Add GTF, PAF, GFA to the type allow-list

hub/utils/data_types.py

@@ -178,6 +178,61 @@ def validate_gff(content):
 
     return True
 
+def validate_gtf(content):
+    if not content:
+        return False
+    lines = content.strip().split('\n')
+    for line in lines:
+        if line.startswith('#') or not line.strip():
+            continue
+        fields = line.split('\t')
+        if len(fields) != 9:
+            return False
+        seqid, source, type_, start, end, score, strand, frame, attributes = fields
+        if not start.isdigit() or not end.isdigit():
+            return False
+        if strand not in ['+', '-', '.']:
+            return False
+        if frame not in ['0', '1', '2', '.']:
+            return False
+        # GTF attribute column uses key "value"; quoted-value pairs separated by ';'
+        if 'gene_id' not in attributes and 'transcript_id' not in attributes:
+            return False
+    return True
+
+def validate_paf(content):
+    if not content:
+        return False
+    lines = content.strip().split('\n')
+    for line in lines:
+        if not line.strip():
+            continue
+        fields = line.split('\t')
+        # PAF requires at least 12 mandatory columns
+        if len(fields) < 12:
+            return False
+        # Numeric fields: query_len, query_start, query_end, target_len,
+        # target_start, target_end, matching_bases, alignment_block_len, mapq
+        for idx in (1, 2, 3, 6, 7, 8, 9, 10, 11):
+            if not fields[idx].lstrip('-').isdigit():
+                return False
+        if fields[4] not in ('+', '-'):
+            return False
+    return True
+
+def validate_gfa(content):
+    if not content:
+        return False
+    lines = content.strip().split('\n')
+    for line in lines:
+        if not line.strip():
+            continue
+        # GFA record types: H (header), S (segment), L (link), C (containment),
+        # P (path), W (walk), J (jump), # (comment)
+        if line[0] not in 'HSLCPWJ#':
+            return False
+    return True
+
 def validate_list(content):
     if not content.strip(): 
         return False 
@@ -236,6 +291,9 @@ def validate_fai(content):
     {'type': 'BED', 'validator': validate_bed},
     {'type': 'LIST', 'validator': validate_list},
     {'type': 'GFF', 'validator': validate_gff},
+    {'type': 'GTF', 'validator': validate_gtf},
+    {'type': 'PAF', 'validator': validate_paf},
+    {'type': 'GFA', 'validator': validate_gfa},
     {'type': 'JSON', 'validator': validate_json},
     {'type': 'FAI', 'validator': validate_fai},
     {'type': 'TEXT', 'validator': lambda x: True},  # Default fallback

hub/utils/type_definitions.py

@@ -151,6 +151,24 @@
         "output": True,
         "example": "seq\t.\tgene\t1\t30\t.\t+\t.\tID=gene1\nseq\t.\tmRNA\t1\t30\t.\t+\t.\tID=tx1;Parent=gene1\nseq\t.\texon\t1\t30\t.\t+\t.\tParent=tx1\nseq\t.\tCDS\t1\t30\t.\t+\t0\tParent=tx1",
     },
+    {
+        "id": "GTF",
+        "input": True,
+        "output": True,
+        "example": 'seq\tStringTie\ttranscript\t1\t30\t1000\t+\t.\tgene_id "gene1"; transcript_id "tx1"; FPKM "12.34";\nseq\tStringTie\texon\t1\t30\t1000\t+\t.\tgene_id "gene1"; transcript_id "tx1"; exon_number "1";',
+    },
+    {
+        "id": "PAF",
+        "input": True,
+        "output": True,
+        "example": "queryA\t500\t10\t490\t+\ttargetA\t1000\t100\t580\t470\t480\t60\nqueryB\t300\t0\t300\t-\ttargetA\t1000\t650\t950\t290\t300\t60",
+    },
+    {
+        "id": "GFA",
+        "input": True,
+        "output": True,
+        "example": "H\tVN:Z:1.0\nS\ts1\tACGTACGTACGT\nS\ts2\tTTACGTACGTAC\nL\ts1\t+\ts2\t+\t4M\nP\tp1\ts1+,s2+\t*",
+    },
     {
         "id": "LIST",
         "input": True,