Add write gtf feature - Issue #21

gtfparse/__init__.py

@@ -13,6 +13,7 @@
 from .attribute_parsing import expand_attribute_strings
 from .create_missing_features import create_missing_features
 from .parsing_error import ParsingError
+from .write_gtf import write_gtf
 from .read_gtf import (
     read_gtf, 
     parse_gtf,

gtfparse/write_gtf.py

@@ -0,0 +1,23 @@
+import polars
+from pathlib import Path
+import typing as t
+
+
+COMMONS_COL = ['seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame']
+
+
+def write_gtf(df: polars.DataFrame, export_path: str | Path, headers:  t.List[str] = None):
+    headers = headers or []
+    with open(export_path, 'w') as f:
+        for header in headers:
+            f.write(f"{header}\n")
+        for row in df.iter_rows(named=True):
+            f.write(f"{commons_cols(row)}\t{custom_fields(row)}\n")
+
+
+def commons_cols(row) -> str :
+    return "\t".join([str(row[field] or '.') for field in COMMONS_COL])
+
+
+def custom_fields(row) -> str:
+    return "; ".join([f'{field} "{row[field]}"' for field in row.keys() if (field not in COMMONS_COL) and (row[field])])

tests/test_write_gtf.py

@@ -0,0 +1,11 @@
+from gtfparse import read_gtf, write_gtf
+from .data import data_path
+from polars import DataFrame
+
+REFSEQ_GTF_PATH = data_path("refseq.ucsc.small.gtf")
+
+
+def test_write_gtf(tmp_path):
+    gtf_dict = read_gtf(REFSEQ_GTF_PATH)
+    write_gtf(gtf_dict, tmp_path/"dummy_gtf.gtf")
+    assert  isinstance(read_gtf(str(tmp_path/"dummy_gtf.gtf")), DataFrame)