Merge pull request galaxyproject#16576 from claudiofr/dt_chain

Support new genome browser chain file format

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -960,6 +960,7 @@
     <datatype extension="shp" type="galaxy.datatypes.gis:Shapefile" mimetype="application/octet-stream" display_in_upload="true" description="geospatial vector data format for geographic information system"/>
     <!-- Flexible Image Transport System (FITS) used in Astronomy https://fits.gsfc.nasa.gov/ https://fits.gsfc.nasa.gov/rfc4047.txt -->
     <datatype extension="fits" type="galaxy.datatypes.binary:FITS" mimetype="application/octet-stream" display_in_upload="true" description="Flexible Image Transport System (FITS) used in Astronomy"/>
+    <datatype extension="chain" type="galaxy.datatypes.chain:Chain" display_in_upload="true"/>
   </registration>
   <sniffers>
     <!--
@@ -1061,6 +1062,7 @@
     <sniffer type="galaxy.datatypes.binary:Pretext"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
+    <sniffer type="galaxy.datatypes.chain:Chain"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.images:Gifti" />

lib/galaxy/datatypes/chain.py

@@ -0,0 +1,129 @@
+"""
+Genome browser chain format class
+"""
+
+import logging
+
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.protocols import DatasetProtocol
+from galaxy.datatypes.sniff import (
+    build_sniff_from_prefix,
+    FilePrefix,
+)
+from galaxy.util import (
+    commaify,
+    compression_utils,
+    nice_size,
+)
+from . import data
+
+log = logging.getLogger(__name__)
+
+
+@build_sniff_from_prefix
+class Chain(data.Text):
+    """Class describing a chain format alignment file"""
+
+    edam_format = "format_3982"
+    file_ext = "chain"
+
+    strands = ["+", "-"]
+
+    MetadataElement(
+        name="chains", default=0, desc="Number of chains", readonly=True, visible=False, optional=False, no_value=0
+    )
+
+    def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
+        """
+        Set the number of chains and the number of data lines in dataset.
+        """
+        data_lines = 0
+        chains = 0
+        with compression_utils.get_fileobj(dataset.file_name) as fh:
+            for line in fh:
+                line = line.strip()
+                if line and line.startswith("#"):
+                    # We don't count comment lines for sequence data types
+                    continue
+                if line and line.startswith("chain"):
+                    chains += 1
+                    data_lines += 1
+                else:
+                    data_lines += 1
+            dataset.metadata.data_lines = data_lines
+            dataset.metadata.chains = chains
+
+    def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            if dataset.metadata.chains:
+                dataset.blurb = f"{commaify(str(dataset.metadata.chains))} chains"
+            else:
+                dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = "file does not exist"
+            dataset.blurb = "file purged from disk"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """
+        Determines whether the file is in chain format
+
+        For complete details see https://genome.ucsc.edu/goldenPath/help/chain.html
+
+        Rules for sniffing as True:
+
+            We don't care about line length (other than empty lines).
+
+            The first non-empty line must start with 'chain' and the Very Next line.strip() must have an alignment data line
+            which consists of either 1 or 3 integers separated by spaces.
+
+            The chain line must have at least 12 tokens representing the chain attributes.
+            The 2 strand attributes must have values + or -. We verify that some of the
+            other numeric attributes such as sequence length start/stop positions are
+            integers.
+
+            We will only check that the first chain and alignment data lines are formatted correctly.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( 'sequence.maf' )
+        >>> Chain().sniff( fname )
+        False
+        >>> fname = get_test_fname( '1.chain' )
+        >>> Chain().sniff( fname )
+        True
+        >>>
+        """
+        fh = file_prefix.string_io()
+        for line in fh:
+            line = line.strip()
+            if line:  # first non-empty line
+                if line.startswith("chain"):
+                    # The next line.strip() must not be '', nor startwith '>'
+                    tokens = line.split()
+                    if not (
+                        len(tokens) in [12, 13]
+                        and tokens[4] in self.strands
+                        and tokens[9] in self.strands
+                        and tokens[3].isdigit()
+                        and tokens[5].isdigit()
+                        and tokens[6].isdigit()
+                    ):
+                        return False
+                    prior_token_len = 0
+                    for line in fh:
+                        line = line.strip()
+                        if line == "":
+                            break
+                        tokens = line.split()
+                        if prior_token_len == 1:
+                            return False
+                        if len(tokens) not in [1, 3]:
+                            return False
+                        if not all(token.isdigit() for token in tokens):
+                            return False
+                        prior_token_len = len(tokens)
+                    if prior_token_len == 1:
+                        return True
+                else:
+                    return False
+        return False