bio 1.3.1 → 1.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (303) hide show
  1. data/ChangeLog +2105 -3728
  2. data/KNOWN_ISSUES.rdoc +35 -3
  3. data/README.rdoc +8 -2
  4. data/RELEASE_NOTES.rdoc +166 -0
  5. data/bin/bioruby +4 -1
  6. data/bioruby.gemspec +146 -1
  7. data/bioruby.gemspec.erb +3 -1
  8. data/doc/ChangeLog-before-1.3.1 +3961 -0
  9. data/doc/Tutorial.rd +154 -22
  10. data/doc/Tutorial.rd.html +125 -68
  11. data/lib/bio.rb +21 -6
  12. data/lib/bio/appl/bl2seq/report.rb +11 -202
  13. data/lib/bio/appl/blast/format0.rb +0 -193
  14. data/lib/bio/appl/blast/report.rb +2 -147
  15. data/lib/bio/appl/blast/wublast.rb +0 -208
  16. data/lib/bio/appl/fasta.rb +4 -19
  17. data/lib/bio/appl/fasta/format10.rb +0 -14
  18. data/lib/bio/appl/genscan/report.rb +0 -176
  19. data/lib/bio/appl/hmmer.rb +1 -15
  20. data/lib/bio/appl/hmmer/report.rb +0 -100
  21. data/lib/bio/appl/meme/mast.rb +156 -0
  22. data/lib/bio/appl/meme/mast/report.rb +91 -0
  23. data/lib/bio/appl/meme/motif.rb +48 -0
  24. data/lib/bio/appl/psort.rb +0 -111
  25. data/lib/bio/appl/psort/report.rb +1 -45
  26. data/lib/bio/appl/pts1.rb +2 -4
  27. data/lib/bio/appl/sosui/report.rb +5 -54
  28. data/lib/bio/appl/targetp/report.rb +1 -104
  29. data/lib/bio/appl/tmhmm/report.rb +0 -36
  30. data/lib/bio/command.rb +94 -10
  31. data/lib/bio/data/aa.rb +1 -77
  32. data/lib/bio/data/codontable.rb +1 -95
  33. data/lib/bio/data/na.rb +1 -26
  34. data/lib/bio/db/aaindex.rb +1 -38
  35. data/lib/bio/db/fasta.rb +1 -134
  36. data/lib/bio/db/fasta/format_qual.rb +204 -0
  37. data/lib/bio/db/fasta/qual.rb +102 -0
  38. data/lib/bio/db/fastq.rb +645 -0
  39. data/lib/bio/db/fastq/fastq_to_biosequence.rb +40 -0
  40. data/lib/bio/db/fastq/format_fastq.rb +175 -0
  41. data/lib/bio/db/genbank/genbank.rb +1 -86
  42. data/lib/bio/db/gff.rb +0 -17
  43. data/lib/bio/db/go.rb +4 -72
  44. data/lib/bio/db/kegg/common.rb +112 -0
  45. data/lib/bio/db/kegg/compound.rb +29 -20
  46. data/lib/bio/db/kegg/drug.rb +74 -34
  47. data/lib/bio/db/kegg/enzyme.rb +26 -5
  48. data/lib/bio/db/kegg/genes.rb +128 -15
  49. data/lib/bio/db/kegg/genome.rb +3 -41
  50. data/lib/bio/db/kegg/glycan.rb +19 -24
  51. data/lib/bio/db/kegg/orthology.rb +16 -56
  52. data/lib/bio/db/kegg/reaction.rb +81 -28
  53. data/lib/bio/db/kegg/taxonomy.rb +1 -52
  54. data/lib/bio/db/litdb.rb +1 -16
  55. data/lib/bio/db/phyloxml/phyloxml.xsd +582 -0
  56. data/lib/bio/db/phyloxml/phyloxml_elements.rb +1174 -0
  57. data/lib/bio/db/phyloxml/phyloxml_parser.rb +954 -0
  58. data/lib/bio/db/phyloxml/phyloxml_writer.rb +228 -0
  59. data/lib/bio/db/prosite.rb +2 -95
  60. data/lib/bio/db/rebase.rb +5 -6
  61. data/lib/bio/db/sanger_chromatogram/abif.rb +120 -0
  62. data/lib/bio/db/sanger_chromatogram/chromatogram.rb +133 -0
  63. data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb +32 -0
  64. data/lib/bio/db/sanger_chromatogram/scf.rb +210 -0
  65. data/lib/bio/io/das.rb +0 -44
  66. data/lib/bio/io/ddbjxml.rb +1 -181
  67. data/lib/bio/io/flatfile.rb +1 -7
  68. data/lib/bio/io/flatfile/autodetection.rb +6 -0
  69. data/lib/bio/io/keggapi.rb +0 -442
  70. data/lib/bio/io/ncbirest.rb +130 -132
  71. data/lib/bio/io/ncbisoap.rb +2 -1
  72. data/lib/bio/io/pubmed.rb +0 -88
  73. data/lib/bio/location.rb +0 -73
  74. data/lib/bio/pathway.rb +0 -171
  75. data/lib/bio/sequence.rb +18 -1
  76. data/lib/bio/sequence/adapter.rb +3 -0
  77. data/lib/bio/sequence/format.rb +16 -0
  78. data/lib/bio/sequence/quality_score.rb +205 -0
  79. data/lib/bio/tree.rb +70 -5
  80. data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -2
  81. data/lib/bio/util/sirna.rb +1 -23
  82. data/lib/bio/version.rb +1 -1
  83. data/sample/demo_aaindex.rb +67 -0
  84. data/sample/demo_aminoacid.rb +101 -0
  85. data/sample/demo_bl2seq_report.rb +220 -0
  86. data/sample/demo_blast_report.rb +285 -0
  87. data/sample/demo_codontable.rb +119 -0
  88. data/sample/demo_das.rb +105 -0
  89. data/sample/demo_ddbjxml.rb +212 -0
  90. data/sample/demo_fasta_remote.rb +51 -0
  91. data/sample/demo_fastaformat.rb +105 -0
  92. data/sample/demo_genbank.rb +132 -0
  93. data/sample/demo_genscan_report.rb +202 -0
  94. data/sample/demo_gff1.rb +49 -0
  95. data/sample/demo_go.rb +98 -0
  96. data/sample/demo_hmmer_report.rb +149 -0
  97. data/sample/demo_kegg_compound.rb +57 -0
  98. data/sample/demo_kegg_drug.rb +65 -0
  99. data/sample/demo_kegg_genome.rb +74 -0
  100. data/sample/demo_kegg_glycan.rb +72 -0
  101. data/sample/demo_kegg_orthology.rb +62 -0
  102. data/sample/demo_kegg_reaction.rb +66 -0
  103. data/sample/demo_kegg_taxonomy.rb +92 -0
  104. data/sample/demo_keggapi.rb +502 -0
  105. data/sample/demo_litdb.rb +42 -0
  106. data/sample/demo_locations.rb +99 -0
  107. data/sample/demo_ncbi_rest.rb +130 -0
  108. data/sample/demo_nucleicacid.rb +49 -0
  109. data/sample/demo_pathway.rb +196 -0
  110. data/sample/demo_prosite.rb +120 -0
  111. data/sample/demo_psort.rb +138 -0
  112. data/sample/demo_psort_report.rb +70 -0
  113. data/sample/demo_pubmed.rb +118 -0
  114. data/sample/demo_sirna.rb +63 -0
  115. data/sample/demo_sosui_report.rb +89 -0
  116. data/sample/demo_targetp_report.rb +135 -0
  117. data/sample/demo_tmhmm_report.rb +68 -0
  118. data/sample/pmfetch.rb +13 -4
  119. data/sample/pmsearch.rb +15 -4
  120. data/sample/test_phyloxml_big.rb +205 -0
  121. data/test/bioruby_test_helper.rb +61 -0
  122. data/test/data/KEGG/1.1.1.1.enzyme +935 -0
  123. data/test/data/KEGG/C00025.compound +102 -0
  124. data/test/data/KEGG/D00063.drug +104 -0
  125. data/test/data/KEGG/G00024.glycan +47 -0
  126. data/test/data/KEGG/G01366.glycan +18 -0
  127. data/test/data/KEGG/K02338.orthology +902 -0
  128. data/test/data/KEGG/R00006.reaction +14 -0
  129. data/test/data/fastq/README.txt +109 -0
  130. data/test/data/fastq/error_diff_ids.fastq +20 -0
  131. data/test/data/fastq/error_double_qual.fastq +22 -0
  132. data/test/data/fastq/error_double_seq.fastq +22 -0
  133. data/test/data/fastq/error_long_qual.fastq +20 -0
  134. data/test/data/fastq/error_no_qual.fastq +20 -0
  135. data/test/data/fastq/error_qual_del.fastq +20 -0
  136. data/test/data/fastq/error_qual_escape.fastq +20 -0
  137. data/test/data/fastq/error_qual_null.fastq +0 -0
  138. data/test/data/fastq/error_qual_space.fastq +21 -0
  139. data/test/data/fastq/error_qual_tab.fastq +21 -0
  140. data/test/data/fastq/error_qual_unit_sep.fastq +20 -0
  141. data/test/data/fastq/error_qual_vtab.fastq +20 -0
  142. data/test/data/fastq/error_short_qual.fastq +20 -0
  143. data/test/data/fastq/error_spaces.fastq +20 -0
  144. data/test/data/fastq/error_tabs.fastq +21 -0
  145. data/test/data/fastq/error_trunc_at_plus.fastq +19 -0
  146. data/test/data/fastq/error_trunc_at_qual.fastq +19 -0
  147. data/test/data/fastq/error_trunc_at_seq.fastq +18 -0
  148. data/test/data/fastq/error_trunc_in_plus.fastq +19 -0
  149. data/test/data/fastq/error_trunc_in_qual.fastq +20 -0
  150. data/test/data/fastq/error_trunc_in_seq.fastq +18 -0
  151. data/test/data/fastq/error_trunc_in_title.fastq +17 -0
  152. data/test/data/fastq/illumina_full_range_as_illumina.fastq +8 -0
  153. data/test/data/fastq/illumina_full_range_as_sanger.fastq +8 -0
  154. data/test/data/fastq/illumina_full_range_as_solexa.fastq +8 -0
  155. data/test/data/fastq/illumina_full_range_original_illumina.fastq +8 -0
  156. data/test/data/fastq/longreads_as_illumina.fastq +40 -0
  157. data/test/data/fastq/longreads_as_sanger.fastq +40 -0
  158. data/test/data/fastq/longreads_as_solexa.fastq +40 -0
  159. data/test/data/fastq/longreads_original_sanger.fastq +120 -0
  160. data/test/data/fastq/misc_dna_as_illumina.fastq +16 -0
  161. data/test/data/fastq/misc_dna_as_sanger.fastq +16 -0
  162. data/test/data/fastq/misc_dna_as_solexa.fastq +16 -0
  163. data/test/data/fastq/misc_dna_original_sanger.fastq +16 -0
  164. data/test/data/fastq/misc_rna_as_illumina.fastq +16 -0
  165. data/test/data/fastq/misc_rna_as_sanger.fastq +16 -0
  166. data/test/data/fastq/misc_rna_as_solexa.fastq +16 -0
  167. data/test/data/fastq/misc_rna_original_sanger.fastq +16 -0
  168. data/test/data/fastq/sanger_full_range_as_illumina.fastq +8 -0
  169. data/test/data/fastq/sanger_full_range_as_sanger.fastq +8 -0
  170. data/test/data/fastq/sanger_full_range_as_solexa.fastq +8 -0
  171. data/test/data/fastq/sanger_full_range_original_sanger.fastq +8 -0
  172. data/test/data/fastq/solexa_full_range_as_illumina.fastq +8 -0
  173. data/test/data/fastq/solexa_full_range_as_sanger.fastq +8 -0
  174. data/test/data/fastq/solexa_full_range_as_solexa.fastq +8 -0
  175. data/test/data/fastq/solexa_full_range_original_solexa.fastq +8 -0
  176. data/test/data/fastq/wrapping_as_illumina.fastq +12 -0
  177. data/test/data/fastq/wrapping_as_sanger.fastq +12 -0
  178. data/test/data/fastq/wrapping_as_solexa.fastq +12 -0
  179. data/test/data/fastq/wrapping_original_sanger.fastq +24 -0
  180. data/test/data/meme/db +0 -0
  181. data/test/data/meme/mast +0 -0
  182. data/test/data/meme/mast.out +13 -0
  183. data/test/data/meme/meme.out +3 -0
  184. data/test/data/phyloxml/apaf.xml +666 -0
  185. data/test/data/phyloxml/bcl_2.xml +2097 -0
  186. data/test/data/phyloxml/made_up.xml +144 -0
  187. data/test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml +65 -0
  188. data/test/data/phyloxml/phyloxml_examples.xml +415 -0
  189. data/test/data/sanger_chromatogram/test_chromatogram_abif.ab1 +0 -0
  190. data/test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf +0 -0
  191. data/test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf +0 -0
  192. data/test/functional/bio/appl/test_pts1.rb +7 -5
  193. data/test/functional/bio/io/test_ensembl.rb +4 -3
  194. data/test/functional/bio/io/test_pubmed.rb +9 -3
  195. data/test/functional/bio/io/test_soapwsdl.rb +5 -4
  196. data/test/functional/bio/io/test_togows.rb +5 -4
  197. data/test/functional/bio/sequence/test_output_embl.rb +6 -4
  198. data/test/functional/bio/test_command.rb +54 -5
  199. data/test/runner.rb +5 -3
  200. data/test/unit/bio/appl/bl2seq/test_report.rb +5 -4
  201. data/test/unit/bio/appl/blast/test_ncbioptions.rb +4 -2
  202. data/test/unit/bio/appl/blast/test_report.rb +5 -4
  203. data/test/unit/bio/appl/blast/test_rpsblast.rb +5 -4
  204. data/test/unit/bio/appl/gcg/test_msf.rb +5 -5
  205. data/test/unit/bio/appl/genscan/test_report.rb +8 -9
  206. data/test/unit/bio/appl/hmmer/test_report.rb +5 -4
  207. data/test/unit/bio/appl/iprscan/test_report.rb +6 -5
  208. data/test/unit/bio/appl/mafft/test_report.rb +6 -5
  209. data/test/unit/bio/appl/meme/mast/test_report.rb +46 -0
  210. data/test/unit/bio/appl/meme/test_mast.rb +103 -0
  211. data/test/unit/bio/appl/meme/test_motif.rb +38 -0
  212. data/test/unit/bio/appl/paml/codeml/test_rates.rb +5 -4
  213. data/test/unit/bio/appl/paml/codeml/test_report.rb +5 -4
  214. data/test/unit/bio/appl/paml/test_codeml.rb +5 -4
  215. data/test/unit/bio/appl/sim4/test_report.rb +5 -4
  216. data/test/unit/bio/appl/sosui/test_report.rb +6 -5
  217. data/test/unit/bio/appl/targetp/test_report.rb +5 -3
  218. data/test/unit/bio/appl/test_blast.rb +5 -4
  219. data/test/unit/bio/appl/test_fasta.rb +4 -2
  220. data/test/unit/bio/appl/test_pts1.rb +4 -2
  221. data/test/unit/bio/appl/tmhmm/test_report.rb +6 -5
  222. data/test/unit/bio/data/test_aa.rb +5 -3
  223. data/test/unit/bio/data/test_codontable.rb +5 -4
  224. data/test/unit/bio/data/test_na.rb +5 -3
  225. data/test/unit/bio/db/biosql/tc_biosql.rb +5 -1
  226. data/test/unit/bio/db/embl/test_common.rb +4 -2
  227. data/test/unit/bio/db/embl/test_embl.rb +6 -6
  228. data/test/unit/bio/db/embl/test_embl_rel89.rb +6 -6
  229. data/test/unit/bio/db/embl/test_embl_to_bioseq.rb +7 -8
  230. data/test/unit/bio/db/embl/test_sptr.rb +6 -8
  231. data/test/unit/bio/db/embl/test_uniprot.rb +6 -5
  232. data/test/unit/bio/db/fasta/test_format_qual.rb +346 -0
  233. data/test/unit/bio/db/kegg/test_compound.rb +146 -0
  234. data/test/unit/bio/db/kegg/test_drug.rb +194 -0
  235. data/test/unit/bio/db/kegg/test_enzyme.rb +241 -0
  236. data/test/unit/bio/db/kegg/test_genes.rb +32 -4
  237. data/test/unit/bio/db/kegg/test_glycan.rb +260 -0
  238. data/test/unit/bio/db/kegg/test_orthology.rb +50 -0
  239. data/test/unit/bio/db/kegg/test_reaction.rb +96 -0
  240. data/test/unit/bio/db/pdb/test_pdb.rb +4 -2
  241. data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +76 -0
  242. data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +98 -0
  243. data/test/unit/bio/db/test_aaindex.rb +6 -6
  244. data/test/unit/bio/db/test_fasta.rb +5 -46
  245. data/test/unit/bio/db/test_fastq.rb +829 -0
  246. data/test/unit/bio/db/test_gff.rb +4 -2
  247. data/test/unit/bio/db/test_lasergene.rb +7 -5
  248. data/test/unit/bio/db/test_medline.rb +4 -2
  249. data/test/unit/bio/db/test_newick.rb +6 -6
  250. data/test/unit/bio/db/test_nexus.rb +4 -2
  251. data/test/unit/bio/db/test_phyloxml.rb +769 -0
  252. data/test/unit/bio/db/test_phyloxml_writer.rb +328 -0
  253. data/test/unit/bio/db/test_prosite.rb +6 -5
  254. data/test/unit/bio/db/test_qual.rb +63 -0
  255. data/test/unit/bio/db/test_rebase.rb +5 -3
  256. data/test/unit/bio/db/test_soft.rb +7 -6
  257. data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -7
  258. data/test/unit/bio/io/flatfile/test_buffer.rb +6 -5
  259. data/test/unit/bio/io/flatfile/test_splitter.rb +4 -4
  260. data/test/unit/bio/io/test_ddbjxml.rb +4 -3
  261. data/test/unit/bio/io/test_ensembl.rb +5 -3
  262. data/test/unit/bio/io/test_fastacmd.rb +4 -3
  263. data/test/unit/bio/io/test_flatfile.rb +6 -5
  264. data/test/unit/bio/io/test_soapwsdl.rb +4 -3
  265. data/test/unit/bio/io/test_togows.rb +4 -2
  266. data/test/unit/bio/sequence/test_aa.rb +5 -3
  267. data/test/unit/bio/sequence/test_common.rb +4 -2
  268. data/test/unit/bio/sequence/test_compat.rb +4 -2
  269. data/test/unit/bio/sequence/test_dblink.rb +5 -3
  270. data/test/unit/bio/sequence/test_na.rb +4 -2
  271. data/test/unit/bio/sequence/test_quality_score.rb +330 -0
  272. data/test/unit/bio/shell/plugin/test_seq.rb +5 -3
  273. data/test/unit/bio/test_alignment.rb +5 -3
  274. data/test/unit/bio/test_command.rb +4 -3
  275. data/test/unit/bio/test_db.rb +5 -3
  276. data/test/unit/bio/test_feature.rb +4 -2
  277. data/test/unit/bio/test_location.rb +4 -2
  278. data/test/unit/bio/test_map.rb +5 -3
  279. data/test/unit/bio/test_pathway.rb +4 -2
  280. data/test/unit/bio/test_reference.rb +4 -2
  281. data/test/unit/bio/test_sequence.rb +5 -3
  282. data/test/unit/bio/test_shell.rb +5 -3
  283. data/test/unit/bio/test_tree.rb +6 -6
  284. data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +4 -2
  285. data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +4 -2
  286. data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +4 -2
  287. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +4 -2
  288. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +4 -2
  289. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +4 -2
  290. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +4 -2
  291. data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +4 -2
  292. data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +4 -2
  293. data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +4 -2
  294. data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +4 -2
  295. data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +4 -2
  296. data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +17 -13
  297. data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +17 -13
  298. data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +4 -2
  299. data/test/unit/bio/util/test_color_scheme.rb +5 -3
  300. data/test/unit/bio/util/test_contingency_table.rb +5 -3
  301. data/test/unit/bio/util/test_restriction_enzyme.rb +4 -2
  302. data/test/unit/bio/util/test_sirna.rb +6 -4
  303. metadata +147 -2
data/test/data/KEGG/R00006.reaction ADDED
@@ -0,0 +1,14 @@
1
+ ENTRY R00006 Reaction
2
+ NAME pyruvate:pyruvate acetaldehydetransferase (decarboxylating);
3
+ 2-acetolactate pyruvate-lyase (carboxylating)
4
+ DEFINITION 2-Acetolactate + CO2 <=> 2 Pyruvate
5
+ EQUATION C00900 + C00011 <=> 2 C00022
6
+ COMMENT TPP-dependent enzymatic reaction (R00014+R03050)
7
+ RPAIR RP: RP00440 C00022_C00900 main
8
+ RP: RP05698 C00011_C00022 leave
9
+ RP: RP12733 C00022_C00900 trans
10
+ PATHWAY PATH: rn00770 Pantothenate and CoA biosynthesis
11
+ ENZYME 2.2.1.6
12
+ ORTHOLOGY KO: K01652 acetolactate synthase I/II/III large subunit
13
+ [EC:2.2.1.6]
14
+ KO: K01653 acetolactate synthase I/III small subunit [EC:2.2.1.6]
data/test/data/fastq/README.txt ADDED
@@ -0,0 +1,109 @@
1
+ This README file describes the FASTQ example files provided as supplementary
2
+ information to the open-access publication:
3
+
4
+ P.J.A. Cock, C.J. Fields, N. Goto, M.L. Heuer and P.M. Rice (2009). The Sanger
5
+ FASTQ file format for sequences with quality scores, and the Solexa/Illumina
6
+ FASTQ variants.
7
+
8
+ These files are provided freely and we encourage anyone writing a FASTQ parser
9
+ to use them as part of your test suite. Permission is granted to freely
10
+ distribute and modify the files. We request (but do not insist) that this
11
+ README file is included, or at least a reference to the above paper. Please
12
+ cite the above paper if appropriate. We also request (but do not insist) that
13
+ the example files are not modified, in order that they may serve as a common
14
+ reference.
15
+
16
+ Invalid FASTQ files
17
+ ===================
18
+
19
+ The archive contains the following sample FASTQ files with names of the form
20
+ error_NAME.fastq, which all contain errors and should be rejected (if parsed
21
+ as any of the three FASTQ variants):
22
+
23
+ error_diff_ids.fastq
24
+ error_double_qual.fastq
25
+ error_double_seq.fastq
26
+ error_long_qual.fastq
27
+ error_no_qual.fastq
28
+ error_qual_del.fastq
29
+ error_qual_escape.fastq
30
+ error_qual_null.fastq
31
+ error_qual_space.fastq
32
+ error_qual_tab.fastq
33
+ error_qual_unit_sep.fastq
34
+ error_qual_vtab.fastq
35
+ error_short_qual.fastq
36
+ error_spaces.fastq
37
+ error_tabs.fastq
38
+ error_trunc_at_seq.fastq
39
+ error_trunc_at_plus.fastq
40
+ error_trunc_at_qual.fastq
41
+ error_trunc_in_title.fastq
42
+ error_trunc_in_seq.fastq
43
+ error_trunc_in_plus.fastq
44
+ error_trunc_in_qual.fastq
45
+
46
+ Of these, those with names error_qual_XXX.fastq would be valid except for the
47
+ inclusion of spaces or non-printing ASCII characters outside the range allowed
48
+ in the quality string. The files named error_trunc_XXX.fastq would be valid
49
+ but for being truncated (e.g. simulating a partial copy over the network).
50
+
51
+ The special cases of FASTQ files which would be valid as one variant, but not
52
+ another, are covered below.
53
+
54
+ Valid FASTQ
55
+ ===========
56
+
57
+ The archive contains the following valid sample FASTQ input files for testing:
58
+
59
+ longreads_original_sanger.fastq
60
+ wrapping_original_sanger.fastq
61
+ illumina_full_range_original_illumina.fastq
62
+ sanger_full_range_original_sanger.fastq
63
+ solexa_full_range_original_solexa.fastq
64
+ misc_dna_original_sanger.fastq
65
+ misc_rna_original_sanger.fastq
66
+
67
+ These all have the form NAME_original_FORMAT.fastq, where NAME is a prefix for
68
+ that example, and FORMAT is one of sanger, solexa or illumina indicating which
69
+ FASTQ variant that example is using. There are three matching files called
70
+ NAME_as_FORMAT.fastq showing how the original file should be converted into
71
+ each of the three FASTQ variants. These converted files are standardised not
72
+ to use line wrapping (so each record has exactly four lines), and omit the
73
+ optional repetition of the read titles on the plus line.
74
+
75
+ The file longreads_original_sanger.fastq is based on real Roche 454 reads from
76
+ the Sanger Institute for the the potato cyst nematodes Globodera pallida. Ten
77
+ of the reads have been presented as FASTQ records, wrapping the sequence and
78
+ the quality lines at 80 characters. This means some of the quality lines start
79
+ with "@" or "+" characters, which may cause problems with naive parsers. Also
80
+ note that the sequence is mixed case (with upper case denoting the trimmed
81
+ region), and furthermore the free format title lines are over 100 characters
82
+ and encode assorted read information (and are repeated on the "+" lines).
83
+
84
+ The wrapping_original_sanger.fastq is based on three real reads from the NCBI
85
+ Short Read Archive, but has been carefully edited to use line wrapping for the
86
+ quality lines (but not the sequence lines) such that the due to the occurrence
87
+ of "@" and "+" on alternating lines, the file may be misinterpreted by a
88
+ simplistic parser. While this is therefore a very artificial example, it
89
+ remains a valid FASTQ file, and is useful for testing purposes.
90
+
91
+ The sanger_full_range_original_sanger.fastq file uses PHRED scores from 0 to
92
+ 93 inclusive, covering ASCII characters from 33 (!) to 126 (~). This means it
93
+ cannot be treated as a Solexa or Illumina 1.3+ FASTQ file, and attempting to
94
+ parse it as such should raise an error.
95
+
96
+ The solexa_full_range_original_solexa.fastq file uses Solexa scores from -5 to
97
+ 62 inclusive, covering ASCII characters from 59 (;) to 126 (~). This means it
98
+ cannot be treated as a Illumina 1.3+ FASTQ file, and attempting to parse it as
99
+ such should raise an error. On the basis of the quality characters, the file
100
+ would also qualify as a valid Sanger FASTQ file.
101
+
102
+ The illumina_full_range_original_illumina.fastq file uses PHRED scores from 0
103
+ to 62 inclusive, covering ASCII characters from 64 (@) to 126 (~). On the
104
+ basis of the quality characters, the file would also qualify as a valid Sanger
105
+ or Solexa FASTQ file.
106
+
107
+ The misc_dna_original_sanger.fastq and misc_rna_original_sanger.fastq files
108
+ are artificial reads using the full range of IUPAC DNA or RNA letters,
109
+ including ambiguous character codes, and both cases.
data/test/data/fastq/error_diff_ids.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_124
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_double_qual.fastq ADDED
@@ -0,0 +1,22 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
14
+ YYYYYYYYYYYYYWYYWYYSYYYSY
15
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ GGAAACAAAGTTTTTCTCAACATAG
17
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
18
+ YYYYYYYYYYYYYYYYYYWWWWYWY
19
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ GTATTATTTAATGGCATACACTCAA
21
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
22
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_double_seq.fastq ADDED
@@ -0,0 +1,22 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ GGAAACAAAGTTTTTCTCAACATAG
17
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
18
+ YYYYYYYYYYYYYYYYYYWWWWYWY
19
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ GTATTATTTAATGGCATACACTCAA
21
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
22
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_long_qual.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWYY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_no_qual.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGC
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+
data/test/data/fastq/error_qual_del.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_qual_escape.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_qual_space.fastq ADDED
@@ -0,0 +1,21 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYY WWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
21
+
data/test/data/fastq/error_qual_tab.fastq ADDED
@@ -0,0 +1,21 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYY YYYYWYWWUWWWQQ
21
+
data/test/data/fastq/error_qual_unit_sep.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_qual_vtab.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYY YYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_short_qual.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYS
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYYYWYYYYWYWWUWWWQQ
data/test/data/fastq/error_spaces.fastq ADDED
@@ -0,0 +1,20 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAA TACCTTTGTA GAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYY YYYYYYYYYW YWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGA AAGAGAAATG AGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYY WYYYYWWYYY WYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTT GATCATGATG ATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYY YYYYWYYWYY SYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAA GTTTTTCTCA ACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYY YYYYYYYYYW WWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTT AATGGCATAC ACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYY YWYYYYWYWW UWWWQQ
data/test/data/fastq/error_tabs.fastq ADDED
@@ -0,0 +1,21 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAA TACCTTTGTA GAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYY YYYYYYYYYW YWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGA AAGAGAAATG AGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYY WYYYYWWYYY WYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTT GATCATGATG ATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYY YYYYWYYWYY SYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAA GTTTTTCTCA ACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYY YYYYYYYYYW WWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTT AATGGCATAC ACTCAA
19
+ +SLXA-B3_649_FC8437_R1_1_1_183_714
20
+ YYYYYYYYY YWYYYYWYWW UWWWQQ
21
+
data/test/data/fastq/error_trunc_at_plus.fastq ADDED
@@ -0,0 +1,19 @@
1
+ @SLXA-B3_649_FC8437_R1_1_1_610_79
2
+ GATGTGCAATACCTTTGTAGAGGAA
3
+ +SLXA-B3_649_FC8437_R1_1_1_610_79
4
+ YYYYYYYYYYYYYYYYYYWYWYYSU
5
+ @SLXA-B3_649_FC8437_R1_1_1_397_389
6
+ GGTTTGAGAAAGAGAAATGAGATAA
7
+ +SLXA-B3_649_FC8437_R1_1_1_397_389
8
+ YYYYYYYYYWYYYYWWYYYWYWYWW
9
+ @SLXA-B3_649_FC8437_R1_1_1_850_123
10
+ GAGGGTGTTGATCATGATGATGGCG
11
+ +SLXA-B3_649_FC8437_R1_1_1_850_123
12
+ YYYYYYYYYYYYYWYYWYYSYYYSY
13
+ @SLXA-B3_649_FC8437_R1_1_1_362_549
14
+ GGAAACAAAGTTTTTCTCAACATAG
15
+ +SLXA-B3_649_FC8437_R1_1_1_362_549
16
+ YYYYYYYYYYYYYYYYYYWWWWYWY
17
+ @SLXA-B3_649_FC8437_R1_1_1_183_714
18
+ GTATTATTTAATGGCATACACTCAA
19
+