Merge pull request #96 from daichengxin/master

Fix bug
bigbio · Jul 28, 2021 · 9902bd0 · 9902bd0
2 parents 1e28afa + 0d29c51
commit 9902bd0
Show file tree

Hide file tree

Showing 2 changed files with 34 additions and 17 deletions.
diff --git a/sdrf_pipelines/openms/openms.py b/sdrf_pipelines/openms/openms.py
@@ -387,6 +387,7 @@ def writeTwoTableExperimentalDesign(self, output_filename, sdrf, file2technical_
         sample_id_map = {}
         sample_id = 1
         pre_frac_group = 1
+        raw_frac = {}
         for _0, row in sdrf.iterrows():
             raw = row["comment[data file]"]
             source_name = row["source name"]
@@ -399,16 +400,24 @@ def writeTwoTableExperimentalDesign(self, output_filename, sdrf, file2technical_
                 offset = offset + int(source_name2n_reps[source_name_list[i]])
 
             fraction_group = offset + int(replicate)
-            if raw in Fraction_group.keys():
-                if fraction_group < Fraction_group[raw]:
+
+            if fraction_group not in raw_frac:
+                raw_frac[fraction_group] = [raw]
+
+                if raw in Fraction_group.keys():
+                    if fraction_group < Fraction_group[raw]:
+                        Fraction_group[raw] = fraction_group
+                else:
                     Fraction_group[raw] = fraction_group
-            else:
-                Fraction_group[raw] = fraction_group
 
-            # make fraction group consecutive
-            if Fraction_group[raw] > pre_frac_group + 1:
-                Fraction_group[raw] = pre_frac_group + 1
-            pre_frac_group = Fraction_group[raw]
+                # make fraction group consecutive
+                if Fraction_group[raw] > pre_frac_group + 1:
+                    Fraction_group[raw] = pre_frac_group + 1
+                pre_frac_group = Fraction_group[raw]
+
+            else:
+                raw_frac[fraction_group].append(raw)
+                Fraction_group[raw] = Fraction_group[raw_frac[fraction_group][0]]
 
             if re.search(sample_identifier_re, source_name) is not None:
                 sample = re.search(sample_identifier_re, source_name).group(1)
@@ -553,6 +562,7 @@ def writeOneTableExperimentalDesign(self, output_filename, legacy, sdrf, file2te
         sample_id_map = {}
         sample_id = 1
         pre_frac_group = 1
+        raw_frac = {}
         for _0, row in sdrf.iterrows():
             raw = row["comment[data file]"]
             source_name = row["source name"]
@@ -566,16 +576,23 @@ def writeOneTableExperimentalDesign(self, output_filename, legacy, sdrf, file2te
 
             fraction_group = offset + int(replicate)
 
-            if raw in Fraction_group.keys():
-                if fraction_group < Fraction_group[raw]:
+            if fraction_group not in raw_frac:
+                raw_frac[fraction_group] = [raw]
+
+                if raw in Fraction_group.keys():
+                    if fraction_group < Fraction_group[raw]:
+                        Fraction_group[raw] = fraction_group
+                else:
                     Fraction_group[raw] = fraction_group
-            else:
-                Fraction_group[raw] = fraction_group
 
-            # make fraction group consecutive
-            if Fraction_group[raw] > pre_frac_group + 1:
-                Fraction_group[raw] = pre_frac_group + 1
-            pre_frac_group = Fraction_group[raw]
+                # make fraction group consecutive
+                if Fraction_group[raw] > pre_frac_group + 1:
+                    Fraction_group[raw] = pre_frac_group + 1
+                pre_frac_group = Fraction_group[raw]
+
+            else:
+                raw_frac[fraction_group].append(raw)
+                Fraction_group[raw] = Fraction_group[raw_frac[fraction_group][0]]
 
             if re.search(sample_identifier_re, source_name) is not None:
                 sample = re.search(sample_identifier_re, source_name).group(1)

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
   name="sdrf-pipelines",
-  version="0.0.17",
+  version="0.0.18",
   author="BigBio Team",
   author_email="ypriverol@gmail.com",
   description="Translate, convert SDRF to configuration pipelines",