Add SeqIO support for GFA files. (#4598)

* Adds tags from segment lines into the annotations dictionary of
  the SeqRecord, handles undefined sequences and sets their length
  according to LN tag, raises a warning on incorrect tag types, and
  adds more links to the format documentation.

* Check for valid tag name and store tag types in annotations

* Tag value may contain colons

* Update NEWS.rst

Bio/SeqIO/GfaIO.py

@@ -0,0 +1,177 @@
+"""Bio.SeqIO support for the Graphical Fragment Assembly format.
+
+This format is output by many assemblers and includes linkage information for
+how the different sequences fit together, however, we just care about the
+segment (sequence) information.
+
+Documentation:
+- Version 1.x: https://gfa-spec.github.io/GFA-spec/GFA1.html
+- Version 2.0: https://gfa-spec.github.io/GFA-spec/GFA2.html
+"""
+
+import warnings
+import hashlib
+import re
+
+from Bio import BiopythonWarning
+from Bio.File import as_handle
+from Bio.Seq import Seq, _UndefinedSequenceData
+from Bio.SeqRecord import SeqRecord
+
+
+def _check_tags(seq, tags):
+    """Check a segment line's tags for inconsistencies (PRIVATE)."""
+    for tag in tags:
+        if tag[:2] == "LN":
+            # Sequence length
+            if len(seq) == 0:
+                # No sequence data, set the sequence length
+                seq._data = _UndefinedSequenceData(int(tag[5:]))
+            elif int(tag[5:]) != len(seq):
+                warnings.warn(
+                    f"Segment line has incorrect length. Expected {tag[5:]} but got {len(seq)}.",
+                    BiopythonWarning,
+                )
+        elif tag[:2] == "SH":
+            # SHA256 checksum
+            checksum = hashlib.sha256(str(seq).encode()).hexdigest()
+            if checksum.upper() != tag[5:]:
+                warnings.warn(
+                    f"Segment line has incorrect checksum. Expected {tag[5:]} but got {checksum}.",
+                    BiopythonWarning,
+                )
+
+
+def _tags_to_annotations(tags):
+    """Build an annotations dictionary from a list of tags (PRIVATE)."""
+    annotations = {}
+    for tag in tags:
+        parts = tag.split(":")
+        if len(parts) < 3:
+            raise ValueError(f"Segment line has invalid tag: {tag}.")
+        if re.fullmatch(r"[A-Za-z][A-Za-z0-9]", parts[0]) is None:
+            warnings.warn(
+                f"Tag has invalid name: {parts[0]}. Are they tab delimited?",
+                BiopythonWarning,
+            )
+        parts[2] = ":".join(parts[2:])  # tag value may contain : characters
+        annotations[parts[0]] = (parts[1], parts[2])
+
+        # Check type of the tag and raise warning on a mismatch. These RegExs
+        # are part of the 1.0 standard.
+        if parts[1] not in "AifZJHB":
+            warnings.warn(f"Tag has invalid type: {parts[1]}", BiopythonWarning)
+        elif parts[1] == "A" and re.fullmatch(r"[!-~]", parts[2]) is None:
+            warnings.warn(
+                f"Tag has incorrect type. Expected printable character, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif parts[1] == "i" and re.fullmatch(r"[-+]?[0-9]+", parts[2]) is None:
+            warnings.warn(
+                f"Tag has incorrect type. Expected signed integer, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif (
+            parts[1] == "f"
+            and re.fullmatch(r"[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?", parts[2])
+            is None
+        ):
+            warnings.warn(
+                f"Tag has incorrect type. Expected float, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif parts[1] == "Z" and re.fullmatch(r"[ !-~]+", parts[2]) is None:
+            warnings.warn(
+                f"Tag has incorrect type. Expected printable string, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif parts[1] == "J" and re.fullmatch(r"[ !-~]+", parts[2]) is None:
+            warnings.warn(
+                f"Tag has incorrect type. Expected JSON excluding new-line and tab characters, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif parts[1] == "H" and re.fullmatch(r"[0-9A-F]+", parts[2]) is None:
+            warnings.warn(
+                f"Tag has incorrect type. Expected byte array in hex format, got {parts[2]}.",
+                BiopythonWarning,
+            )
+        elif (
+            parts[1] == "B"
+            and re.fullmatch(
+                r"[cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+", parts[2]
+            )
+            is None
+        ):
+            warnings.warn(
+                f"Tag has incorrect type. Expected array of integers or floats, got {parts[2]}.",
+                BiopythonWarning,
+            )
+    return annotations
+
+
+def Gfa1Iterator(source):
+    """Parser for GFA 1.x files.
+
+    Documentation: https://gfa-spec.github.io/GFA-spec/GFA1.html
+    """
+    with as_handle(source) as handle:
+        for line in handle:
+            if line == "\n":
+                warnings.warn("GFA data has a blank line.", BiopythonWarning)
+                continue
+
+            fields = line.strip("\n").split("\t")
+            if fields[0] != "S":
+                continue
+            if len(fields) < 3:
+                raise ValueError(
+                    f"Segment line must have name and sequence fields: {line}."
+                )
+
+            if fields[2] == "*":
+                seq = Seq(None, length=0)
+            else:
+                seq = Seq(fields[2])
+
+            tags = fields[3:]
+            _check_tags(seq, tags)
+            annotations = _tags_to_annotations(tags)
+
+            yield SeqRecord(seq, id=fields[1], name=fields[1], annotations=annotations)
+
+
+def Gfa2Iterator(source):
+    """Parser for GFA 2.0 files.
+
+    Documentation for version 2: https://gfa-spec.github.io/GFA-spec/GFA2.html
+    """
+    with as_handle(source) as handle:
+        for line in handle:
+            if line == "\n":
+                warnings.warn("GFA data has a blank line.", BiopythonWarning)
+                continue
+
+            fields = line.strip("\n").split("\t")
+            if fields[0] != "S":
+                continue
+            if len(fields) < 4:
+                raise ValueError(
+                    f"Segment line must have name, length, and sequence fields: {line}."
+                )
+            try:
+                int(fields[2])
+            except ValueError:
+                raise ValueError(
+                    f"Segment line must have an integer length: {line}."
+                ) from None
+
+            if fields[3] == "*":
+                seq = Seq(None, length=0)
+            else:
+                seq = Seq(fields[3])
+
+            tags = fields[4:]
+            _check_tags(seq, tags)
+            annotations = _tags_to_annotations(tags)
+
+            yield SeqRecord(seq, id=fields[1], name=fields[1], annotations=annotations)

Bio/SeqIO/__init__.py

@@ -291,6 +291,10 @@ names are also used in Bio.AlignIO and include the following:
     - gck     - Gene Construction Kit's format.
     - genbank - The GenBank or GenPept flat file format.
     - gb      - An alias for "genbank", for consistency with NCBI Entrez Utilities
+    - gfa1     - Graphical Fragment Assemblyv versions 1.x. Only segment lines
+      are parsed and all linkage information is ignored.
+    - gfa2    - Graphical Fragement Assembly version 2.0. Only segment lines are
+      parsed and all linkage information is ignored.
     - ig      - The IntelliGenetics file format, apparently the same as the
       MASE alignment format.
     - imgt    - An EMBL like format from IMGT where the feature tables are more
@@ -380,6 +384,7 @@ from Bio.SeqIO import AbiIO
 from Bio.SeqIO import AceIO
 from Bio.SeqIO import FastaIO
 from Bio.SeqIO import GckIO
+from Bio.SeqIO import GfaIO
 from Bio.SeqIO import IgIO  # IntelliGenetics or MASE format
 from Bio.SeqIO import InsdcIO  # EMBL and GenBank
 from Bio.SeqIO import NibIO
@@ -420,6 +425,8 @@ _FormatToIterator = {
     "gck": GckIO.GckIterator,
     "genbank": InsdcIO.GenBankIterator,
     "genbank-cds": InsdcIO.GenBankCdsFeatureIterator,
+    "gfa1": GfaIO.Gfa1Iterator,
+    "gfa2": GfaIO.Gfa2Iterator,
     "imgt": InsdcIO.ImgtIterator,
     "nib": NibIO.NibIterator,
     "cif-seqres": PdbIO.CifSeqresIterator,

NEWS.rst

@@ -63,11 +63,17 @@ The wwPDB organization announced that they plan to deprecate the FTP
 server by the end of the year. See the announcement
 `here <https://www.wwpdb.org/news/news?year=2023#65562f0ad78e004e766a96c1>`_.
 
+``Bio.SeqIO`` now supports reading sequences from the Graphical Fragment
+Assembly (GFA) files with the formats ``gfa1`` and ``gfa2`` (for GFA 1.x and
+GFA 2.0 files respectively). All data outside of segment lines are ignored, such
+as linkage information.
+
 Many thanks to the Biopython developers and community for making this release
 possible, especially the following contributors:
 
 - Anil Tuncel (first contribution)
 - Fabio Zanini (first contribution)
+- Michael M. (first contribution)
 - Michiel de Hoon
 - Peter Cock
 - Will Tyler (first contribution)

Tests/GFA/corrupt_checksum.gfa

@@ -0,0 +1 @@
+S	fake	AAA	SH:H:FFFFFFFFFFFFFFF69566510EE712661F9F14B83385006EF92AEC47F523A38358

Tests/GFA/corrupt_len.gfa

@@ -0,0 +1 @@
+S	fake	AAA	LN:i:2

Tests/GFA/corrupt_segment_fields.gfa

@@ -0,0 +1 @@
+S	fake

Tests/GFA/corrupt_tag_name.gfa

@@ -0,0 +1 @@
+S	fake	AAA	~~:i:0

Tests/GFA/corrupt_tag_type.gfa

@@ -0,0 +1 @@
+S	fake	AAA	AB:i:C

Tests/GFA/fake_gfa2.gfa

@@ -0,0 +1 @@
+S	fake	3	AAA

Tests/GFA/fake_with_checksum.gfa

@@ -0,0 +1 @@
+S	fake	AAA	SH:H:CB1AD2119D8FAFB69566510EE712661F9F14B83385006EF92AEC47F523A38358

Tests/GFA/no_seq.gfa

@@ -0,0 +1,21 @@
+S	232	*	LN:i:528	KC:i:51170
+S	277	*	LN:i:893	KC:i:50561
+S	280	*	LN:i:895	KC:i:37634
+S	282	*	LN:i:1819	KC:i:106341
+S	283	*	LN:i:1854	KC:i:82138
+S	289	*	LN:i:163	KC:i:14624
+S	297	*	LN:i:4149	KC:i:248525
+S	333	*	LN:i:4399	KC:i:191002
+S	6	*	LN:i:89	KC:i:9779
+L	6	+	277	-	81M
+L	6	+	280	+	81M
+L	232	+	277	+	81M
+L	280	+	232	-	81M
+L	282	+	6	+	81M
+L	283	+	6	+	81M
+L	289	+	282	+	81M
+L	289	+	283	+	81M
+L	297	-	232	+	81M
+L	297	+	289	+	81M
+L	333	-	232	+	81M
+L	333	+	289	+	81M

Tests/GFA/seq_with_len.gfa

@@ -0,0 +1,21 @@
+S	232	CCTTATACGAAGCCCAGGTTAATCCTGGGCTTTTTGTTGAATCTGATCATTGGTAGCAAACAGATCAGGATTGGTAATTTTGATGTTTTCCTGACAACTCCTGCAAAGCATCAGCCCAGCAAAAAGTTGTACATGTTCCGTTGATTCACAGAAGGCACATGGCTTAGGAAAAGAGATGATATTGGCTGAATTGACTAATTCTGTTGACATAAGAAGTAACCTTGGATTGTACATATTTATTTTTAATAAATTTCAATACTTTATACCTAATTTAGCCACTAAAATTTGTACATTATTGTATAATCCATGTGTACATATTATTTTTTATAATTTTCATTCACTTAGACCCAAAATAGTATTTATTTTTGTACAACACCATGTACAGAACAATAATCATATAAATCAAATTTTTAGCATAAAAAAGTCCATTAATTTTGTACACAATTCTGAAACTTAAAAATCTAAACTTTCATCAATTTTTTTCATAATTTCAATAAATTAACCTTAATTTTAAGATATATTCTGAAA	LN:i:528	RC:i:51170
+S	277	TGAAACTTAAAAATCTAAACTTTCATCAATTTTTTTCATAATTTCAATAAATTAACCTTAATTTTAAGATATATTCTGAAATTTGGTTTGAAAGCTGTTTTTACATTATATTTCAATACTTTAAATCAAAAAATTGGATATTTTTTGAAAAACTCAATGAAAGTTTATTTTTTATTTAAAAACAACTAGTTATATTAGTTTTTATCCATTTTTTTGAAACAGTTTCTATATGATAAAAAAACCTATAAAAACCATATCTAGCAAAGGTTTGAGGGTTATCATCTTTAGATGCGTGGTGTGTGACAAAAAAATCCCGGCATGTGCCGGATTCTGGATTAGAAAATTGGCTAAAGTGACGTAGGACTGGTGCTTGGTTTTACATGGAAAAAAGTATTTATTTTCTGGTTTATAAAAACGTAAAAAGATCAGTTTTTGTTCATTCATCCAGGTTAAAAATTTCAACCTAAAACTTTAATTATGAAAAGCTTCACAGAAAGCATTCAAATGCGATTTAAGAGCCTTTATCTAAAAAACATAGATCTTATAGCGAAAAACAGAAAACAGCTCAAAAAACGCAAAAGAGAGTGAAGTAAAGAGATGTTTTGACTTTAGATAGCTGCATAGAGCGAGTGTCTACGAGCGAACTATCAAAATTTGCGTCTAGACTCTCTGAAAAACATTTTTTTGCCCTCTTTAGCCTAAGAAAGCTTAATTTTCATGCAGAAATTTGCTCCTGGACCGAGCGTAGCGAGAAAAAAAGCTCATGAGCGAAGCGAATTCCGAGTTGCTTTTGCTTTTTCTTAAAGTCACGCAAGTATTAACCAAAAAATTGCCCCGACGAACTGAGCGAAAGCGAAGTTCAATAGAGTTTGAGCGAAGCGAAAACCAAGGGC	LN:i:893	RC:i:50561
+S	280	GCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGTTAATACTTACGTGATTTTAAGAAAAAGCAAAAACAACTCGGAATTCGCTTCGCTCATAAAACTTTTTTACTCGCTACGCTCGGTCTAGGAACAAATTTCTGCATAAAACTTACGCTTTCTTAGGCTAAAAAGCCCCAAAAACTGTTTTTCAGAAAGGCTGAGAGGCAAATTTTATAAGTTCGCTCGTAGACACTCGCTCTATGAATCTATCTAGAATCAAAATCCCTCTTTATTTCGCGCTCATTTGCGTTTTTTGAGCTGTTTTCTGTTTTTCACTATAAGACCTATGTTTTTTACTTAAAGGCTCTTAAATCGCATTTGAATGCTTTCTGTGAAAATTTCCATAATTAAAATTTTAGTTTGAAATTTTTAATTTGGATGAACGGACAAAAAATGATTTTTTTACGTTTTTCTAAACCAAGAAATAAATACTTTTTTCTATATAAAACCAAGCACCAGTCCTACGTCACTTTAGCCAATTTTCTAATCAAGGATCCGGCACATGCCGGGATTTTTTTGTCACACACCACGCATCTAAAGATGATAACCCTCAAACCTTTGCTAGTTATGGTTTTTATAGGTTTTTTTATCATATAGAAACTGTTTCAAAAAAATGGATAAAAAATAATATAACTAGTTGTTTTTAAATAAAAAATAAACTCTCATTGAGTTTTTCAAAAAATATCCAATTTTTTGATTTAAAGCATTGAAATATAATGTAAAAACAACTTTCAAACCAACTTTCAGAATATATCTTAAAATTAAGGTTAATTTATTGAAATTATGAAAAAAATTGATGAAAGTTTAGATTTTTAAGTTTCA	LN:i:895	RC:i:37634
+S	282	AGAAGCCACGCTTTTTAGGCTCTGGTTCAACATGCTCTGGAACAGGAATGCGCTTATTCTCTGGAGTAGTCAATCCGTCATGTTTAGGATCATCAATATTAGGTTCTGGCTGTACTTGAGCTACATTCGCTTGCGACTGTTCTTGATCGGTAAACGTAGTCATATTGGCTTTTGGTGCTTCTAGTAAGCGCTGCATGGCCTCGATCTGATCTTGATAAAACGATTCACGTTCTAGTGATTGATTTTCTCTAAACAGTGCTTGATTTAACTGTTTTTCCAGTATGTCAACTTGACGTTTTAATAGGTCAACTTCTGTCAAGTTTTGACTGTTAATTGATTGACTTTGATTGACATTAGTATCTTTCTTTTGTGGTTCCCCAAAAACTCTTATGGCTTCTGCGAAGTCAATTAATCCATCAGATCCTTTAGATAAATTTCCTTTGTTTATATGGGCATATATGGCTTGTCGTGAATATCCGTAAAGCTTAGCCAACTCTGAAACTGACAGTTTTTTCATTATGTAAACCAGTTTTCAATTTGTGTTAATACTTGACTGTCAACTTTACAATGTCAATTGACATCATTTATTGAAAGCCAACTTTTCGAAGTAATGGAGTAAGTTCTTTTAATTTCTCCGGCTGTTTTAGCATATCTGCAATCCGTACAGCAAATTGTTCATAGCTTTCGGTGCCTTGTGAAAGTTTTCCCATTTCTGGAAGCTCTGACAATTTACTCGCAAATGAATAGCGTTGTGCATCTGTTAAAGTGATCGTTATATCTTCGCTTACACCTATACTTTTAGCTGACTTCGTTACTGATTTTTTTTGTTTAAAGCTAAATGAAAAACCTGTAATTGATCTACCAGTCTTATGCTGTTCAACTTTAACAGTAATGTCGGTATGTTCATTTACTTGCTTTAATGCAATGTCTAAGACATATTTTTTAAAGTCATACATTCGTTTGTATTCAGTATCGAGTACACCTATTTTTTGTCTGAAATCAGACAAAGTTATAAGAGGCGTTTTTCCTGTACTACGCCATGCAATCAATATCTCATATAACCGAACGGCATAAGCACTTGTTAAATTGCTTATTTGTTGTATTTCATACTTTGTAAATTGTTCTTCTAGTCTTGTAATTAAAGGCACGATAGCGGGAGCAAAAATAAGTCTAACAACCGCTTCATTATCAATATAAGCGACTTCACTCACCCATCTTGACTTGTGATTAATAATGTTGCCTTTTTCACTAAGACTTTGATAACTGAATTGTCTTGCAAATAGATCATCACAAGCATCTTTTAATGCCTGATAAGCCGTGTTTCGATGTACACCAAATTGATTGATGTAGCTTTCAGCATGAACTGTTAATGGATCATTAGCATTTATTCCCTTACCCGATTCCCTTGCTTCAACGATAGCTAGAAGAATTAACCGTTGCTCGACTAAATCAAGGTTATAACTGGCATTAATTAATGCATTATCTTTAACTATTAGTTCTGTTTTCATATGAAAAGGTTATATTTTTAATTCAATAAGACGAGGCTATATCATAAACTCGCTTAATGCAAGGTAAACCTCGTTTTAATGCAAGGTAAACCTCGTTTTAATGCAAGGTAAACCTCGTTTTAATGCAAGGTAAACCTCGTTTTATAGTCTCTAAGAATTTTATAAATAAAGGCTTTCAGCATGTCTAAAAGCATTTAAAAGATTTAAAAATATTTAAAAGCTCAGGTCATGAAAAATTGCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGT	LN:i:1819	RC:i:106341
+S	283	AGAAGCCACGCTTTTTAGGCTCTGGTTCAACATGCTCTGGAACAGGAATGCGCTTATTCTCTGGAGTAGTCAATCCGTCATCTTTAGGTGGAACAACTATCACCTGCTCCTTCATTTCTACAATGGGAGCTGATTGAGGGAGTTCGGGTTCACTAGGCTCTTGGATCTCAGGTTTAGGTGCTTCCAGTAGACGTTGCATTGTCTCAATTTGATTTTGATAAAAGGATTCACGCTCTTTTGCATCATCAAGCTGATTTTGCAGCATGTTTATCTGTTGTCTAAGTAGTAAAACTTCTGTCGATATTGGACTGTCTATTTTTACAGATTCTTTTACATCCTGTTTTTTTGAAGGTTCACCAAAAACACGGATAGCCTCGGCTAGATCAATTTTATTATCAGAATTTTTACTTAAAATTCCTTTCTTTATGTTGTTGTAAATCGTTTGTCTATTGATATTGTAAAGCTTAGAAAGCTCAAGAACTGTAAGGCTTTTCATGTTGTAAATCTATGTCTAAACCTGTCAAAAGTTGTTGTCTATTAGACTGCCTAATAGACAAATGATCAAGCATAAATTTTAGGCAGCTTGATAGCCAACTTTTTGAAGATAAGGAAATAATTCTTGGAATTTTTGATAATCTTGGAGCATTTCTGCAATGCGTATAGCAAATTGTTGGAAACTTTCGGTGCCTTCTGAATATTGCCCCATCTCAGGTAATTCAGAAAGTTTGTTGGCAAAGAGATGACGTTGTTTATCACTCATTTTGGTGAAAAGGGCTAATGTATCCGTTCCCTTAATTACTTTGTCAGAGTTGGTTTTTTTCTGCTTAAAACTGAAAGAAAAACCGGAAATTGAACGTCCTTTTTTATGTTGTTCATATTTAGCCTTTACATCGGTTAACTCATTTACTTGCTTGAGGGCAAAATCTAAAACATACGTTTTAAAATTACTCATTGTTTTGTATTGATGAGCTTCGACACCAAGTTGTTGTCTAAAGATCGATAGATCAAAAATTGGCGTTTTACCAGCAGATCTCCATTGAATTAATAACTCGTATAACCGAATAGCATAAGAGCTAGTTAATCTCGAAACCTGCTCCAATTCATATTTAGTAAAGTTTTCTTCCAGTCGAGTTATGAGTGGAACAATGTCTTGCGTGAAACGTAGGAAAACGATCCCGGATTGAGGTTCATATCCAATTTTATCGACCCAACGACAGTGAAAGCTACGATCCTTACCAGTCTTAGGATTAATGTCATGATACGTGACATAGCGATCAAACAAGCTTTTAGATGCATCCCTAAGCACGGTATAAGCAGTGTGTTTCTCGACATTAAAGGTATTGATATAACTACTTGCATGTACTTCTAAAAGGCTATTTTCAGTTATCCCGTGCCCTGTTTCCCGAGCTTCAGCAATGGCTAATAGGATCAGCCTTTGTTCAACTGTATCTAGGGTATAGCTAGCTTGAATTAAAGCATTATCCTTTACGATTAATTCACTCATTTCTAATAATAAATTTATAATTAAACTAGGTTGTACAATAGACTATTTTAATTGAATTGTAAATCGACTTAATTTGGGGTCGATAAACCTAGTTTTAAGGTCGATAAACCTAGTTTTAAGGGTCGATAAACCTAGTTTTAAGGGTCGATAAACCTAGTTTTAAGGGTCGATAAACCTAGGTTTATTAACTCTAAAACTATTATGAATAAAGGGTTACAGCTTACTTAAAAGCATTTAAAAGATTAAAAATAATTAAAAGCCTAGGTAAAGAAAAATTGCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGT	LN:i:1854	RC:i:82138
+S	289	CACGTTCCACGCTTATTTATTGAGCAATGTTCCACGGTTTTATTTAGCCTAAGTTAACCATATGGAAGAAAAAAACGACTCCAGAAGCCACGCTTTTTAGGCTCTGGTTCAACATGCTCTGGAACAGGAATGCGCTTATTCTCTGGAGTAGTCAATCCGTCAT	LN:i:163	RC:i:14624
+S	297	AAAATTACCAATCCTGATCTGTTTGCTACCAATGATCAGATTCAACAAAAAGCCCAGGATTAACCTGGGCTTCGTATAAGGTGTATTATGTTAATTTTAGAAATTATTAAATGATTCCAAGATTTTCTAGCGACTTATAAGTAATTTCATTACGAATAGAACCAGACATTCCTTCTTTCATTTCTAAGTTGAGCGAAAAGGGGATTTTTTTTCCATTAGCTTGCTCCACCCAACCAGTCAACCAACCTACCTGTGGAGTAACATCCATTCCCCATCCACTTTTTGCATAAATCTTACTACCATTTACTTCTTTAATTAGAAGCATTTTTTTAACTTCTTCTTGAGTTTCTAATTTAAAAGGTAATCGGTTATGTGCAAGGTCATCGGCAAAATTAACTTCTTGTACTGGTGTAATTTTAAGGGGGCCAACTAACCAAAAATTATCGACCTGTGTTCCAATATTTGTATTTCCAAAATTAACCCGCTTTACTTCTTTCTGCATTAGCTCTAGGCCAGTCCGTCTTGCAAGCTCTTGATATACTGGAACTGCTGACAATGCCATTGCCTCACCTAAAGTCATATCTTTCTCCCACATAGGATAAGTTCTTTTTTTACCATCCCATTTGAAAATCTCATTTGTTGTTGCTTTATGATTTTCTAGCCCGATTAAAGCATTTAGCATCTTAAATGTTGATGCAGGGACATATTCTTTATTTGCTCGTGCAAGAGCATTACCATAGGTGCTAAGATTTTTACCCTCTTTAATAATAATTACACCCTGTGTTTGAGCTTCATCAAAATAGCTTTTAATAGCTTTTTCATGTTGCTGAGAAGAAATATGAAAATTATCTTCAGATTTAGTTTTAATAGATGAACATGCACTGAGAGAAACTAGAATAGAAATGCTGAATATAGGAAGTATAAATTTTTTCATTACAAATTCATGTTAGGGGAAATTTTGGGGCTTAGAGCATAATATTTTTATTAAAAAAGTTAAAACTCTTTTAATTTAACATAATGGGCGTTATCCGAAATGGCCCTTTAAGTTTACTTTAAGATCAACAACTTACATTGAGTTAAACCCCTGGAACGATCTCGTTCAACCGATTTAGAAATAAATCGGTTTTTTTATGTTCAATTCTGATACTTCTTGCCAATAAAATTGGTTAAAAAATGATCAAAAATACCAATTCCATAGAGTTTGTAAGCCTTTTTTACCCAAAAGAATCCACAATTTCTGCGGATAACCATTGGGATAAATTTTGATTATTTTTTGTACGTTTTGGCTTACAGCGTTTCACGAAATTGTCTGTATCTATCCCCCGATGAAGCTCTTATGATCGATCTATATGGACAGGATGTTCAATGACTTAAAACAACAATAATAATCAGTCAGGCACCATGACCATCAGGTAGTCAGCCCTACCTATGCGCTCCATACCGAAAAATCCCGACATGACGTCGGGATTTTTTATTGCCATTTGCAAAGTCATTCAATCAGATTTAATATATAGACTGTAATCTATATTGTGATTGTAATATGTGGACAGTCATTACAACGGATCTGTTTAATGAATGGCTTGAACAGCAAGATGAAGCAACACAAGAGAAAGTCTTAGCTGCATTGGTTGTTCTACAACAGCAAGGGCCTAGTTTAGGTCGTCCTTTAGTAGATACCGTCTACGATTCTAAATTTACCAATATGAAGGAACTACGTGTTCAGCATCGTGGTAAACCGTTAAGGGCATTTTTTGCATTCGATCCCCTAAGACAAGCGATTGTGCTGTGTATTGGTGATAAGAGTAATAAAAAGCGTTTTTATACAGAGATGCTAGCAATTGCAGATGAGCAATACGCACTTCATCTCTCAACTTTAGGAGATCAATCTAATGGCTAAGAGCTTACAAGAATTATTGGCTAGTCGCTCTCCAGAGAGTCAAGCTCGTATTCAAAAAATGGCTGATGAATTACTTTTAGAAAGTCAGCTTCACCTTATCCGAGAAGAGTTAGAAATTTCCCAGAAAGAACTAGCTGCAACCCTTGGAATTAAACAGCCGTCATTATCAGCAATCGAAAATCGTGGTCATGATCTTAAAATTTCAACGATGAAAAAGTATGTTGAAGCAATGGGTGGAAAACTTCGTATTGATGTAGAGCTTCCAACAGGAAAACACATAGGGTTCAATGTCTAATAATAAACCTTTGAAAAATAGTACTAAATTACTTGTTAACTTAGACAAGTTTATATTTTTAGTCAATGCTGCCGATAGCCTAGAAGAAATTGAAATTATTAGAGATTTATGCTGTGAATATTTTTCACATTGTAAGAGGCCAAGCTATTACATTGATATTTTTGACAATGCTTATTGGATAAAATATTACGAAATAGCTTAATCCTTCTAGATTCACATAGGAGTTTCTATGTTAAATAGGACTAAAAATATACTCTAATTTTAGAGTTTTCTTTTAGGTATGATGTAAAAACATACAAGCCTAAGAGTTTAATTTAAAGGTTAAGAATTGAATAAATTAGTAAATATTTTTATGGCTTTAGGAGTTTGCCTTTCAATGGAAACATTTGCAGAACCTGTTTTTTCTAATGATTTATTAGCGAAAGCAGAAAGTGGAGATACTTCTGCCCAGTTAGAATTAGCTGAGATTTATCTATATGGTCATGGTGTTGATTCAGATGAAAATCAAGCTGAAATTTGGGCTATTAAATCAGCTGAAAATGGAAATGTAGCAGCAATGTTTTGGTTAGCTGATGGATATGTTACCTATGCTAGATTAATAGAGGATGATGACAAAAACGATTCTTTAGAACATTTCCAAAAAGCTTTTAAGTGGTTTCAGAAAGCTTCAGAAAATGGTCATTCTGAATCAATGGTTGAGTTAGCTGACCTATATACTCGCGCAGCTAGCGGAATAGAAGTTAATATTAAGAAAGCTTTAGAACTTCGTGAAAAGGCTGCAAAGTTAGGTAATAAGAAAGCAATGCGAAGTCTTTCCGTTATGTATCGTGATGGTATAGGCATTCCTAAAAATACTGATTTAGCTCAAAGTTGGTGGGATAAGTCTGAAAATTAATTTTAGTAAAAGTTAAGGATTTTTTAAGAGTCTAATAAATGAATAGTGTTCATGAAATTATAGAAAAAATACATAATGAATGGGAGATTGAACCTAAGAAAGCTATTCAGAGAGGTATGGAATGTCCCTTTCCTTTGCAGTGTTCATTAAACCTAAAAAGCAAAATTTACCCACAAATACCCCAAGTACTTTTACCAAAAGTATTAGAGGATTTTTATACAGTATCTAATGGTGCAGATCTATTTAAAGATCAAGAATACGGACAATGGGGCTTAAAATTATATTCTATTGAGGAAGTAATTTTTGCTTCAAAAATTTATAAAAGTAATCGTAATAATGACGCTCTTCAAAGTGACTTAATTATTGGAGAATTCTATGGAGATTCAGACTTATTGTTAGTTCGATGTGATCCTAATAGTGATGATTACGGCTCTATTTTTGTTGTCTTACCTATAGATCAAAGACAAGATTGGTACATTGTTGCTAATACTTTTCAAGAATTCATTAGTAAATTTTATGAAACTCAGGGTGATAAATTCTGGGAACCTTAAAATTATATGGCCGATATAAGCTCTATTTAACTTATGTTCACCTAAAATTTATTTAATTATCACAAAAATAGTATCATTTTTTGAATTTCATATAACGCCCATTATGTTAAATGGCTTAATCAAAATAACCTAAAATTGCTAAAGTAGGTATAAAAAAGATCGTAAATACAGCAAAATATTGAATCATCTTTTTATGTCTGAAATCTCGTTTAGAAATGATCAAAAGCAATGCCGAAAAAAAAATGACTATGAATGTCCATGAAATTGAATACATACTTAAATCCTAATTAATTATGTTGAGTTTTAAATTTCTCTAAAATTAACATAATACACCTTATACGAAATGCTTTTAATTTCTCTTGAAAATTCAACGCTGTAGTTTCTAGTTTATAGCCCATCTTCCCCAAGGTGGGTTTTTTTTATGATTTTTCACGTTCCACGCTTATTTATTGAGCAATGTTCCACGGTTTTATTTAGCCTAAGTTAACCATATGGAAGAAAAAAACGACTC	LN:i:4149	RC:i:248525
+S	333	AAAATTACCAATCCTGATCTGTTTGCTACCAATGATCAGATTCAACAAAAAGCCCAGGATTAACCTGGGCTTCGTATAAGGCGTATTATGTTAATTTTAATGGAACTTTATAATTAGACGTTGTTGTTGATATATAGCGAATGCCATCATGGTGGGCACTATATTTTATGTAGATTGAATACCCACAATCTAAATTACACCATTTTTCAGAGTACAGACTTTCTCTTACATCATCTGGGCTTCCCAATAGATCATGAATTTCAACCTTAGACATGTCAAAATTAAGTCCTTTAGGTAGAAGCTCTCTATATTTATTAAATCCTTCAACATTTTGATTATAAAAAAATATTGTTTGAAAAAATAAGTTTTTACCTAACATTGCTGTATTACTAAGATGATCTAAGCAACTAGCTTCATCTCGAAAAAGTAAACAAATACCTTTTTCTTCATTAGCTATATATAAAGTATCTTCATCTAAAGGTTCATTATCCTCATCTAATAAAGGAATATAAAGATTAGGTTCTGTAATTAATTGATTATTTAATAAAAAATAAATCAACTCCTTATCATGATTACTTGTACCCAAAAATTCTAAAAGCTTTTCGGTCATAATATTTTTCTATATTTTCGACTGACAAATTTTAGAAGAAATCCCATGTAAAAGTCATCTACATCGACCCATTTAACATAATAGAGCTTATGCGAAACCACTCTTAATTATTTTAATTAAATCAATTGTTTGTGAATTTTACATAACGCAAAAAAACACCAAAAAGCCGACTTAGAAACAAGTCGGCTGCTTTTTAAGCAAGTTTGTCATATTCTGCCAATAAAATCGGTTAAAAAATGCTCAAAATTTCAATTTTTCCTGATTTCTAAAGGCTCTCTTTTCTGAAATTATCCCCATTTCCTGCGGACAATTCTTGGGATAATTTGAGGATATTTCCTTGTACGTTCTGGCGTACAACAATTCAGGAAAATTGCCCCAATTGGTTGTGCGGTAGATTTTGTGTGTAGGCTTCTTCATTTGAAAATTATATCGCTGAAAAAGCCTTTACAGATAGGTTTGTGCAACAAAGCCTTTCATAAATAAAACTAAAATTTAATGTAAAAGCGTTGAGAATATCCTGCACCATTTTCCCATTTATCAGTCTCTATGTCTAAAGATAGGTTCTTTACTGTTGTCTGTTTATTCGTTTTGTTTTTTATAGCATTTTTTAAAACAGATGGGAGTTCTTGATTAGCAACTTCCTTGTATATGCTTTCAGACATTTTTATAAATTCAGTCTCTGCTGATTTCTTATATTTTGAGTCATTAACATTTAAAACAACTTTCAATTCTTTAATACTACTTTCAGTACCTTCTACATAATAAGCAAGATTATTTGGATTTTCTCCATTTTGAGGATCAGGAGAAATATCAATATATGAAGAAATACAACGATAGGTACCTTCTCCCATTGTGTCTTTCCAGCTAGTCATACCTGGTAAATTCAGCATAGAACATGCTTCACTCACCGATATACTAATGTCTTCTGCTTCTACGTTTCCTGTATCTTTACTTTCTGCTTCTACATTTCCTATATCTTTACTTTCTACTTCCACGCTTTTTTCCTCTACTTCTTTATTCTGAATCGAAGAATCACAAGCTGAAAAAAATAAAGGTAATAACATCACAGCAATAAATTTATTTCTCATAACAATCCTATAAGCTACTAATATTAATTAATTTTTAACTGTAATTTTCCAGTTACCACCAACATCTGCTAGTTCGTATCTATAATTGTAATTATTACACACTAAATGATATCCAACACTTCTAACAAAAGGTAAAGTTGATGTTACAGAATCACACTTATAACCATTTAATTTAACCATGACTGCCATTTGCTTAGCCCCTTGTACTCCTGTAGCTTTATCAATTTTGGCACCCGATTCAATTTTTACTGATTTCATCATCTCTTGTAATACTTTTTCTTGTAATGGAGTTGCAAAAGTATTTACTGAGCATAATGTAGAGATAGCTAATACAATTTTGATAGATAATTTCATGATTATTAAGTAATTAAAAAAATGATATATTATATATAGTTAAAAATTTAGCAATATTTATATTGGTAAGTCCTTTATGGTTCTAGGCGGTTGGCGGGTTTCGGGGGGCTTGTCCCCCTGAACAAGGTCACGATAGGTAACTTTGAAAATAACGCAGTTATTTGAAAAAGTACCTATTGTGTATCCTTGCTTATTTTTGAATAAGCACTAGTTTAATATAATATTTAAATAAATTCCTGTGTAGGTTTGTTTTTGGGTTTTAGTTAGTGAACTATTTTTTATAATTGAACAAGAAAAAGGAAATATAAAAAATATAGCTCAGGTATTTGAATATCACCATTGAAAAACAAGGCTTCACGGTATGGAGCCGCTGTCGCTTTCAAATCGGTATGCTTGGGTTGCGTTACAGTCCAAGTCACAAGAAAGTATTTAGAAGTCTGACTACTTCCCCTGCACACGCATTATCTCTCTACAACACATGCTCGTATCTTGTGCCGATCATCTCGTACATCTATTTACGATTACATGCGCTATTCCCTGCGTCCTTTACCTAGTGTAATACATCAGTGGTAAAGCGGTTTTAGTCTTTAATGCCTGCCGTCGCTTGTCCACCTTCACATTAAAGCCACCAAAGACTAAGCCGATATATAAAAATATCGCAGTACCCATTGATTCGCATAGTCTCTATTTGCCGCCACCTCATTCCCAGCAAAATCATTTTTAATTTTATTTGTTGTCACTGCTTTTTTAGGAGAACTTTCTACTATCTTTTCCCAGTCAAATAGTGCCTCACCACTGTCTATCCATGTAGTAAAATCATCATAAATCATAATATTTTTTATGGCTTCTTCTTTATTTGCAAAAGTAAATGATGATGTAGTTAATAATAATGTCGGGATCAGAAGGTATTTCATAAAAAGATACTCTAAAATTAATTTTAAGTTAGAATCTTATAAAACAATGACTTAATTAAAAGCAATTTTTTTGCTTTAGGGAATAGTGTATGTCTTTAATAAATTGTCCAGAATGCAACCATTCTGTTAGTGATAAAGCCTTAGATTGTCCATCTTGTGGGGCTAGATTAAGGAAACCTAAAAGAGGTTTCTTTGGTAAGATTTTTAAATGGCTCTTTATTCTTTTTAACCTTTTTATGCTAGTTATGACATTTAAATCTTGTGGAAGTGCTTCAGAAATTATTGCTTCTAGCCAAAATGAATATGAACAAGCAGGAGCTACATTAGGCTCTACATTAGGCTTAGGGATGGTGATAATTTTCTGGGCATTAGTAGATGTAATACTTGGATTATTTGTACTATTCACACGACCAAAGCGATAAAAATAGGGAGATATTCTCCTTATTTTTCAAATAGCTAAGCGTAAATTAAGGGCTTTAACAACTTTTATAACAGTGTCAAAACTAGGATTAACATCCCCAGATAGAGCTTTGTAAAGACTTTCTCTTCCTAAGCCAGTTTCTTTTGATAGTTGAGTCATACCTTTAGCTTTAGCAATGTTTCCTAGTGCTTTAGCGATAAAGGCTGCATCACCGTTGGATTCATCAATACATGCTTGTAAGTAAGCTTGCATATCCTCTTCTGTTTTGAGGTGCTCTGCACTATCCCACTTACGAAGTTTAATAGCCATTTATAGTTCCTCCTCTAGGTCTTTTGCTAGCTTCAAGGCGAGTTTTATATCTTTACTTTGGGTGGTTTTATCACCGCCTGCTAATAAAATAATAACTCTTTGTCCTTGTTGGCAATAATAAACTCTATAACCAGGACCGAAGAAAAAACGTAGTTCAGAAACACCTTCGCCCACAGGCTCAGTATCTCCAAAATTGCCATCTTCAACCCGATCGATACGAACTTGTATGCGTCTTTTTGCCTGTTGGTCTTTAAGTTTGTCAAACCAATCATCAAAGACTTCGGTGGTGTATATTGAGTACATAAGCAAAATGTATCCTATAGGATACATTTGTGCAAGACATAAACTTGGTTTTTTAGGCCTGAGGCACTGATGTTATTCCCAAGTAGAAAAGTCCTACCTAATAACTAAATAGAAATGTCCTATACAGGCATTTCCGGCCAGTGAGCCTATCAAAGTCCTCATGCATGAAGCCAAAGAAGAAATAATTTATTATTGAGTTTCGCTAAAATTAACATAATACACCTTATACGAAATGCGTTATAATTATCTATAGAAATCAATGCTGTAGTTTCTAGTTTATAGCCCATCTTCCCCAAGGTGGGTTTTTTTTATGATTTTACACGTTCCACGCTTATTTATTGAGCAATGTTCCACGGTTTTATTTAGCCTAAGTTAACCATATGGAAGAAAAAAACGACTC	LN:i:4399	RC:i:191002
+S	6	GAAAAATTGCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGTTAATACTT	LN:i:89	RC:i:9779
+L	6	+	277	-	81M
+L	6	+	280	+	81M
+L	232	+	277	+	81M
+L	280	+	232	-	81M
+L	282	+	6	+	81M
+L	283	+	6	+	81M
+L	289	+	282	+	81M
+L	289	+	283	+	81M
+L	297	-	232	+	81M
+L	297	+	289	+	81M
+L	333	-	232	+	81M
+L	333	+	289	+	81M

Tests/test_SeqIO.py

@@ -28,7 +28,7 @@ from Bio.SeqRecord import SeqRecord
 # warnings to stdout and verifying via the print-and-compare check. However,
 # there was some frustrating cross-platform inconsistency I couldn't resolve.
 
-possible_unknown_seq_formats = {"embl", "genbank", "gb", "imgt", "qual"}
+possible_unknown_seq_formats = {"embl", "genbank", "gb", "imgt", "qual", "gfa1", "gfa2"}
 
 # List of formats including alignment only file formats we can read AND write.
 # The list is initially hard coded to preserve the original order of the unit
@@ -1844,6 +1844,61 @@ class TestSeqIO(SeqIOTestBaseClass):
             messages,
         )
 
+    def test_gfa1(self):
+        sequences = [
+            "GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCT...ACATTAT",
+            "TATAATAAACACCCTCACCACTACAATCTTCCTAGGAACA...CTACTCT",
+            "GGGGTAAATGATGGGTTGGGCCAAGGGGTTAATTAGTACG...TATTAAG",
+            "ACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGC...TCTGAGC",
+            "ATTCTACCACTCCAGCCTAGCCCCCACCCCTCAACTTGGA...TATAAAC",
+            "CTTTTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGA...AGCCCAA",
+            "TTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCC...AAAGACC",
+            "ACATCATCGAAACCGCAAACATATCATACACAAACGCCTG...CACGATG",
+        ]
+        ids = [
+            "MTh0",
+            "MTh4001",
+            "MTo3426",
+            "MTh4502",
+            "MTo8961",
+            "MTh9505",
+            "MTh13014",
+            "MTh13516",
+        ]
+        names = ids
+        lengths = [4001, 501, 501, 5003, 502, 3509, 502, 3053]
+        molecule_types = {
+            "embl": "DNA",
+            "genbank": "DNA",
+            "imgt": "DNA",
+            "seqxml": "DNA",
+            "nexus": "DNA",
+        }
+        alignment = None
+        messages = {
+            "fastq": "No suitable quality scores found in letter_annotations of SeqRecord (id=MTh13516).",
+            "fastq-illumina": "No suitable quality scores found in letter_annotations of SeqRecord (id=MTh13516).",
+            "fastq-solexa": "No suitable quality scores found in letter_annotations of SeqRecord (id=MTh13516).",
+            "nib": "More than one sequence found",
+            "phd": "No suitable quality scores found in letter_annotations of SeqRecord (id=MTh13516).",
+            "qual": "No suitable quality scores found in letter_annotations of SeqRecord (id=MTh13516).",
+            "sff": "Missing SFF flow information",
+            "xdna": "More than one sequence found",
+        }
+        self.perform_test(
+            "gfa1",
+            False,
+            "GFA/seq.gfa",
+            8,
+            ids,
+            names,
+            sequences,
+            lengths,
+            alignment,
+            messages,
+            molecule_types=molecule_types,
+        )
+
     def test_nexus1(self):
         sequences = [
             "A-C-G-Tc-gtgtgtgctct-t-t------ac-gtgtgtgctct-t-t",

Tests/test_SeqIO_Gfa.py

@@ -0,0 +1,77 @@
+"""Tests for SeqIO GFA module."""
+import unittest
+
+from Bio import BiopythonWarning
+from Bio import SeqIO
+
+
+class TestRead(unittest.TestCase):
+    def test_read_GFA1(self):
+        """Test parsing valid GFA 1.x files."""
+        records = list(SeqIO.parse("GFA/seq.gfa", "gfa1"))
+        self.assertEqual(len(records), 8)
+        self.assertEqual(records[6].id, "MTh13014")
+        self.assertEqual(
+            records[6].seq,
+            "TTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACC",
+        )
+        self.assertEqual(records[0].annotations["SN"], ("Z", "MT_human"))
+        self.assertEqual(records[0].annotations["SO"], ("i", "0"))
+
+        records = list(SeqIO.parse("GFA/seq_with_len.gfa", "gfa1"))
+        self.assertEqual(len(records), 9)
+        self.assertEqual(
+            records[8].seq,
+            "GAAAAATTGCCCTTGGTTTTCGCTTCGCTCAAACTCTATTGAACTTCGCTTTCGCTCAGTTCGTCGGGGCAATTTTTTGGTTAATACTT",
+        )
+
+        records = list(SeqIO.parse("GFA/fake_with_checksum.gfa", "gfa1"))
+        self.assertEqual(len(records), 1)
+        self.assertEqual(records[0].seq, "AAA")
+
+        records = list(SeqIO.parse("GFA/no_seq.gfa", "gfa1"))
+        self.assertEqual(len(records), 9)
+        self.assertEqual(len(records[0]), 528)
+
+    def test_read_GFA2(self):
+        """Test parsing valid GFA 2.0 files."""
+        records = list(SeqIO.parse("GFA/fake_gfa2.gfa", "gfa2"))
+        self.assertEqual(len(records), 1)
+        self.assertEqual(records[0].seq, "AAA")
+
+
+class TestCorrupt(unittest.TestCase):
+    def test_corrupt_gfa2(self):
+        """Check a GFA 1.x file does not parse in GFA 2."""
+        with self.assertRaises(ValueError):
+            list(SeqIO.parse("GFA/seq.gfa", "gfa2"))
+
+    def test_corrupt_segment_fields(self):
+        """Check a GFA file with invalid fields on a segment line."""
+        with self.assertRaises(ValueError):
+            list(SeqIO.parse("GFA/corrupt_segment_fields.gfa", "gfa1"))
+
+    def test_corrupt_len(self):
+        """Check a GFA file with an incorrect length."""
+        with self.assertWarns(BiopythonWarning):
+            list(SeqIO.parse("GFA/corrupt_len.gfa", "gfa1"))
+
+    def test_corrupt_checksum(self):
+        """Check a GFA file with an incorrect checksum."""
+        with self.assertWarns(BiopythonWarning):
+            list(SeqIO.parse("GFA/corrupt_checksum.gfa", "gfa1"))
+
+    def test_corrupt_tag_name(self):
+        """Check a GFA file with an invalid tag name."""
+        with self.assertWarns(BiopythonWarning):
+            list(SeqIO.parse("GFA/corrupt_tag_name.gfa", "gfa1"))
+
+    def test_corrupt_tag_type(self):
+        """Check a GFA file with an incorrect tag type."""
+        with self.assertWarns(BiopythonWarning):
+            list(SeqIO.parse("GFA/corrupt_tag_type.gfa", "gfa1"))
+
+
+if __name__ == "__main__":
+    runner = unittest.TextTestRunner(verbosity=2)
+    unittest.main(testRunner=runner)