Commit 2dd0d58b authored by Andreas Tille's avatar Andreas Tille
Browse files

Lots of more python to python3 conversions

parent 84e500a0

debian/patches/python3.patch

+816 −0

File changed.

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debian/patches/yaml_load.patch

+69 −0
Original line number Diff line number Diff line
@@ -14,6 +14,42 @@ Description: Specify yaml loader 
         dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))

         support.pretty_print_reads(dataset_data, log)

 

@@ -425,7 +425,7 @@ def fill_cfg(options_to_parse, log, seco

     if load_processed_dataset:

         if os.path.isfile(processed_dataset_fpath):

             try:

-                existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'))

+                existing_dataset_data = pyyaml.load(open(processed_dataset_fpath, 'r'), Loader=pyyaml.FullLoader)

             except pyyaml.YAMLError:

                 existing_dataset_data = None

     if existing_dataset_data is not None:

@@ -433,7 +433,7 @@ def fill_cfg(options_to_parse, log, seco

     else:

         if options_storage.dataset_yaml_filename:

             try:

-                dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'))

+                dataset_data = pyyaml.load(open(options_storage.dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)

             except pyyaml.YAMLError:

                 _, exc, _ = sys.exc_info()

                 support.error('exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))

@@ -792,7 +792,7 @@ def main(args):

             if os.path.isfile(corrected_dataset_yaml_filename) and options_storage.continue_mode \

                     and not options_storage.restart_from == "ec":

                 if not bh_cfg.gzip_output or \

-                        support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))):

+                        support.dataset_has_gzipped_reads(pyyaml.load(open(corrected_dataset_yaml_filename, 'r')), Loader=pyyaml.FullLoader):

                     log.info("\n===== Skipping %s (already processed). \n" % STAGE_NAME)

                     ec_is_needed = False

                 else:

@@ -869,7 +869,7 @@ def main(args):

                     support.continue_from_here(log)

 

                 if os.path.isfile(corrected_dataset_yaml_filename):

-                    dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'))

+                    dataset_data = pyyaml.load(open(corrected_dataset_yaml_filename, 'r'), Loader=pyyaml.FullLoader)

                     dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(corrected_dataset_yaml_filename))

                 if spades_cfg.disable_rr:

                     spades_cfg.__dict__["rr_enable"] = False

--- a/assembler/src/spades_pipeline/hammer_logic.py

+++ b/assembler/src/spades_pipeline/hammer_logic.py

@@ -94,7 +94,7 @@ def prepare_config_ih(filename, cfg, ext
@@ -34,3 +70,36 @@ Description: Specify yaml loader 
     remove_not_corrected_reads(cfg.output_dir)

     is_changed = False

     if cfg.gzip_output:

--- a/assembler/src/spades_pipeline/spades_logic.py

+++ b/assembler/src/spades_pipeline/spades_logic.py

@@ -94,7 +94,7 @@ def get_read_length(output_dir, K, ext_p

             import pyyaml2 as pyyaml

         elif sys.version.startswith('3.'):

             import pyyaml3 as pyyaml

-        est_params_data = pyyaml.load(open(est_params_filename, 'r'))

+        est_params_data = pyyaml.load(open(est_params_filename, 'r'), Loader=pyyaml.FullLoader)

         max_read_length = int(est_params_data['nomerge max read length'])

         log.info("Max read length detected as %d" % max_read_length)

     if max_read_length == 0:

--- a/assembler/src/spades_pipeline/corrector_logic.py

+++ b/assembler/src/spades_pipeline/corrector_logic.py

@@ -24,7 +24,7 @@ def prepare_config_corr(filename, cfg, e

         import pyyaml2 as pyyaml

     elif sys.version.startswith('3.'):

         import pyyaml3 as pyyaml

-    data = pyyaml.load(open(filename, 'r'))

+    data = pyyaml.load(open(filename, 'r'), Loader=pyyaml.FullLoader)

     data["dataset"] = cfg.dataset

     data["output_dir"] = cfg.output_dir

     data["work_dir"] = cfg.tmp_dir

--- a/assembler/src/tools/reads_utils/reads_quality.py

+++ b/assembler/src/tools/reads_utils/reads_quality.py

@@ -148,7 +148,7 @@ print("Analyzing datasets")

 for dataset in datasets:

 

     try:

-        dataset_data = pyyaml.load(file(dataset, 'r'))

+        dataset_data = pyyaml.load(file(dataset, 'r'), Loader=pyyaml.FullLoader)

     except pyyaml.YAMLError, exc:

         support.warning('skipping ' + dataset + ': exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))

         continue