZG_B 6LZG_A +1R42_A 6YLA_E 6M0J_A 6M0J_E +6YLA_E 1R42_A 6M0J_E 6M0J_A +6AT5_A 5EJB_D 6ILF_A 6ILF_C +4L8S_C 6AT5_A 6ILF_B 6ILF_A +4L8S_C 5EJB_D 6ILF_B 6ILF_C +5EJB_D 6AT5_A 6ILF_C 6ILF_A +5EJB_D 4L8S_C 6ILF_C 6ILF_B \ No newline at end of file |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/hhr.ffdata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/hhr.ffdata Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,8976 @@\n+Query sp|Q9BYF1|ACE2_HUMAN Angiotensin-converting enzyme 2 OS=Homo sapiens (Human) OX=9606 GN=ACE2 PE=1 SV=2\n+Match_columns 805\n+No_of_seqs 1 out of 1\n+Neff 1\n+Searched_HMMs 82491\n+Date Sat Oct 10 23:55:36 2020\n+Command hhsearch -e 0.001 -i /galaxy-repl/main/files/046/047/dataset_46047478.dat -d hhdb -o /galaxy-repl/main/files/046/091/dataset_46091622.dat \n+\n+ No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n+ 1 6M18_B Sodium-dependent neutra 100.0 4E-194 5E-199 1504.8 0.0 804 2-805 3-814 (814)\n+ 2 1R42_A angiotensin I convertin 100.0 3.4E-78 4.2E-83 582.0 0.0 615 1-615 1-615 (615)\n+ 3 6LZG_A Angiotensin-converting 100.0 5.4E-74 6.6E-79 545.9 0.0 597 19-615 1-597 (597)\n+ 4 3D0I_B Crystal structure of sp 100.0 1.2E-73 1.5E-78 545.2 0.0 596 20-615 2-597 (597)\n+ 5 5AMB_A ANGIOTENSIN-CONVERTING 100.0 1.2E-69 1.5E-74 524.2 0.0 595 20-625 12-614 (629)\n+ 6 6H5W_A Angiotensin-converting 100.0 4.4E-61 5.4E-66 455.7 0.0 579 22-613 5-588 (591)\n+ 7 6S1Y_A Angiotensin-converting 100.0 4.6E-59 5.5E-64 450.3 0.0 579 21-610 11-600 (621)\n+ 8 4CA5_A ANGIOTENSIN-CONVERTING 100.0 3.9E-58 4.7E-63 435.5 0.0 578 22-612 5-587 (589)\n+ 9 5A2R_A ANGIOTENSIN-CONVERTING 100.0 2.8E-56 3.4E-61 425.1 0.0 579 22-611 5-594 (598)\n+ 10 4ASR_A ANGIOTENSIN-CONVERTING 100.0 2.9E-56 3.5E-61 426.4 0.0 578 22-611 6-595 (598)\n+ 11 4CA7_A ANGIOTENSIN-CONVERTING 100.0 3.2E-56 3.9E-61 426.0 0.0 578 22-611 6-595 (598)\n+ 12 2C6F_A ANGIOTENSIN-CONVERTING 100.0 2.3E-52 2.7E-57 400.7 0.0 579 22-611 14-599 (612)\n+ 13 5GIV_E Carboxypeptidase; M32 c 100.0 4.3E-52 5.2E-57 399.6 0.0 474 19-597 3-502 (503)\n+ 14 5GIV_F Carboxypeptidase; M32 c 100.0 4.3E-52 5.2E-57 399.6 0.0 474 19-597 3-502 (503)\n+ 15 3HQ2_B Bacillus subtilis M32 c 100.0 1.1E-47 1.3E-52 361.2 0.0 473 22-597 3-500 (501)\n+ 16 1K9X_B m32 carboxypeptidase; H 100.0 1.1E-46 1.3E-51 357.8 0.0 470 20-593 4-499 (499)\n+ 17 1KA2_A M32 carboxypeptidase; H 100.0 1.1E-46 1.3E-51 357.8 0.0 470 20-593 4-499 (499)\n+ 18 5E3X_A Thermostable carboxypep 100.0 2.4E-46 2.9E-51 356.7 0.0 456 27-597 2-486 (489)\n+ 19 3HOA_A Thermostable carboxypep 100.0 1.1E-45 1.3E-50 356.9 0.0 468 22-594 3-507 (509)\n+ 20 3DWC_B Metallocarboxypeptidase 100.0 2E-44 2.4E-49 343.9 0.0 459 23-593 3-501 (505)\n+ 21 5WVU_C Thermostable carboxypep 100.0 8.4E-44 1E-48 344.0 0.0 469 22-595 3-508 (510)\n+ 22 3SKS_A Putative Oligoendopepti 100.0 1.7E-38 2.1E-43 300.7 0.0 506 22-600 36-564 (567)\n+ 23 3AHN_A Oligopeptidase; HYDROLA 100.0 2.6E-38 3.2E-43 299.3 0.0 505 22-601 33-562 (564)\n+ 24 2QR4_A Peptidase M3B, oligoend 100.0 2E-33 2.4E-38 267.6 0.0 506 23-603 34-578 (587)\n+ 25 2O36_A Thimet oligopeptidase ( 99.9 5E-30 6.1E-35 254.5 0.0 518 26-588 47-660 (674)\n+ 26 3CE2_A Crystal structure of pu 99.9 1.1E-29 1.4E-34 244.3 0.0 507 23-601 67-609 (618)\n+ 27 2O3E_A Neurolysin (E.C.3.4.24. 99.9 9.4E-29 1.1E-33 246.4 0.0 515 31-588 68-676 (678)\n+ 28 5LV0_A Neurolysin, mitochondri 99.9 6.2E-28 7.6E-33 240.2 0.0 504 41-589 83-682 (686)\n+ 29 1S4B_P Thimet oligopeptidase ( 99.9 1.6E-27 2E-32 236.8 0.0 516 26-588 47-660 (674)\n+ 30 5L44_A K-26 dipeptidyl carboxy 99.8 4.9E-23 6E-28 205.4 0.0 512 28-589 76-681 (683)\n+ 31 5L43_B K-26 dipeptidyl carboxy 99.8 4.9E-23 6E-28 205.4 0.0 512 28-589 76-681 (683)\n+ 32 1Y79_1 Peptidyl-Dipeptidase Dc 99.4 4.5E-17 5.4E-22 163.2 0.0 501 41-588 70-676 (680)\n+ 33 4KA7_A Oligopeptidase A, short 99.4 5.8E-17 7.1E-22 163.7 0.0 407 144-589 239-706 (714)\n+ 34 2KNC_B Integrin alpha-IIb, Int 92.7 0.036 4.4E-07 45.3 0.0 31 733-763 2-32 (79)\n+ 35 2L8S_A Integrin alpha-1; Integ 87.6 0.29 '..b'sp TTCHHHHHHHHHHHHHHHHHHHHHHHGGGTCSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTC\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 4555666666666666555555554432222 23445666666666666666666666666665543\n+\n+\n+No 128\n+>6W08_B NSP15 endoribnuclease; Tripartite pore forming toxin, Cytotoxin; HET: EDO; 1.75A {Vibrio cholerae O1 biovar El Tor str. N16961}\n+Probab=20.88 E-value=87 Score=32.75 Aligned_cols=55 Identities=15% Similarity=0.317 Sum_probs=27.7 Template_Neff=9.500\n+\n+Q sp|P0DTC2|SPIK 1139 DPLQPELDSFKEELDKYFKNHTSPDVDLGD--------ISGINASVVNIQKEIDRLNEVAKNL 1193 (1273)\n+Q Consensus 1139 dplqpeldsfkeeldkyfknhtspdvdlgd--------isginasvvniqkeidrlnevaknl 1193 (1273)\n+ +.++.+++.|+..|..+...-..-.-++.. ..+.++.+..++++|++|++-.+.+\n+T Consensus 122 ~~~~~~~~~~~~~l~~f~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~L~~~I~~l~~~i~~~ 184 (359)\n+T 6W08_B 122 QSLTSNIKRYDEGLNAWARQVEDAHNTLQQTIAQIQQEEVSIQAEIIATNAQIDLMKQQIAAF 184 (359)\n+T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHHH\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 456666667777666554442222222322 1334445556666666665544433\n+\n+\n+No 129\n+>3OGI_C Putative ESAT-6-like protein 6, Putative; Structural Genomics, PSI-2, Protein Structure; HET: MSE; 2.549A {Mycobacterium tuberculosis}\n+Probab=20.43 E-value=90 Score=26.79 Aligned_cols=66 Identities=14% Similarity=0.137 Sum_probs=31.7 Template_Neff=9.500\n+\n+Q sp|P0DTC2|SPIK 921 KLIANQFNSAIGKIQDSLSSTASALGKLQDV-VNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDK 986 (1273)\n+Q Consensus 921 klianqfnsaigkiqdslsstasalgklqdv-vnqnaqalntlvkqlssnfgaissvlndilsrldk 986 (1273)\n+ .-.++.+....+.|++.++.....+..|.+. ....+++......++...+..+...|+++-..|+.\n+T Consensus 11 ~~~a~~l~~~~~~l~~~~~~l~~~~~~l~~~W~G~a~~af~~~~~~~~~~~~~~~~~l~~~~~~l~~ 77 (101)\n+T 3OGI_C 11 DAHGAMIRAQAGLLEAEHQAIVRDVLAAGDFWGGAGSVACQEFITQLGRNFQVIYEQANAHGQKVQA 77 (101)\n+T ss_dssp --CHHHHHHHHHHHHHHHHHHHHHHHHTGGGTTCTTSHHHHHHHHHHHHHHHHHTTCC---------\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+Confidence 3455666666666666666555555555332 22345555566666666666666666666555544\n+\n+\n+No 130\n+>5HJ3_L Envelope glycoprotein, KZ52 Antibody Fragment; Ebola virus, EOV, Ebolavirus, GP; HET: MAN, NAG, BMA; 3.3A {Ebola virus sp.}\n+Probab=20.10 E-value=93 Score=31.85 Aligned_cols=35 Identities=17% Similarity=0.174 Sum_probs=23.0 Template_Neff=5.300\n+\n+Q sp|P0DTC2|SPIK 930 AIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVK 964 (1273)\n+Q Consensus 930 aigkiqdslsstasalgklqdvvnqnaqalntlvk 964 (1273)\n+ .+....++++.....+..+..+|-||..||.-|.-\n+T Consensus 60 ~~n~t~~al~~L~~~l~sl~~vvLQNR~aLD~Lla 94 (136)\n+T 5HJ3_L 60 LANETTQALQLFLRATTELRTFSILNRKAIDFLLQ 94 (136)\n+T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHHHH\n+Confidence 33444455555555566677888999999887653\n+\n+\n+No 131\n+>6RX1_A Syncytin-1; HUMAN PLACENTAL PROTEIN, MEMBRANE FUSION; 2.1A {Homo sapiens}\n+Probab=20.03 E-value=93 Score=30.99 Aligned_cols=53 Identities=26% Similarity=0.386 Sum_probs=30.7 Template_Neff=5.000\n+\n+Q sp|P0DTC2|SPIK 908 GIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVK 964 (1273)\n+Q Consensus 908 gigvtqnvlyenqklianqfnsaigkiqdslsstasalgklqdvvnqnaqalntlvk 964 (1273)\n+ |.|+++.-+. .+..+....+....++++.....+..+..+|-||..||.-|.-\n+T Consensus 12 ~~~~~~~~l~----~L~~~l~~~~n~t~~al~~L~~~l~sl~~vvLQNR~aLD~Ll~ 64 (108)\n+T 6RX1_A 12 FQSTSTQFYY----KLSQELNGDMERVADSLVTLQDQLNSLAAVVLQNRRALDLLTA 64 (108)\n+T ss_dssp ------CHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTG\n+T ss_pred ccchhhHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhchhHHHHHHH\n+Confidence 5555553222 2333444445556666777777777788899999999887653\n+\n+\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/hhr.ffindex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/hhr.ffindex Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +sp|Q9BYF1|ACE2_HUMAN 0 287957 +sp|P0DTC2|SPIKE_SARS2 287958 391533 \ No newline at end of file |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/log.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#namea nameb springscore tmscore energy clashes zscore templatea templateb +sp|Q9BYF1|ACE2_HUMAN sp|P0DTC2|SPIKE_SARS2 0.91 0.82 -8.92 0.00 406.00 6LZG_A 6LZG_B |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/pairs.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/pairs.txt Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +sp|Q9BYF1|ACE2_HUMAN sp|P0DTC2|SPIKE_SARS2 \ No newline at end of file |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/pdb_structures.ffdata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/pdb_structures.ffdata Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,122458 @@\n+HEADER HYDROLASE/VIRAL PROTEIN 01-AUG-05 2AJF \n+TITLE STRUCTURE OF SARS CORONAVIRUS SPIKE RECEPTOR-BINDING DOMAIN COMPLEXED \n+TITLE 2 WITH ITS RECEPTOR \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: ANGIOTENSIN-CONVERTING ENZYME-RELATED CARBOXYPEPTIDASE \n+COMPND 3 (ACE2); \n+COMPND 4 CHAIN: A, B; \n+COMPND 5 FRAGMENT: RESIDUES 19-615; \n+COMPND 6 SYNONYM: ACE-RELATED CARBOXYPEPTIDASE, ANGIOTENSIN-CONVERTING ENZYME \n+COMPND 7 HOMOLOG, ACEH; \n+COMPND 8 EC: 3.4.17.-; \n+COMPND 9 ENGINEERED: YES; \n+COMPND 10 MOL_ID: 2; \n+COMPND 11 MOLECULE: SARS-CORONAVIRUS SPIKE PROTEIN; \n+COMPND 12 CHAIN: E, F; \n+COMPND 13 FRAGMENT: RECEPTOR-BINDING DOMAIN, RESIDUES 323-502; \n+COMPND 14 SYNONYM: SPIKE GLYCOPROTEIN, PEPLOMER PROTEIN, E2; \n+COMPND 15 ENGINEERED: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; \n+SOURCE 3 ORGANISM_COMMON: HUMAN; \n+SOURCE 4 ORGANISM_TAXID: 9606; \n+SOURCE 5 GENE: ACE2; \n+SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; \n+SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; \n+SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; \n+SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; \n+SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; \n+SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC 1; \n+SOURCE 12 MOL_ID: 2; \n+SOURCE 13 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; \n+SOURCE 14 ORGANISM_TAXID: 227859; \n+SOURCE 15 STRAIN: SARS; \n+SOURCE 16 GENE: S; \n+SOURCE 17 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; \n+SOURCE 18 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; \n+SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7108; \n+SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: SF9; \n+SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; \n+SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PFASTBAC 1 \n+KEYWDS ANTIPARALLEL BETA SHEET, EXTENDED LOOP, HYDROLASE-VIRAL PROTEIN \n+KEYWDS 2 COMPLEX \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR F.LI,W.LI,M.FARZAN,S.C.HARRISON \n+REVDAT 4 29-JUL-20 2AJF 1 COMPND REMARK HETNAM LINK \n+REVDAT 4 2 1 SITE ATOM \n+REVDAT 3 13-JUL-11 2AJF 1 VERSN \n+REVDAT 2 24-FEB-09 2AJF 1 VERSN \n+REVDAT 1 20-SEP-05 2AJF 0 '..b' \n+CONECT 996410377 \n+CONECT 999321543 \n+CONECT1005410901 \n+CONECT10377 9964 \n+CONECT1090110054 \n+CONECT1099811403 \n+CONECT1140310998 \n+CONECT1159611687 \n+CONECT1168711596 \n+CONECT1178711845 \n+CONECT1184511787 \n+CONECT1225012417 \n+CONECT1229112331 \n+CONECT1233112291 \n+CONECT1241712250 \n+CONECT13940 2390 \n+CONECT1430114387 \n+CONECT1438714301 \n+CONECT1468615044 \n+CONECT1504414686 \n+CONECT1597216085 \n+CONECT1608515972 \n+CONECT1686416937 \n+CONECT1693716864 \n+CONECT1722017427 \n+CONECT1742717220 \n+CONECT1756717980 \n+CONECT17596 6337 \n+CONECT1765718504 \n+CONECT1798017567 \n+CONECT1850417657 \n+CONECT1860119006 \n+CONECT1900618601 \n+CONECT1919919290 \n+CONECT1929019199 \n+CONECT1939019448 \n+CONECT1944819390 \n+CONECT1985320020 \n+CONECT1989419934 \n+CONECT1993419894 \n+CONECT2002019853 \n+CONECT21543 9993 \n+CONECT2190421990 \n+CONECT2199021904 \n+CONECT2228922647 \n+CONECT2264722289 \n+MASTER 1140 0 0 66 180 0 0 622806 3 78 294 \n+END \n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/pdb_structures.ffindex --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/pdb_structures.ffindex Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +2ajf.pdb 0 1135053 +6cs2.pdb 1135053 2523474 +6ilf.pdb 3658527 548208 +6lzg.pdb 4206735 1136349 +6m0j.pdb 5343084 583362 +6m18.pdb 5926446 1974699 +6x29.pdb 7901145 2017953 |
| b |
| diff -r 000000000000 -r dbbcc7cd889f test-data/model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb Tue Mar 23 13:55:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,20118 @@\n+ATOM 1 N THR 0 15 -27.319 51.435 -1.110 0.00 0.00\n+ATOM 2 CA THR 0 15 -28.530 51.067 -0.470 0.00 0.00\n+ATOM 3 CB THR 0 15 -29.354 52.407 -0.327 0.00 0.00\n+ATOM 4 OG1 THR 0 15 -28.715 53.127 0.778 0.00 0.00\n+ATOM 5 CG2 THR 0 15 -30.852 52.264 -0.069 0.00 0.00\n+ATOM 6 C THR 0 15 -29.362 50.054 -1.295 0.00 0.00\n+ATOM 7 O THR 0 15 -29.898 49.095 -0.751 0.00 0.00\n+ATOM 8 N ILE 0 21 -29.424 50.247 -2.611 0.00 0.00\n+ATOM 9 CA ILE 0 21 -30.123 49.325 -3.448 0.00 0.00\n+ATOM 10 CB ILE 0 21 -30.114 49.825 -4.911 0.00 0.00\n+ATOM 11 CG1 ILE 0 21 -30.880 51.152 -5.038 0.00 0.00\n+ATOM 12 CG2 ILE 0 21 -30.700 48.731 -5.781 0.00 0.00\n+ATOM 13 CD1 ILE 0 21 -30.867 51.814 -6.394 0.00 0.00\n+ATOM 14 C ILE 0 21 -29.475 47.880 -3.367 0.00 0.00\n+ATOM 15 O ILE 0 21 -30.167 46.873 -3.263 0.00 0.00\n+ATOM 16 N GLU 0 22 -28.145 47.821 -3.403 0.00 0.00\n+ATOM 17 CA GLU 0 22 -27.493 46.566 -3.298 0.00 0.00\n+ATOM 18 CB GLU 0 22 -25.991 46.780 -3.509 0.00 0.00\n+ATOM 19 CG GLU 0 22 -25.673 47.438 -4.846 0.00 0.00\n+ATOM 20 CD GLU 0 22 -24.187 47.737 -5.079 0.00 0.00\n+ATOM 21 OE1 GLU 0 22 -23.418 47.883 -4.097 0.00 0.00\n+ATOM 22 OE2 GLU 0 22 -23.798 47.857 -6.266 0.00 0.00\n+ATOM 23 C GLU 0 22 -27.751 45.870 -1.935 0.00 0.00\n+ATOM 24 O GLU 0 22 -27.999 44.670 -1.884 0.00 0.00\n+ATOM 25 N GLU 0 23 -27.738 46.637 -0.847 0.00 0.00\n+ATOM 26 CA GLU 0 23 -28.030 46.081 0.439 0.00 0.00\n+ATOM 27 CB GLU 0 23 -27.820 47.163 1.504 0.00 0.00\n+ATOM 28 CG GLU 0 23 -26.410 47.741 1.483 0.00 0.00\n+ATOM 29 CD GLU 0 23 -26.166 48.875 2.484 0.00 0.00\n+ATOM 30 OE1 GLU 0 23 -27.131 49.565 2.898 0.00 0.00\n+ATOM 31 OE2 GLU 0 23 -24.979 49.096 2.835 0.00 0.00\n+ATOM 32 C GLU 0 23 -29.425 45.478 0.476 0.00 0.00\n+ATOM 33 O GLU 0 23 -29.645 44.349 0.936 0.00 0.00\n+ATOM 34 N GLN 0 24 -30.375 46.236 -0.068 0.00 0.00\n+ATOM 35 CA GLN 0 24 -31.780 45.738 -0.095 0.00 0.00\n+ATOM 36 CB GLN 0 24 -32.710 46.859 -0.568 0.00 0.00\n+ATOM 37 CG GLN 0 24 -32.659 48.088 0.347 0.00 0.00\n+ATOM 38 CD GLN 0 24 -33.536 49.233 -0.121 0.00 0.00\n+ATOM 39 OE1 GLN 0 24 -34.759 49.106 -0.202 0.00 0.00\n+ATOM 40 NE2 GLN 0 24 -32.912 50.366 -0.430 0.00 0.00\n+ATOM 41 C GLN 0 24 -31.878 44.524 -0.995 0.00 0.00\n+ATOM 42 O GLN 0 24 -32.633 43.594 -0.716 0.00 0.00\n+ATOM 43 N ALA 0 25 -31.076 44.510 -2.059 0.00 0.00\n+ATOM 44 CA ALA 0 25 -31.058 43.363 -2.984 0.00 0.00\n+ATOM 45 CB ALA 0 25 -30.239 43.619 -4.246 0.00 0.00\n+ATOM 46 C ALA 0 25 -30.612 42.107 -2.275 0.00 0.00\n+ATOM 47 O ALA 0 25 -31.222 41.070 -2.511 0.00 0.00\n+ATOM 48 N LYS 0 26 -29.646 42.164 -1.359 0.00 0.00\n+ATOM 49 CA LYS 0 26 -29.220 41.049 -0.581 0.00 0.00\n+ATOM 50 CB LYS 0 26 -27.942 41.271 0.211 0.00 0.00\n+ATOM 51 CG LYS 0 26 -26.740 41.494 -0.714 0.00 0.00\n+ATOM 52 CD LYS 0 26 -25.449 41.501 0.065 0.00 0.00\n+ATOM 53 CE LYS 0 26 -24.207 41.790 -0.767 0.00 0.00\n+ATOM 54 NZ LYS 0 26 -23.295 42.725 -0.035 0.00 0.00\n+ATOM 55 C LYS 0 26 -30.366 40.551 0.269 0.00 0.00\n+ATOM 56 O LYS 0 26 -30.498 39.332 0.340 0.00 0.00\n+ATOM 57 N THR 0 27 -31.223 41.403 0.815 0.00 0.00\n+ATOM 58 CA THR 0 27 -32.383 41.146 1.544 0.00 0.00\n+ATOM 59 CB THR 0 27 -33'..b'LEU B 518 -27.092 35.368 39.831 1.00 1.00\n+ATOM 6355 N HIS B 519 -24.490 34.792 44.136 1.00 1.00\n+ATOM 6356 CA HIS B 519 -24.133 34.802 45.555 1.00 1.00\n+ATOM 6357 C HIS B 519 -25.434 34.562 46.317 1.00 1.00\n+ATOM 6358 O HIS B 519 -26.069 35.478 46.846 1.00 1.00\n+ATOM 6359 CB HIS B 519 -23.472 36.116 45.960 1.00 1.00\n+ATOM 6360 CG HIS B 519 -22.571 36.702 44.913 1.00 1.00\n+ATOM 6361 ND1 HIS B 519 -22.447 38.062 44.723 1.00 1.00\n+ATOM 6362 CD2 HIS B 519 -21.734 36.121 44.020 1.00 1.00\n+ATOM 6363 CE1 HIS B 519 -21.585 38.293 43.749 1.00 1.00\n+ATOM 6364 NE2 HIS B 519 -21.138 37.132 43.305 1.00 1.00\n+ATOM 6365 N ALA B 520 -25.864 33.306 46.220 1.00 1.00\n+ATOM 6366 CA ALA B 520 -27.143 32.918 46.841 1.00 1.00\n+ATOM 6367 C ALA B 520 -27.192 31.422 47.130 1.00 1.00\n+ATOM 6368 O ALA B 520 -26.193 30.724 46.949 1.00 1.00\n+ATOM 6369 CB ALA B 520 -28.299 33.350 45.973 1.00 1.00\n+ATOM 6370 N PRO B 521 -28.397 30.923 47.428 1.00 1.00\n+ATOM 6371 CA PRO B 521 -28.665 29.559 47.872 1.00 1.00\n+ATOM 6372 C PRO B 521 -27.834 28.356 47.421 1.00 1.00\n+ATOM 6373 O PRO B 521 -27.348 27.705 48.296 1.00 1.00\n+ATOM 6374 CB PRO B 521 -30.088 29.297 47.361 1.00 1.00\n+ATOM 6375 CG PRO B 521 -30.406 30.509 46.518 1.00 1.00\n+ATOM 6376 CD PRO B 521 -29.634 31.618 47.193 1.00 1.00\n+ATOM 6377 N ALA B 522 -27.700 28.151 46.112 1.00 1.00\n+ATOM 6378 CA ALA B 522 -27.109 26.958 45.451 1.00 1.00\n+ATOM 6379 C ALA B 522 -28.060 25.806 45.747 1.00 1.00\n+ATOM 6380 O ALA B 522 -27.901 25.149 46.754 1.00 1.00\n+ATOM 6381 CB ALA B 522 -25.671 26.664 45.789 1.00 1.00\n+ATOM 6382 N THR B 523 -29.050 25.637 44.878 1.00 1.00\n+ATOM 6383 CA THR B 523 -30.113 24.648 45.141 1.00 1.00\n+ATOM 6384 C THR B 523 -30.027 23.457 44.203 1.00 1.00\n+ATOM 6385 O THR B 523 -30.712 22.475 44.517 1.00 1.00\n+ATOM 6386 CB THR B 523 -31.507 25.262 45.014 1.00 1.00\n+ATOM 6387 OG1 THR B 523 -31.448 26.305 44.050 1.00 1.00\n+ATOM 6388 CG2 THR B 523 -32.047 25.787 46.324 1.00 1.00\n+ATOM 6389 N VAL B 524 -29.323 23.554 43.070 1.00 1.00\n+ATOM 6390 CA VAL B 524 -29.279 22.285 42.337 1.00 1.00\n+ATOM 6391 C VAL B 524 -27.894 21.661 42.482 1.00 1.00\n+ATOM 6392 O VAL B 524 -26.978 22.017 41.725 1.00 1.00\n+ATOM 6393 CB VAL B 524 -29.651 22.494 40.857 1.00 1.00\n+ATOM 6394 CG1 VAL B 524 -29.511 21.199 40.054 1.00 1.00\n+ATOM 6395 CG2 VAL B 524 -31.058 23.051 40.743 1.00 1.00\n+ATOM 6396 N CYS B 525 -27.684 20.766 43.453 1.00 1.00\n+ATOM 6397 CA CYS B 525 -26.359 20.149 43.477 1.00 1.00\n+ATOM 6398 C CYS B 525 -26.224 18.882 42.631 1.00 1.00\n+ATOM 6399 O CYS B 525 -25.431 18.840 41.686 1.00 1.00\n+ATOM 6400 CB CYS B 525 -25.982 19.850 44.930 1.00 1.00\n+ATOM 6401 SG CYS B 525 -25.751 21.332 45.937 1.00 1.00\n+ATOM 6402 N GLY B 526 -27.018 17.888 43.011 1.00 1.00\n+ATOM 6403 CA GLY B 526 -27.110 16.586 42.340 1.00 1.00\n+ATOM 6404 C GLY B 526 -25.875 15.708 42.445 1.00 1.00\n+ATOM 6405 O GLY B 526 -24.991 15.861 41.632 1.00 1.00\n+ATOM 6406 N PRO B 527 -25.747 14.782 43.409 1.00 1.00\n+ATOM 6407 CA PRO B 527 -24.645 13.836 43.380 1.00 1.00\n+ATOM 6408 C PRO B 527 -24.736 13.069 42.055 1.00 1.00\n+ATOM 6409 O PRO B 527 -25.756 12.483 41.857 1.00 1.00\n+ATOM 6410 CB PRO B 527 -24.973 12.903 44.547 1.00 1.00\n+ATOM 6411 CG PRO B 527 -25.641 13.812 45.523 1.00 1.00\n+ATOM 6412 CD PRO B 527 -26.500 14.705 44.646 1.00 1.00\n+TER\n' |
| b |
| diff -r 000000000000 -r dbbcc7cd889f tool-data/ffindex_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ffindex_indices.loc.sample Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# ffindex collection, you can add multiple indices here and seperate them via the type (last column) +# The path should point to a directory and the file-prefix ('pdb_prefix'). +# The folder needs to contain two files pdb_prefix.ffindex and pdb_prefix.ffdata +# +#identifer description from the PDB set /mnt/pdb_indices/pdb/pdb_prefix pdb +#identifer description from the HHR set /mnt/hhr/hhr_prefix hhr + |
| b |
| diff -r 000000000000 -r dbbcc7cd889f tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="ffindex_indices" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path, type</columns> + <file path="tool-data/ffindex_indices.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r dbbcc7cd889f tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Mar 23 13:55:42 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of ffindex indexes for testing --> + <table name="ffindex_indices" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path, type</columns> + <file path="${__HERE__}/test-data/ffindex_indices.loc" /> + </table> +</tables> |
