allow relative paths in yaml config

ablab · Nov 6, 2023 · e915594 · e915594
1 parent 05af068
commit e915594
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 7 deletions.
diff --git a/src/file_utils.py b/src/file_utils.py
@@ -39,3 +39,10 @@ def merge_files(file_names, merged_file_name, stats_file_names=None, ignore_read
             outf.write("__no_feature\t%d\n" % not_assigned_reads)
             outf.write("__not_aligned\t%d\n" % not_aligned_reads)
 
+
+def normalize_path(config_path, file_path):
+    if os.path.isabs(file_path):
+        return os.path.normpath(file_path)
+    else:
+        return os.path.normpath(os.path.join(os.path.dirname(config_path), file_path))
+
diff --git a/src/input_data_storage.py b/src/input_data_storage.py
@@ -9,6 +9,8 @@
 import yaml
 from collections import defaultdict
 
+from .file_utils import normalize_path
+
 
 logger = logging.getLogger('IsoQuant')
 
@@ -191,16 +193,14 @@ def get_samples_from_file(self, file_name):
     def has_replicas(self):
         return any(len(sample.file_list) > 1 for sample in self.samples)
 
-    def get_samples_from_yaml(self, file_name):
+    def get_samples_from_yaml(self, yaml_file_path):
         # TODO: allow relative paths, i.e. introduce "path fixer" for non-abosulte paths (relative to YAML file)
         sample_files = []
         experiment_names = []
         illumina_bam = []
         readable_names_dict = defaultdict(lambda: defaultdict(str))
-        yaml_file = open(file_name, 'r')
+        yaml_file = open(yaml_file_path, 'r')
         con = yaml.safe_load(yaml_file)
-        current_sample = []
-        current_sample_name = self.experiment_prefix
         current_index = 0
         t = con[0]
         if not 'data format' in t.keys():
@@ -235,7 +235,7 @@ def get_samples_from_yaml(self, file_name):
                 logger.critical("Experiment %s does not contain any files" %current_sample_name)
                 exit(-2)
             else:
-                current_sample = sample['long read files']
+                current_sample = [normalize_path(yaml_file_path, b) for b in sample['long read files']]
                 names = 'labels' in sample.keys()
                 if names and not len(sample['labels']) == len(current_sample):
                     logger.critical("The number of file aliases differs from the number of files")
@@ -254,7 +254,7 @@ def get_samples_from_yaml(self, file_name):
                 sample_files.append([current_sample])
                 experiment_names.append(current_sample_name)
                 if 'illumina bam' in sample.keys():
-                    illumina_bam.append(sample['illumina bam'])
+                    illumina_bam.append([normalize_path(yaml_file_path, ib) for ib in sample['illumina bam']])
                 else:
                     illumina_bam.append(None)
 

diff --git a/tests/console_test.py b/tests/console_test.py
@@ -122,7 +122,7 @@ def test_with_illumina():
                              "-o", out_dir,
                              "--data_type", "nanopore",
                              "--bam", os.path.join(data_dir, "chr9.4M.ont.sim.polya.bam"),
-                             "--illumina_bam", os.path.join(data_dir, "chr9.4M.Illumina.bam")
+                             "--illumina_bam", os.path.join(data_dir, "chr9.4M.Illumina.bam"),
                              "--genedb", os.path.join(data_dir, "chr9.4M.gtf.gz"), "--complete_genedb",
                              "-r",  os.path.join(data_dir, "chr9.4M.fa.gz"),
                              "-t", "2",