protk 1.3.1.pre2 → 1.3.1.pre3
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- checksums.yaml +4 -4
- data/bin/protxml_to_psql.rb +19 -3
- metadata +41 -40
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 7d5d14d3a6fdd45c7ac3be6f122a9a30dd5e3823
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4
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+
data.tar.gz: c77c6b6a83386426ad8a727866f0c0ca8a0c42b5
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 62ddf0c0d8b42a12a34a0f81b866b823a85af7a8cb7908ea6080604fcc64e9fb8c3ad24eb3f7aa8ef6ffc8333d004d778e563fab4e152d054a2dca266c9d0287
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7
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+
data.tar.gz: 19bfc66be4caace10de8c4c602a9ff9ed9d397db2f836b60351350ecade6abf9f046de53b2b717ac1a49e483f470a15337cecb27f6b654b8bd9b51d09bb65c62
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data/bin/protxml_to_psql.rb
CHANGED
@@ -301,7 +301,7 @@ def lookup_spectra_from_files(file_list,matched_spectra)
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|
301
301
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total_spectra=0
|
302
302
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|
303
303
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file_list.each do |file|
|
304
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-
mzml_parser = MzMLParser.new(file)
|
304
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+
mzml_parser = MzMLParser.new(find_file(file))
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305
305
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|
306
306
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spec = mzml_parser.next_spectrum
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307
307
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@@ -334,7 +334,22 @@ def lookup_spectra_from_files(file_list,matched_spectra)
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334
334
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|
335
335
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end
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336
336
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|
337
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-
|
337
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+
def find_file(path)
|
338
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+
if File.exists? path
|
339
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+
return path
|
340
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+
else # Search in search paths
|
341
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+
filename = Pathname.new(path).basename.to_s
|
342
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+
$search_paths.each do |sp|
|
343
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+
pth = File.join(sp,filename)
|
344
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+
if File.exists? pth
|
345
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+
return pth
|
346
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+
end
|
347
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+
end
|
348
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+
end
|
349
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+
return nil
|
350
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+
end
|
351
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+
|
352
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+
# Setup specific command-line options for this tool. Other options are inherited
|
338
353
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#
|
339
354
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tool=Tool.new([:explicit_output,:over_write])
|
340
355
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tool.option_parser.banner = "Convert a protXML file to a sqlite database.\n\nUsage: protxml_to_psql.rb [options] file1.protXML"
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@@ -347,6 +362,7 @@ exit unless tool.check_options(true,[:explicit_output])
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|
347
362
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|
348
363
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input_file=ARGV.shift
|
349
364
|
|
365
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+
$search_paths = [Pathname.new(input_file).dirname.to_s,Pathname.new(".").realpath.to_s]
|
350
366
|
|
351
367
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if File.exists? tool.explicit_output
|
352
368
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throw "Cant overwrite existing db #{tool.explicit_output}" unless tool.over_write
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@@ -386,7 +402,7 @@ matched_spectra=[]
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|
386
402
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headers_with_inputs.each do |header|
|
387
403
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pepxml_files = header.attributes['source_files'].split(",")
|
388
404
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pepxml_files.each do |pepxml_file|
|
389
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-
matched_spectra.concat insert_psms_from_file(pepxml_file)
|
405
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+
matched_spectra.concat insert_psms_from_file(find_file(pepxml_file))
|
390
406
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end
|
391
407
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end
|
392
408
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|
metadata
CHANGED
@@ -1,7 +1,7 @@
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|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: protk
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 1.3.1.
|
4
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+
version: 1.3.1.pre3
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5
5
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platform: ruby
|
6
6
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authors:
|
7
7
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- Ira Cooke
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@@ -216,38 +216,7 @@ extensions:
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|
216
216
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- ext/decoymaker/extconf.rb
|
217
217
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extra_rdoc_files: []
|
218
218
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files:
|
219
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-
-
|
220
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-
- lib/protk/bio_sptr_extensions.rb
|
221
|
-
- lib/protk/command_runner.rb
|
222
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-
- lib/protk/constants.rb
|
223
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-
- lib/protk/convert_util.rb
|
224
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-
- lib/protk/data/make_uniprot_table.rb
|
225
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-
- lib/protk/fastadb.rb
|
226
|
-
- lib/protk/galaxy_stager.rb
|
227
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-
- lib/protk/galaxy_util.rb
|
228
|
-
- lib/protk/gffdb.rb
|
229
|
-
- lib/protk/manage_db_tool.rb
|
230
|
-
- lib/protk/mascot_util.rb
|
231
|
-
- lib/protk/mzml_parser.rb
|
232
|
-
- lib/protk/omssa_util.rb
|
233
|
-
- lib/protk/openms_defaults.rb
|
234
|
-
- lib/protk/peptide.rb
|
235
|
-
- lib/protk/pepxml.rb
|
236
|
-
- lib/protk/plasmodb.rb
|
237
|
-
- lib/protk/prophet_tool.rb
|
238
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-
- lib/protk/protein.rb
|
239
|
-
- lib/protk/protein_to_genome_mapper.rb
|
240
|
-
- lib/protk/protxml_to_gff_tool.rb
|
241
|
-
- lib/protk/randomize.rb
|
242
|
-
- lib/protk/search_tool.rb
|
243
|
-
- lib/protk/setup_tool.rb
|
244
|
-
- lib/protk/swissprot_database.rb
|
245
|
-
- lib/protk/tandem_search_tool.rb
|
246
|
-
- lib/protk/tool.rb
|
247
|
-
- lib/protk/uniprot_mapper.rb
|
248
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-
- lib/protk.rb
|
249
|
-
- lib/protk/manage_db_rakefile.rake
|
250
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-
- lib/protk/setup_rakefile.rake
|
219
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+
- README.md
|
251
220
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- bin/add_retention_times.rb
|
252
221
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- bin/augustus_to_proteindb.rb
|
253
222
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- bin/interprophet.rb
|
@@ -271,14 +240,22 @@ files:
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|
271
240
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- bin/tandem_to_pepxml.rb
|
272
241
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- bin/unimod_to_loc.rb
|
273
242
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- bin/uniprot_mapper.rb
|
274
|
-
-
|
275
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-
-
|
276
|
-
- lib/protk
|
277
|
-
- lib/protk/
|
243
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+
- ext/decoymaker/decoymaker.c
|
244
|
+
- ext/decoymaker/extconf.rb
|
245
|
+
- lib/protk.rb
|
246
|
+
- lib/protk/bio_gff3_extensions.rb
|
247
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+
- lib/protk/bio_sptr_extensions.rb
|
248
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+
- lib/protk/command_runner.rb
|
249
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+
- lib/protk/constants.rb
|
250
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+
- lib/protk/convert_util.rb
|
278
251
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- lib/protk/data/ExecutePipeline.trf
|
279
252
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- lib/protk/data/FeatureFinderCentroided.ini
|
280
253
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- lib/protk/data/FeatureFinderIsotopeWavelet.ini
|
254
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+
- lib/protk/data/apt-get_packages.yaml
|
255
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+
- lib/protk/data/brew_packages.yaml
|
256
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+
- lib/protk/data/default_config.yml
|
281
257
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- lib/protk/data/galaxyenv.sh
|
258
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+
- lib/protk/data/make_uniprot_table.rb
|
282
259
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- lib/protk/data/predefined_db.crap.yaml
|
283
260
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- lib/protk/data/predefined_db.sphuman.yaml
|
284
261
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- lib/protk/data/predefined_db.swissprot_annotation.yaml
|
@@ -293,8 +270,31 @@ files:
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|
293
270
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- lib/protk/data/uniprot_accessions_table.txt
|
294
271
|
- lib/protk/data/uniprot_input_accessions.loc
|
295
272
|
- lib/protk/data/yum_packages.yaml
|
296
|
-
-
|
297
|
-
-
|
273
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+
- lib/protk/fastadb.rb
|
274
|
+
- lib/protk/galaxy_stager.rb
|
275
|
+
- lib/protk/galaxy_util.rb
|
276
|
+
- lib/protk/gffdb.rb
|
277
|
+
- lib/protk/manage_db_rakefile.rake
|
278
|
+
- lib/protk/manage_db_tool.rb
|
279
|
+
- lib/protk/mascot_util.rb
|
280
|
+
- lib/protk/mzml_parser.rb
|
281
|
+
- lib/protk/omssa_util.rb
|
282
|
+
- lib/protk/openms_defaults.rb
|
283
|
+
- lib/protk/peptide.rb
|
284
|
+
- lib/protk/pepxml.rb
|
285
|
+
- lib/protk/plasmodb.rb
|
286
|
+
- lib/protk/prophet_tool.rb
|
287
|
+
- lib/protk/protein.rb
|
288
|
+
- lib/protk/protein_to_genome_mapper.rb
|
289
|
+
- lib/protk/protxml_to_gff_tool.rb
|
290
|
+
- lib/protk/randomize.rb
|
291
|
+
- lib/protk/search_tool.rb
|
292
|
+
- lib/protk/setup_rakefile.rake
|
293
|
+
- lib/protk/setup_tool.rb
|
294
|
+
- lib/protk/swissprot_database.rb
|
295
|
+
- lib/protk/tandem_search_tool.rb
|
296
|
+
- lib/protk/tool.rb
|
297
|
+
- lib/protk/uniprot_mapper.rb
|
298
298
|
homepage: http://rubygems.org/gems/protk
|
299
299
|
licenses:
|
300
300
|
- LGPL-2.1
|
@@ -315,8 +315,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
315
315
|
version: 1.3.1
|
316
316
|
requirements: []
|
317
317
|
rubyforge_project:
|
318
|
-
rubygems_version: 2.
|
318
|
+
rubygems_version: 2.2.1
|
319
319
|
signing_key:
|
320
320
|
specification_version: 4
|
321
321
|
summary: Proteomics Toolkit
|
322
322
|
test_files: []
|
323
|
+
has_rdoc:
|