Merge pull request #196 from griffithlab/flask

Merge flask branch into develop

.gitignore

@@ -18,3 +18,4 @@ nytprof.out
 *.o
 *.bs
 /_eumm/
+__pycache__

pvacseq.egg-info/PKG-INFO

@@ -0,0 +1,15 @@
+Metadata-Version: 1.1
+Name: pvacseq
+Version: 3.0.5
+Summary: Personalized Variant Antigens by Cancer Sequencing (pVAC-Seq)
+Home-page: https://github.com/griffithlab/pVAC-Seq
+Author: Jasreet Hundal, Susanna Kiwala, Aaron Graubert, Jason Walker, Chris Miller, Malachi Griffith and Elaine Mardis
+Author-email: pvacseq-support@genome.wustl.edu
+License: NPOSL-3.0
+Description: A cancer immunotherapy pipeline for the identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq)
+Keywords: antigens neoantigens cancer sequencing variant variants
+Platform: UNKNOWN
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python :: 3.5

pvacseq.egg-info/SOURCES.txt

@@ -0,0 +1,63 @@
+pvacseq/__init__.py
+pvacseq/pvacseq.py
+pvacseq.egg-info/PKG-INFO
+pvacseq.egg-info/SOURCES.txt
+pvacseq.egg-info/dependency_links.txt
+pvacseq.egg-info/entry_points.txt
+pvacseq.egg-info/requires.txt
+pvacseq.egg-info/top_level.txt
+pvacseq/VEP_plugins/Wildtype.pm
+pvacseq/example_data/Test_21.key
+pvacseq/example_data/genes.fpkm_tracking
+pvacseq/example_data/input.vcf
+pvacseq/example_data/isoforms.fpkm_tracking
+pvacseq/example_data/class_i/Test.chop.tsv
+pvacseq/example_data/class_i/Test.combined.parsed.tsv
+pvacseq/example_data/class_i/Test.filtered.binding.tsv
+pvacseq/example_data/class_i/Test.filtered.coverage.tsv
+pvacseq/example_data/class_i/Test.final.tsv
+pvacseq/example_data/class_i/Test.stab.tsv
+pvacseq/example_data/class_i/Test.tsv
+pvacseq/example_data/class_i/Test_21.fa
+pvacseq/example_data/class_i/tmp/Test.HLA-E*01:01.10.parsed.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.HLA-E*01:01.9.parsed.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.HLA-G*01:09.10.parsed.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.HLA-G*01:09.9.parsed.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.ann.HLA-E*01:01.10.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.ann.HLA-E*01:01.9.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.pickpocket.HLA-E*01:01.10.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.pickpocket.HLA-E*01:01.9.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.pickpocket.HLA-G*01:09.10.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test.pickpocket.HLA-G*01:09.9.tsv_1-200
+pvacseq/example_data/class_i/tmp/Test_21.fa.split_1-200
+pvacseq/example_data/class_i/tmp/Test_21.fa.split_1-200.key
+pvacseq/example_data/class_ii/Test.chop.tsv
+pvacseq/example_data/class_ii/Test.combined.parsed.tsv
+pvacseq/example_data/class_ii/Test.filtered.binding.tsv
+pvacseq/example_data/class_ii/Test.filtered.coverage.tsv
+pvacseq/example_data/class_ii/Test.final.tsv
+pvacseq/example_data/class_ii/Test.tsv
+pvacseq/example_data/class_ii/Test_31.fa
+pvacseq/example_data/class_ii/tmp/Test.H2-IAb.parsed.tsv_1-200
+pvacseq/example_data/class_ii/tmp/Test.nn_align.H2-IAb.tsv_1-200
+pvacseq/example_data/class_ii/tmp/Test_31.fa.split_1-200
+pvacseq/example_data/class_ii/tmp/Test_31.fa.split_1-200.key
+pvacseq/lib/__init__.py
+pvacseq/lib/binding_filter.py
+pvacseq/lib/call_iedb.py
+pvacseq/lib/combine_parsed_outputs.py
+pvacseq/lib/convert_vcf.py
+pvacseq/lib/coverage_filter.py
+pvacseq/lib/download_example_data.py
+pvacseq/lib/generate_fasta.py
+pvacseq/lib/generate_fasta_key.py
+pvacseq/lib/install_vep_plugin.py
+pvacseq/lib/main.py
+pvacseq/lib/net_chop.py
+pvacseq/lib/netmhc_stab.py
+pvacseq/lib/parse_output.py
+pvacseq/lib/pipeline.py
+pvacseq/lib/prediction_class.py
+pvacseq/lib/valid_alleles.py
+pvacseq/server/__init__.py
+pvacseq/server/app.py

pvacseq.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pvacseq.egg-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+pvacseq = pvacseq.pvacseq:main
+pvacseq-ui = pvacseq.server.app:main
+

pvacseq.egg-info/requires.txt

@@ -0,0 +1,3 @@
+PyVCF
+requests
+connexion

pvacseq.egg-info/top_level.txt

@@ -0,0 +1 @@
+pvacseq

pvacseq/lib/pipeline.py

@@ -56,6 +56,7 @@ def tsv_file_path(self):
 
     def convert_vcf(self):
         print("Converting VCF to TSV")
+        sys.stdout.flush()
         convert_params = [
             self.input_file,
             self.tsv_file_path(),
@@ -107,19 +108,23 @@ def split_fasta_file_and_create_key_files(self):
             if split_end > entry_count:
                 split_end = entry_count
             print("Splitting FASTA into smaller chunks - Entries %d-%d" % (split_start, split_end))
+
             split_fasta_file_path = "%s_%d-%d"%(self.split_fasta_basename(), split_start, split_end)
             if os.path.exists(split_fasta_file_path):
                 print("Split FASTA file for Entries %d-%d already exists. Skipping." % (split_start, split_end))
+
                 [entry for entry in chunk]
             else:
                 split_writer = open(split_fasta_file_path, mode='w')
                 split_writer.writelines(chunk)
                 split_writer.close()
                 print("Completed")
             print("Generating FASTA Key File - Entries %d-%d" % (split_start, split_end))
+
             split_fasta_key_file_path = split_fasta_file_path + '.key'
             if os.path.exists(split_fasta_key_file_path):
                 print("Split FASTA Key File for Entries %d-%d already exists. Skipping." % (split_start, split_end))
+
             else:
                 lib.generate_fasta_key.main([
                     split_fasta_file_path,
@@ -141,6 +146,7 @@ def combined_parsed_path(self):
 
     def combined_parsed_outputs(self, split_parsed_output_files):
         print("Combining Parsed IEDB Output Files")
+        sys.stdout.flush()
         lib.combine_parsed_outputs.main([
             *split_parsed_output_files,
             self.combined_parsed_path()
@@ -152,6 +158,7 @@ def binding_filter_out_path(self):
 
     def binding_filter(self):
         print("Running Binding Filters")
+        sys.stdout.flush()
         lib.binding_filter.main(
             [
                 self.combined_parsed_path(),
@@ -168,6 +175,7 @@ def coverage_filter_out_path(self):
 
     def coverage_filter(self):
         print("Running Coverage Filters")
+        sys.stdout.flush()
         coverage_params = [
             self.binding_filter_out_path(),
             self.coverage_filter_out_path(),
@@ -194,6 +202,7 @@ def net_chop_out_path(self):
 
     def net_chop(self):
         print("Submitting remaining epitopes to NetChop")
+        sys.stdout.flush()
         lib.net_chop.main([
             self.coverage_filter_out_path(),
             self.net_chop_out_path(),
@@ -209,6 +218,7 @@ def netmhc_stab_out_path(self):
 
     def call_netmhc_stab(self):
         print("Running NetMHCStabPan")
+        sys.stdout.flush()
         lib.netmhc_stab.main([
             self.net_chop_out_path(),
             self.netmhc_stab_out_path(),
@@ -265,11 +275,11 @@ def execute(self):
         for symlink in symlinks_to_delete:
             os.unlink(symlink)
 
+
         print("\n")
-        print("Done: pvacseq has completed. File", self.final_path(),
-              "contains list of filtered putative neoantigens")
+        print("Done: pvacseq has completed. File %s contains list of filtered putative neoantigens" % self.final_path())
         print("We recommend appending coverage information and running `pvacseq coverage_filter` to filter based on sequencing coverage information")
-
+        sys.stdout.flush()
         if self.keep_tmp_files is False:
             shutil.rmtree(self.tmp_dir)
 
@@ -320,6 +330,7 @@ def call_iedb_and_parse_outputs(self, chunks):
                             split_iedb_output_files.append(split_iedb_out)
                             continue
                         print("Running IEDB on Allele %s and Epitope Length %s with Method %s - Entries %s" % (a, epl, method, chunk))
+                        sys.stdout.flush()
                         lib.call_iedb.main([
                             split_fasta_file_path,
                             split_iedb_out,
@@ -351,7 +362,6 @@ def call_iedb_and_parse_outputs(self, chunks):
                         lib.parse_output.main(params)
                         print("Completed")
                         split_parsed_output_files.append(split_parsed_file_path)
-
         return split_parsed_output_files
 
 class MHCIIPipeline(Pipeline):
@@ -395,6 +405,7 @@ def call_iedb_and_parse_outputs(self, chunks):
                         split_iedb_output_files.append(split_iedb_out)
                         continue
                     print("Running IEDB on Allele %s with Method %s - Entries %s" % (a, method, chunk))
+                    sys.stdout.flush()
                     lib.call_iedb.main([
                         split_fasta_file_path,
                         split_iedb_out,
@@ -438,4 +449,3 @@ def split_file(reader, lines=400):
             tmp = next(reader)
         except StopIteration:
             return
-

pvacseq/server/.gitignore

@@ -0,0 +1 @@
+pvacseq-ui