sequenceserver 0.8.5 → 0.8.6

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Files changed (30) hide show
  1. data/lib/sequenceserver.rb +1 -1
  2. data/public/js/jquery.activity.js +1 -1
  3. data/sequenceserver.gemspec +1 -1
  4. metadata +31 -59
  5. data/lib/blast.rb~ +0 -200
  6. data/lib/sequenceserver/database_formatter.rb~ +0 -190
  7. data/public/css/beige.css~ +0 -226
  8. data/public/js/sequenceserver.js~ +0 -250
  9. data/tests/chromedriver.log +0 -98
  10. data/tests/database/nucleotide/head.fa +0 -10
  11. data/tests/database/nucleotide/head.faVno_parse.html +0 -96
  12. data/tests/database/nucleotide/head.faVparse.html +0 -96
  13. data/tests/database/nucleotide/headVno_parse.archive +0 -151
  14. data/tests/database/nucleotide/headVno_parse.archive.csv +0 -1
  15. data/tests/database/nucleotide/headVparse.archive +0 -148
  16. data/tests/database/nucleotide/headVparse.archive.csv +0 -1
  17. data/tests/database/nucleotide/no_parse.fa +0 -5486
  18. data/tests/database/nucleotide/no_parse.fa.nhr +0 -0
  19. data/tests/database/nucleotide/no_parse.fa.nin +0 -0
  20. data/tests/database/nucleotide/no_parse.fa.nsq +0 -0
  21. data/tests/database/nucleotide/no_parse.info +0 -7
  22. data/tests/database/nucleotide/parse.fa +0 -5486
  23. data/tests/database/nucleotide/parse.fa.nhr +0 -0
  24. data/tests/database/nucleotide/parse.fa.nin +0 -0
  25. data/tests/database/nucleotide/parse.fa.nog +0 -0
  26. data/tests/database/nucleotide/parse.fa.nsd +0 -946
  27. data/tests/database/nucleotide/parse.fa.nsi +0 -0
  28. data/tests/database/nucleotide/parse.fa.nsq +0 -0
  29. data/tests/database/nucleotide/parse.info +0 -7
  30. data/views/search.erb~ +0 -164
data/tests/database/nucleotide/head.faVparse.html DELETED
@@ -1,96 +0,0 @@
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- <HTML>
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- <TITLE>BLAST Search Results</TITLE>
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- <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
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- <PRE>
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-
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- <b>BLASTN 2.2.25+</b>
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-
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-
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- <b><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10890397&dopt=Citation">Reference</a>:</b>
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- Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000),
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- "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000;
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- 7(1-2):203-14.
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-
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-
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-
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- Database: parse.fa
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- 473 sequences; 287,752 total letters
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-
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-
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-
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- <b>Query=</b> SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2
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-
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- Length=540
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- Score E
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- Sequences producing significant alignments: (Bits) Value
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-
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- lcl|SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2 <a href=#SI2.2.0_06267> 998</a> 0.0
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-
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-
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- <script src="blastResult.js"></script>>lcl|SI2.2.0_06267<a name=SI2.2.0_06267></a> Si_gnF.scaffold02592[1282609..1284114].pep_2
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- Length=597
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-
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- Score = 998 bits (540), Expect = 0.0
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- Identities = 540/540 (100%), Gaps = 0/540 (0%)
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- Strand=Plus/Plus
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-
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- Query 1 ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG 60
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 1 ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATG 60
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-
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- Query 61 GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT 120
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 61 GTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCT 120
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-
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- Query 121 CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG 180
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 121 CTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGG 180
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-
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- Query 181 ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT 240
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 181 ACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGT 240
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-
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- Query 241 TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA 300
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 241 TGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAA 300
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-
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- Query 301 TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT 360
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 301 TCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGAT 360
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-
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- Query 361 ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG 420
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 361 ATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATG 420
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-
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- Query 421 TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT 480
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 421 TTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTT 480
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-
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- Query 481 TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG 540
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- ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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- Sbjct 481 TACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG 540
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-
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-
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-
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- Lambda K H
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- 1.33 0.621 1.12
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-
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- Gapped
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- Lambda K H
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- 1.28 0.460 0.850
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-
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- Effective search space used: 145236565
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-
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-
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- Database: parse.fa
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- Posted date: Sep 25, 2011 10:05 AM
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- Number of letters in database: 287,752
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- Number of sequences in database: 473
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-
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-
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-
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- Matrix: blastn matrix 1 -2
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- Gap Penalties: Existence: 0, Extension: 2.5
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- </PRE>
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- </BODY>
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- </HTML>
data/tests/database/nucleotide/headVno_parse.archive DELETED
@@ -1,151 +0,0 @@
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- Blast4-archive ::= {
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- request {
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- ident "",
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- body queue-search {
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- program "blastn",
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- service "megablast",
7
- queries bioseq-set {
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- seq-set {
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- seq {
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- id {
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- local str "Query_1"
12
- },
13
- descr {
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- title "SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2",
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- user {
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- type str "CFastaReader",
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- data {
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- {
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- label str "DefLine",
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- data str ">SI2.2.0_06267
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- Si_gnF.scaffold02592[1282609..1284114].pep_2"
22
- }
23
- }
24
- }
25
- },
26
- inst {
27
- repr raw,
28
- mol na,
29
- length 540,
30
- seq-data ncbi2na '38315DE9DDFCEA3CD5AC27D5F01F4EBBF8460A38DE4249
31
- B3E888D7C493177A4BCDF628554163344987CCCE03CA1835F4C47F9651650503ECF79D634BED80
32
- 83007AD1E8E8613FCD8C005AE0DFB56F043C7E4F7A7DFA779038C1A334408C03E803DE1B843168
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- CF01D30EFD70225B316787A39E97D22FBCF59FC4EB7E9DDD90FCD1F37DE35C32FA62'H
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- }
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- }
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- }
37
- },
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- subject database "no_parse.fa",
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- algorithm-options {
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- {
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- name "EvalueThreshold",
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- value cutoff e-value { 1, 10, 1 }
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- },
44
- {
45
- name "MaskAtHash",
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- value boolean TRUE
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- },
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- {
49
- name "DustFilteringLevel",
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- value integer 20
51
- },
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- {
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- name "DustFilteringWindow",
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- value integer 64
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- },
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- {
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- name "DustFilteringLinker",
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- value integer 1
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- },
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- {
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- name "UngappedMode",
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- value boolean FALSE
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- },
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- {
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- name "ForceMbIndex",
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- value boolean FALSE
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- },
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- {
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- name "MbIndexName",
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- value string "no_parse.fa"
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- },
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- {
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- name "HitlistSize",
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- value integer 250
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- },
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- {
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- name "EffectiveSearchSpace",
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- value big-integer 145236565
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- }
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- }
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- }
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- },
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- results {
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- alignments {
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- {
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- type partial,
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- dim 2,
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- score {
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- {
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- id str "score",
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- value int 540
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- },
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- {
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- id str "e_value",
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- value real { 0, 10, 0 }
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- },
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- {
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- id str "bit_score",
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- value real { 998311106496169, 10, -12 }
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- },
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- {
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- id str "num_ident",
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- value int 540
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- }
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- },
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- segs denseg {
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- dim 2,
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- numseg 1,
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- ids {
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- local str "Query_1",
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- general {
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- db "BL_ORD_ID",
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- tag id 0
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- }
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- },
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- starts {
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- 0,
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- 0
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- },
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- lens {
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- 540
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- },
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- strands {
124
- plus,
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- plus
126
- }
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- }
128
- }
129
- },
130
- masks {
131
- },
132
- ka-blocks {
133
- {
134
- lambda { 133270576282382, 10, -14 },
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- k { 620991117264207, 10, -15 },
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- h { 112409184650115, 10, -14 },
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- gapped FALSE
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- },
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- {
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- lambda { 128, 10, -2 },
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- k { 46, 10, -2 },
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- h { 85, 10, -2 },
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- gapped TRUE
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- }
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- },
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- search-stats {
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- "Effective search space: 145236565",
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- "Effective search space used: 145236565"
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- }
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- }
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- }
data/tests/database/nucleotide/headVno_parse.archive.csv DELETED
@@ -1 +0,0 @@
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- SI2.2.0_06267 0 SI2.2.0_06267 SI2.2.0_06267 540 SI2.2.0_06267 SI2.2.0_06267 0 0 SI2.2.0_06267 SI2.2.0_06267 SI2.2.0_06267 597 1 540 1 540 ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATGGTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCTCTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGGACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGTTGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAATCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGATATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATGTTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTTTACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATGGTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCTCTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGGACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGTTGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAATCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGATATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATGTTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTTTACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG 0.0 998 540 540 100.00 540 0 540 0 0 100.00 1/1 1 1 540
data/tests/database/nucleotide/headVparse.archive DELETED
@@ -1,148 +0,0 @@
1
- Blast4-archive ::= {
2
- request {
3
- ident "",
4
- body queue-search {
5
- program "blastn",
6
- service "megablast",
7
- queries bioseq-set {
8
- seq-set {
9
- seq {
10
- id {
11
- local str "Query_1"
12
- },
13
- descr {
14
- title "SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2",
15
- user {
16
- type str "CFastaReader",
17
- data {
18
- {
19
- label str "DefLine",
20
- data str ">SI2.2.0_06267
21
- Si_gnF.scaffold02592[1282609..1284114].pep_2"
22
- }
23
- }
24
- }
25
- },
26
- inst {
27
- repr raw,
28
- mol na,
29
- length 540,
30
- seq-data ncbi2na '38315DE9DDFCEA3CD5AC27D5F01F4EBBF8460A38DE4249
31
- B3E888D7C493177A4BCDF628554163344987CCCE03CA1835F4C47F9651650503ECF79D634BED80
32
- 83007AD1E8E8613FCD8C005AE0DFB56F043C7E4F7A7DFA779038C1A334408C03E803DE1B843168
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- CF01D30EFD70225B316787A39E97D22FBCF59FC4EB7E9DDD90FCD1F37DE35C32FA62'H
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- }
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- }
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- }
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- },
38
- subject database "parse.fa",
39
- algorithm-options {
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- {
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- name "EvalueThreshold",
42
- value cutoff e-value { 1, 10, 1 }
43
- },
44
- {
45
- name "MaskAtHash",
46
- value boolean TRUE
47
- },
48
- {
49
- name "DustFilteringLevel",
50
- value integer 20
51
- },
52
- {
53
- name "DustFilteringWindow",
54
- value integer 64
55
- },
56
- {
57
- name "DustFilteringLinker",
58
- value integer 1
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- },
60
- {
61
- name "UngappedMode",
62
- value boolean FALSE
63
- },
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- {
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- name "ForceMbIndex",
66
- value boolean FALSE
67
- },
68
- {
69
- name "MbIndexName",
70
- value string "parse.fa"
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- },
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- {
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- name "HitlistSize",
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- value integer 250
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- },
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- {
77
- name "EffectiveSearchSpace",
78
- value big-integer 145236565
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- }
80
- }
81
- }
82
- },
83
- results {
84
- alignments {
85
- {
86
- type partial,
87
- dim 2,
88
- score {
89
- {
90
- id str "score",
91
- value int 540
92
- },
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- {
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- id str "e_value",
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- value real { 0, 10, 0 }
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- },
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- {
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- id str "bit_score",
99
- value real { 998311106496169, 10, -12 }
100
- },
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- {
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- id str "num_ident",
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- value int 540
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- }
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- },
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- segs denseg {
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- dim 2,
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- numseg 1,
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- ids {
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- local str "Query_1",
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- local str "SI2.2.0_06267"
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- },
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- starts {
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- 0,
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- 0
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- },
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- lens {
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- 540
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- },
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- strands {
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- plus,
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- plus
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- }
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- }
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- }
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- },
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- masks {
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- },
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- ka-blocks {
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- {
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- lambda { 133270576282382, 10, -14 },
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- k { 620991117264207, 10, -15 },
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- h { 112409184650115, 10, -14 },
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- gapped FALSE
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- },
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- {
137
- lambda { 128, 10, -2 },
138
- k { 46, 10, -2 },
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- h { 85, 10, -2 },
140
- gapped TRUE
141
- }
142
- },
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- search-stats {
144
- "Effective search space: 145236565",
145
- "Effective search space used: 145236565"
146
- }
147
- }
148
- }
data/tests/database/nucleotide/headVparse.archive.csv DELETED
@@ -1 +0,0 @@
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- SI2.2.0_06267 0 SI2.2.0_06267 SI2.2.0_06267 540 SI2.2.0_06267 SI2.2.0_06267 0 0 SI2.2.0_06267 SI2.2.0_06267 SI2.2.0_06267 597 1 540 1 540 ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATGGTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCTCTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGGACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGTTGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAATCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGATATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATGTTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTTTACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG ATGAATACCCTCTGGCTCTCTTTATGGGATTATCCCGGTAAGCTTCCCTTAAACTTCATGGTGTTTGACACGAAGGATGATCTGCAAGCAGCGTATTGGAGAGATCCTTACAGCATACCTCTGGCAGTTATCTTCGAGGACCCCCAACCGATATCACAGCGACTTATATATGAAATTAGGACGAATCCTTCATACACTTTGCCGCCACCGCCAACCAAATTGTATTCTGCTCCGATCAGTTGTCGAAAGAATAAAACTGGTCACTGGATGGACGACATTTTATCGATAAAAACCGGTGAATCTTGTCCCGTTAACAATTACTTGCATTCTGGCTTCTTGGCTCTGCAAATGATAACGGATATCACAAAGATAAAATTGGAAAATTCTGACGTGACAATACCGGATATTAAACTCATAATGTTTCCTAAAGAGCCGTATACCGCTGACTGGATGCTGGCCTTCAGAGTTGTTATTCCGCTTTACATGGTCTTGGCTCTCTCGCAATTTATCACTTATCTTCTGATCCTAATAGTTGGCGAG 0.0 998 540 540 100.00 540 0 540 0 0 100.00 1/1 1 1 540