Hsp alignment download reformat

.codeclimate.yml

@@ -15,6 +15,41 @@ plugins:
     enabled: true
   stylelint:
     enabled: true
+  duplication:
+    enabled: true
+    # dump_ast and debug are optional for debugging to show the parsing tree
+    config:
+      # dump_ast: true
+      # debug: true
+      languages:
+        javascript:
+          # Filter for sidebar.js to prevent duplication call by the following pattern
+          # Reads like this: "An ExpressionStatement node, with a expression node and an
+          # AssignmentExpression node with any value, that contains a left MemberExpression node
+          # with an object and any Identifier and a property with any Identifier plus a right
+          # MemberExpression node with an object and any Identifier and a property with any Identifier
+          filters:
+          - "(ExpressionStatement (expression (AssignmentExpression _ (left(MemberExpression\
+          (object (Identifier _))(property (Identifier _))false))(right(MemberExpression(object\
+          (Identifier _))(property (Identifier _))false)))))"
+
+          # Filter parsing tree explicitly for the generate_fasta function inside alignment_exporter.js
+          # to prevent duplication call
+          - "(ExpressionStatement(expression(AssignmentExpression _(left(Identifier _))(right\
+          (BinaryExpression(left(BinaryExpression(left(BinaryExpression(left(BinaryExpression(left(BinaryExpression\
+          (left(BinaryExpression(left(BinaryExpression(left(BinaryExpression(left(BinaryExpression(left(BinaryExpression(left\
+          (StringLiteral _ _ _))_(right(MemberExpression(object (Identifier _))(property (Identifier _))false))))_(right\
+          (StringLiteral _ _ _))))_(right(MemberExpression(object (Identifier _))(property (Identifier _))false))))_(right\
+          (StringLiteral _ _ _))))_(right(MemberExpression(object (Identifier _))(property (Identifier _))false))))_(right\
+          (StringLiteral _ _ _))))_(right(MemberExpression(object (Identifier _))(property (Identifier _))false))))_\
+          (right, (StringLiteral _ _ _))))_(right(CallExpression(callee (Identifier _))(arguments(MemberExpression\
+          (object (Identifier _))(property (Identifier _))false))))))_(right (StringLiteral _ _ _)))))))"
+
+          # 45 is default from codeclimate as long as there is no explicit reason to change, we should keep it
+          mass_threshold: 45
+        ruby:
+          # default from codeclimate
+          mass_threshold: 25
 exclude_patterns:
 - public/css/sequenceserver.min.css
 - public/sequenceserver-*.min.js

public/js/alignment_exporter.js

@@ -1,5 +1,6 @@
 import * as Exporter from './exporter';
 import _ from 'underscore';
+import { toLetters } from './visualisation_helpers';
 export default class AlignmentExporter {
     constructor() {}
 
@@ -23,12 +24,13 @@ export default class AlignmentExporter {
         var fasta = '';
 
         _.each(hsps, _.bind(function (hsp) {
-            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'\n';
+            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'_hit_'+hsp.hit_number+'_hsp_'+toLetters(hsp.number)+'\n';
             fasta += hsp.qseq+'\n';
-            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'_alignment_'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
+            fasta += '>'+hsp.query_id+':'+hsp.qstart+'-'+hsp.qend+'_hit_'+hsp.hit_number+'_hsp_'+toLetters(hsp.number)+
+            '_alignment_'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
             fasta += hsp.midline+'\n';
-            fasta += '>'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'\n';
-            fasta += hsp.sseq+'\n';
+            fasta += '>'+hsp.hit_id+':'+hsp.sstart+'-'+hsp.send+'_hit_'+hsp.hit_number+'_hsp_'+toLetters(hsp.number)+'\n';
+            fasta += hsp.sseq+'\n\n';
         }, this));
         return fasta;
     }

public/js/hit.js

@@ -89,6 +89,7 @@ export default class extends Component {
         var hsps = _.map(this.props.hit.hsps, _.bind(function (hsp) {
             hsp.query_id = this.props.query.id;
             hsp.hit_id = this.props.hit.id;
+            hsp.hit_number = this.props.hit.number;
             return hsp;
         }, this));
 

public/js/sidebar.js

@@ -66,6 +66,7 @@ export default class extends Component {
                     hit.hsps.forEach((hsp) => {
                         hsp.query_id = query.id;
                         hsp.hit_id = hit.id;
+                        hsp.hit_number = hit.number;
                         hsps_arr.push(hsp);
                     });
                 }
@@ -91,6 +92,7 @@ export default class extends Component {
                     _.each(hit.hsps, function (hsp) {
                         hsp.hit_id = hit.id;
                         hsp.query_id = query.id;
+                        hsp.hit_number = hit.number;
                         hsps_arr.push(hsp);
                     });
                 }

spec/sequences/MH011443_1_gi_1486783306_gb_MH011443_1.txt

@@ -1,6 +1,7 @@
->MH011443.1:1-123
+>MH011443.1:1-123_hit_1_hsp_a
 TGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCGTGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAT
->MH011443.1:1-123_alignment_gi|1486783306|gb|MH011443.1|:1-123
+>MH011443.1:1-123_hit_1_hsp_a_alignment_gi|1486783306|gb|MH011443.1|:1-123
 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
->gi|1486783306|gb|MH011443.1|:1-123
+>gi|1486783306|gb|MH011443.1|:1-123_hit_1_hsp_a
 TGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCGTGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGAT
+

spec/sequences/MH011443_1_gi_1486783307_gb_AYF55702_1.txt

@@ -1,6 +1,7 @@
->MH011443.1:1-123
+>MH011443.1:1-123_hit_1_hsp_a
 WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:1-123_alignment_gi|1486783307|gb|AYF55702.1|:1-41
+>MH011443.1:1-123_hit_1_hsp_a_alignment_gi|1486783307|gb|AYF55702.1|:1-41
 WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->gi|1486783307|gb|AYF55702.1|:1-41
+>gi|1486783307|gb|AYF55702.1|:1-41_hit_1_hsp_a
 WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
+

spec/sequences/MH011443_1_gi_1528997474_gb_MH447967_1.txt

@@ -1,30 +1,35 @@
->MH011443.1:1-123
+>MH011443.1:1-123_hit_2_hsp_a
 WVDSTPPPGTRVRAVAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:1-123_alignment_gi|1528997474|gb|MH447967.1|:34-156
+>MH011443.1:1-123_hit_2_hsp_a_alignment_gi|1528997474|gb|MH447967.1|:34-156
 WVDSTPPPGTRVRA+AIYKQSQHMTEVVRRCPHHERCSDSD
->gi|1528997474|gb|MH447967.1|:34-156
+>gi|1528997474|gb|MH447967.1|:34-156_hit_2_hsp_a
 WVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSD
->MH011443.1:2-121
+
+>MH011443.1:2-121_hit_2_hsp_b
 RYLSSAHGGGSASQPPSCAVTACRWPRRGRGCRAGVWNQP
->MH011443.1:2-121_alignment_gi|1528997474|gb|MH447967.1|:35-154
+>MH011443.1:2-121_hit_2_hsp_b_alignment_gi|1528997474|gb|MH447967.1|:35-154
 RYLSSAHGGGSASQPPSCAVTACRWP RGRGCRAGVWNQP
->gi|1528997474|gb|MH447967.1|:35-154
+>gi|1528997474|gb|MH447967.1|:35-154_hit_2_hsp_b
 RYLSSAHGGGSASQPPSCAVTACRWPWRGRGCRAGVWNQP
->MH011443.1:3-122
+
+>MH011443.1:3-122_hit_2_hsp_c
 SLSEQRSWWGQRLTTSVMCCDCL*MATARTRVPGGGVEST
->MH011443.1:3-122_alignment_gi|1528997474|gb|MH447967.1|:36-155
+>MH011443.1:3-122_hit_2_hsp_c_alignment_gi|1528997474|gb|MH447967.1|:36-155
 SLSEQRSWWGQRLTTSVMCCDCL*MA ARTRVPGGGVEST
->gi|1528997474|gb|MH447967.1|:36-155
+>gi|1528997474|gb|MH447967.1|:36-155_hit_2_hsp_c
 SLSEQRSWWGQRLTTSVMCCDCL*MAMARTRVPGGGVEST
->MH011443.1:3-86
+
+>MH011443.1:3-86_hit_2_hsp_d
 G*FHTPARHPRPRRGHLQAVTAHDGGCE
->MH011443.1:3-86_alignment_gi|1528997474|gb|MH447967.1|:36-119
+>MH011443.1:3-86_hit_2_hsp_d_alignment_gi|1528997474|gb|MH447967.1|:36-119
 G*FHTPARHPRPR GHLQAVTAHDGGCE
->gi|1528997474|gb|MH447967.1|:36-119
+>gi|1528997474|gb|MH447967.1|:36-119_hit_2_hsp_d
 G*FHTPARHPRPRHGHLQAVTAHDGGCE
->MH011443.1:80-121
+
+>MH011443.1:80-121_hit_2_hsp_e
 L*GAAPTMSAAQIA
->MH011443.1:80-121_alignment_gi|1528997474|gb|MH447967.1|:113-154
+>MH011443.1:80-121_hit_2_hsp_e_alignment_gi|1528997474|gb|MH447967.1|:113-154
 L*GAAPTMSAAQIA
->gi|1528997474|gb|MH447967.1|:113-154
+>gi|1528997474|gb|MH447967.1|:113-154_hit_2_hsp_e
 L*GAAPTMSAAQIA
+

spec/sequences/Query_1_SI2_2_0_06267.txt

@@ -1,6 +1,7 @@
->Query_1:1-199
+>Query_1:1-199_hit_1_hsp_a
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
->Query_1:1-199_alignment_SI2.2.0_06267:1-199
+>Query_1:1-199_hit_1_hsp_a_alignment_SI2.2.0_06267:1-199
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
->SI2.2.0_06267:1-199
+>SI2.2.0_06267:1-199_hit_1_hsp_a
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
+

spec/sequences/alignment-2_hits.txt

@@ -1,12 +1,14 @@
->Query_1:1-199
+>Query_1:1-199_hit_1_hsp_a
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
->Query_1:1-199_alignment_SI2.2.0_06267:1-199
+>Query_1:1-199_hit_1_hsp_a_alignment_SI2.2.0_06267:1-199
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
->SI2.2.0_06267:1-199
+>SI2.2.0_06267:1-199_hit_1_hsp_a
 MNTLWLSLWDYPGKLPLNFMVFDTKDDLQAAYWRDPYSIPLAVIFEDPQPISQRLIYEIRTNPSYTLPPPPTKLYSAPISCRKNKTGHWMDDILSIKTGESCPVNNYLHSGFLALQMITDITKIKLENSDVTIPDIKLIMFPKEPYTADWMLAFRVVIPLYMVLALSQFITYLLILIVGEKENKIKEGMKMMGLNDSVF
->SI2.2.0_13722:1-186
+
+>SI2.2.0_13722:1-186_hit_1_hsp_a
 MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP
->SI2.2.0_13722:1-186_alignment_SI2.2.0_13722:1-186
+>SI2.2.0_13722:1-186_hit_1_hsp_a_alignment_SI2.2.0_13722:1-186
 MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP
->SI2.2.0_13722:1-186
+>SI2.2.0_13722:1-186_hit_1_hsp_a
 MSANRLNVLVTLMLAVALLVTESGNAQVDGYLQFNPKRSAVSSPQKYCGKKLSNALQIICDGVYNSMFKKSGQDFPPQNKRHIAHRINGNEEESFTTLKSNFLNWCVEVYHRHYRFVFVSEMEMADYPLAYDISPYLPPFLSRARARGMLDGRFAGRRYRRESRGIHEECCINGCTINELTSYCGP
+