1 files changed, 31 insertions, 14 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index dfa84ba..0ef487f 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -16,7 +16,7 @@ from r_qtl.exceptions import InvalidFormat, MissingFileException
 
 FILE_TYPES = (
     "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap",
-    "phenose")
+    "phenose", "phenonum")
 
 __CONTROL_FILE_ERROR_MESSAGE__ = (
     "The zipped bundle that was provided does not contain a valid control file "
@@ -411,22 +411,19 @@ def file_data(zfile: ZipFile,
 
     try:
         if isinstance(cdata[member_key], list):
-            for row in (line for lines in
+            yield from (line for lines in
                         (file_data(
                             zfile, member_key, {**cdata, member_key: innerfile},
                             process_value, process_transposed_value)
                          for innerfile in cdata[member_key])
-                        for line in lines):
-                yield row
+                        for line in lines)
             return
         if not cdata.get(f"{member_key}_transposed", False):
-            for row in with_non_transposed(zfile, member_key, cdata, process_value):
-                yield row
+            yield from with_non_transposed(zfile, member_key, cdata, process_value)
             return
 
-        for row in with_transposed(
-                zfile, member_key, cdata, process_transposed_value):
-            yield row
+        yield from with_transposed(
+            zfile, member_key, cdata, process_transposed_value)
     except KeyError as exc:
         raise MissingFileException(*exc.args) from exc
 
@@ -477,8 +474,7 @@ def raw_file_data(zipfilepath: Union[str, Path],
     with (ZipFile(str(zipfilepath), "r") as zfile,
           zfile.open(memberfilename) as innerfile):
         wrappedfile = io.TextIOWrapper(innerfile)
-        for  line in wrappedfile:
-            yield line
+        yield from wrappedfile
 
 def strip_comments(rawdata: Iterator[str], commentchar) -> Iterator[str]:
     """Remove comments from raw text."""
@@ -568,15 +564,36 @@ def load_samples(zipfilepath: Union[str, Path],
 def read_text_file(filepath: Union[str, Path]) -> Iterator[str]:
     """Read the raw text from a text file."""
     with open(filepath, "r", encoding="utf8") as _file:
-        for  line in _file:
-            yield line
+        yield from _file
 
 
 def read_csv_file(filepath: Union[str, Path],
                   separator: str = ",",
                   comment_char: str = "#") -> Iterator[tuple[str, ...]]:
-    """Read a file as a csv file."""
+    """Read a file as a csv file. This does not process the N/A values."""
     for line in read_text_file(filepath):
         if line.startswith(comment_char):
             continue
         yield tuple(field.strip() for field in line.split(separator))
+
+
+def read_csv_file_headers(
+        filepath: Union[str, Path],
+        transposed: bool,
+        separator: str = ",",
+        comment_char: str = "#"
+) -> tuple[str, ...]:
+    """Read the 'true' headers of a CSV file."""
+    headers = tuple()
+    for line in read_text_file(filepath):
+        if line.startswith(comment_char):
+            continue
+
+        line = tuple(field.strip() for field in line.split(separator))
+        if not transposed:
+            return line
+
+        headers = headers + (line[0],)
+        continue
+
+    return headers