Hicpro: fix parsing scientific notation in hicpro-ashic. Thanks @Just…

…-Roma (#2126) * Hicpro: fix parsing numbers is scientific notation. Thanks @Just-Roma * [automated] Update CHANGELOG.md --------- Co-authored-by: MultiQC Bot <multiqc-bot@seqera.io> Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
MultiQC · Oct 16, 2023 · 21aded9 · 21aded9
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Showing 2 changed files with 14 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,7 @@
 ### Module updates
 
 - **FastQC**: Add top overrepresented sequences table ([#2075](https://github.com/ewels/MultiQC/pull/2075))
+- **HiCPro**: fix parsing scientific notation in hicpro-ashic. Thanks @Just-Roma ([#2126](https://github.com/ewels/MultiQC/pull/2126))
 - **Picard**: MarkDuplicates: Fix parsing mixed strings/numbers, account for missing trailing `0` ([#2083](https://github.com/ewels/MultiQC/pull/2083), [#2094](https://github.com/ewels/MultiQC/pull/2094))
 - **WhatsHap**: Process truncated input with no ALL chromosome ([#2095](https://github.com/ewels/MultiQC/pull/2095))
 

diff --git a/multiqc/modules/hicpro/hicpro.py b/multiqc/modules/hicpro/hicpro.py
@@ -140,7 +140,7 @@ def __init__(self):
             self.add_section(
                 name="Capture analysis",
                 anchor="hicpro-cap",
-                description="Selection of interactions overlaping the targeted region(s).",
+                description="Selection of interactions overlapping the targeted region(s).",
                 helptext="""
                 Description of capture efficiency. Valid interactions with either two (capture-capture) or
                 one (capture-reporter) interactors overlapping with the target(s) are reported.""",
@@ -159,7 +159,18 @@ def parse_hicpro_stats(self, f, rsection):
                 s = l.split("\t")
                 if s[0] in self.hicpro_data[s_name]:
                     log.debug("Duplicated keys found! Overwriting: {}".format(s[0]))
-                self.hicpro_data[s_name][s[0]] = int(s[1])
+                # Try to convert the extracted value to a number and store it in hicpro_data.
+                # try-block is used to prevent program crash, because there is no
+                # guarantee that the value (s[1]) can be always converted to integer.
+                try:
+                    self.hicpro_data[s_name][s[0]] = int(s[1])
+                except ValueError:
+                    # Convert to float (also works for inf and scientific (exponential) notation).
+                    try:
+                        self.hicpro_data[s_name][s[0]] = float(s[1])
+                    # Otherwise just store the value as is.
+                    except ValueError:
+                        self.hicpro_data[s_name][s[0]] = s[1]
 
     def hicpro_stats_table(self):
         """Add HiC-Pro stats to the general stats table"""
@@ -300,7 +311,6 @@ def hicpro_mapping_chart(self):
         config = {
             "id": "hicpro_mapping_stats_plot",
             "title": "HiC-Pro: Mapping Statistics",
-            "ylab": "# Reads",
             "ylab": "# Reads: Read 1",
             "data_labels": [
                 {"name": "Read 1", "ylab": "# Reads: Read 1"},