# HG changeset patch
# User iuc
# Date 1732173629 0
# Node ID 80414c33a59a328b3541edf667aa2af8eab0fb59
# Parent  5cc8e93ee98f211e89339599107e2f63c7b336de
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296

diff -r 5cc8e93ee98f -r 80414c33a59a extract_genomic_dna.py
--- a/extract_genomic_dna.py	Fri Dec 06 15:24:00 2019 -0500
+++ b/extract_genomic_dna.py	Thu Nov 21 07:20:29 2024 +0000
@@ -11,24 +11,47 @@
 import extract_genomic_dna_utils as egdu  # noqa: I100,I202
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--input_format', dest='input_format', help="Input dataset format")
-parser.add_argument('--input', dest='input', help="Input dataset")
-parser.add_argument('--genome', dest='genome', help="Input dataset genome build")
-parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff")
-parser.add_argument('--columns', dest='columns', help="Columns to use in input file")
-parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file")
-parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file")
-parser.add_argument('--output_format', dest='output_format', help="Output format")
-parser.add_argument('--fasta_header_type', dest='fasta_header_type', default=None, help="Fasta header format")
-parser.add_argument('--fasta_header_delimiter', dest='fasta_header_delimiter', default=None, help="Fasta header field delimiter")
-parser.add_argument('--output', dest='output', help="Output dataset")
+parser.add_argument("--input_format", dest="input_format", help="Input dataset format")
+parser.add_argument("--input", dest="input", help="Input dataset")
+parser.add_argument("--genome", dest="genome", help="Input dataset genome build")
+parser.add_argument(
+    "--interpret_features",
+    dest="interpret_features",
+    default=None,
+    help="Interpret features if input format is gff",
+)
+parser.add_argument("--columns", dest="columns", help="Columns to use in input file")
+parser.add_argument(
+    "--reference_genome_source",
+    dest="reference_genome_source",
+    help="Source of reference genome file",
+)
+parser.add_argument(
+    "--reference_genome", dest="reference_genome", help="Reference genome file"
+)
+parser.add_argument("--output_format", dest="output_format", help="Output format")
+parser.add_argument(
+    "--fasta_header_type",
+    dest="fasta_header_type",
+    default=None,
+    help="Fasta header format",
+)
+parser.add_argument(
+    "--fasta_header_delimiter",
+    dest="fasta_header_delimiter",
+    default=None,
+    help="Fasta header field delimiter",
+)
+parser.add_argument("--output", dest="output", help="Output dataset")
 args = parser.parse_args()
 
-input_is_gff = args.input_format == 'gff'
+input_is_gff = args.input_format == "gff"
 interpret_features = input_is_gff and args.interpret_features == "yes"
-if len(args.columns.split(',')) == 5:
+if len(args.columns.split(",")) == 5:
     # Bed file.
-    chrom_col, start_col, end_col, strand_col, name_col = egdu.parse_cols_arg(args.columns)
+    chrom_col, start_col, end_col, strand_col, name_col = egdu.parse_cols_arg(
+        args.columns
+    )
 else:
     # Gff file.
     chrom_col, start_col, end_col, strand_col = egdu.parse_cols_arg(args.columns)
@@ -47,13 +70,13 @@
 first_invalid_line = 0
 invalid_lines = []
 warnings = []
-warning = ''
+warning = ""
 twobitfile = None
 line_count = 1
 file_iterator = open(args.input)
 if interpret_features:
     file_iterator = egdu.GFFReaderWrapper(file_iterator, fix_strand=False)
-out = open(args.output, 'wt')
+out = open(args.output, "wt")
 
 for feature in file_iterator:
     # Ignore comments, headers.
@@ -70,9 +93,9 @@
         strand = feature.strand
     else:
         # Processing lines, either interval or GFF format.
-        line = feature.rstrip('\r\n')
+        line = feature.rstrip("\r\n")
         if line and not line.startswith("#"):
-            fields = line.split('\t')
+            fields = line.split("\t")
             try:
                 chrom = fields[chrom_col]
                 start = int(fields[start_col])
@@ -99,9 +122,9 @@
                     first_invalid_line = line_count
                 skipped_lines += len(invalid_lines)
                 continue
-            if strand not in ['+', '-']:
-                strand = '+'
-            sequence = ''
+            if strand not in ["+", "-"]:
+                strand = "+"
+            sequence = ""
         else:
             continue
     # Open sequence file and get sequence for feature/interval.
@@ -109,11 +132,16 @@
         if chrom in nibs:
             nib = nibs[chrom]
         else:
-            nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, chrom)))
+            nibs[chrom] = nib = bx.seq.nib.NibFile(
+                open("%s/%s.nib" % (seq_path, chrom))
+            )
         try:
             sequence = nib.get(start, end - start)
-        except Exception as e:
-            warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " % (start, end - start, args.genome)
+        except Exception:
+            warning = (
+                "Unable to fetch the sequence from '%d' to '%d' for build '%s'. "
+                % (start, end - start, args.genome)
+            )
             warnings.append(warning)
             if not invalid_lines:
                 invalid_lines = egdu.get_lines(feature)
@@ -121,18 +149,23 @@
             skipped_lines += len(invalid_lines)
             continue
     elif os.path.isfile(seq_path):
-        if not(twobitfile):
+        if not (twobitfile):
             twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
         try:
             if interpret_features:
                 # Create sequence from intervals within a feature.
-                sequence = ''
+                sequence = ""
                 for interval in feature.intervals:
-                    sequence += twobitfile[interval.chrom][interval.start:interval.end]
+                    sequence += twobitfile[interval.chrom][
+                        interval.start: interval.end
+                    ]
             else:
                 sequence = twobitfile[chrom][start:end]
         except Exception:
-            warning = "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. " % (start, end - start, chrom)
+            warning = (
+                "Unable to fetch the sequence from '%d' to '%d' for chrom '%s'. "
+                % (start, end - start, chrom)
+            )
             warnings.append(warning)
             if not invalid_lines:
                 invalid_lines = egdu.get_lines(feature)
@@ -140,15 +173,21 @@
             skipped_lines += len(invalid_lines)
             continue
     else:
-        warning = "Chromosome by name '%s' was not found for build '%s'. " % (chrom, args.genome)
+        warning = "Chromosome by name '%s' was not found for build '%s'. " % (
+            chrom,
+            args.genome,
+        )
         warnings.append(warning)
         if not invalid_lines:
             invalid_lines = egdu.get_lines(feature)
             first_invalid_line = line_count
         skipped_lines += len(invalid_lines)
         continue
-    if sequence == '':
-        warning = "Chrom: '%s', start: '%d', end: '%d' is either invalid or not present in build '%s'. " % (chrom, start, end, args.genome)
+    if sequence == "":
+        warning = (
+            "Chrom: '%s', start: '%d', end: '%d' is either invalid or not present in build '%s'. "
+            % (chrom, start, end, args.genome)
+        )
         warnings.append(warning)
         if not invalid_lines:
             invalid_lines = egdu.get_lines(feature)
@@ -161,15 +200,18 @@
         if input_is_gff:
             start, end = egdu.convert_bed_coords_to_gff([start, end])
         if args.fasta_header_type == "bedtools_getfasta_default":
-            out.write(">%s\n" % egdu.get_bedtools_getfasta_default_header(str(chrom),
-                                                                          str(start),
-                                                                          str(end),
-                                                                          strand,
-                                                                          includes_strand_col))
+            out.write(
+                ">%s\n"
+                % egdu.get_bedtools_getfasta_default_header(
+                    str(chrom), str(start), str(end), strand, includes_strand_col
+                )
+            )
         else:
             # args.fasta_header_type == "char_delimited":
             fields = [args.genome, str(chrom), str(start), str(end), strand]
-            field_delimiter = egdu.get_fasta_header_delimiter(args.fasta_header_delimiter)
+            field_delimiter = egdu.get_fasta_header_delimiter(
+                args.fasta_header_delimiter
+            )
             meta_data = field_delimiter.join(fields)
             if name.strip():
                 out.write(">%s %s\n" % (meta_data, name))
@@ -184,20 +226,24 @@
     else:
         # output_format == "interval".
         if interpret_features:
-            meta_data = "\t".join([feature.chrom,
-                                   "galaxy_extract_genomic_dna",
-                                   "interval",
-                                   str(feature.start),
-                                   str(feature.end),
-                                   feature.score,
-                                   feature.strand,
-                                   ".",
-                                   egdu.gff_attributes_to_str(feature.attributes, "GTF")])
+            meta_data = "\t".join(
+                [
+                    feature.chrom,
+                    "galaxy_extract_genomic_dna",
+                    "interval",
+                    str(feature.start),
+                    str(feature.end),
+                    feature.score,
+                    feature.strand,
+                    ".",
+                    egdu.gff_attributes_to_str(feature.attributes, "GTF"),
+                ]
+            )
         else:
             # Here fields was set up around line 73.
             meta_data = "\t".join(fields)
         if input_is_gff:
-            format_str = "%s seq \"%s\";\n"
+            format_str = '%s seq "%s";\n'
         else:
             format_str = "%s\t%s\n"
         out.write(format_str % (meta_data, str(sequence)))
@@ -214,7 +260,10 @@
     print(warn_msg)
 if skipped_lines:
     # Error message includes up to the first 10 skipped lines.
-    print('Skipped %d invalid lines, 1st is #%d, "%s"' % (skipped_lines, first_invalid_line, '\n'.join(invalid_lines[:10])))
+    print(
+        'Skipped %d invalid lines, 1st is #%d, "%s"'
+        % (skipped_lines, first_invalid_line, "\n".join(invalid_lines[:10]))
+    )
 
 if args.reference_genome_source == "history":
     os.remove(seq_path)
diff -r 5cc8e93ee98f -r 80414c33a59a extract_genomic_dna.xml
--- a/extract_genomic_dna.xml	Fri Dec 06 15:24:00 2019 -0500
+++ b/extract_genomic_dna.xml	Thu Nov 21 07:20:29 2024 +0000
@@ -1,10 +1,13 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy2">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy3">
     <description>using coordinates from assembled/unassembled genomes</description>
     <requirements>
         <requirement type="package" version="0.7.1">bx-python</requirement>
         <requirement type="package" version="1.13.0">six</requirement>
         <requirement type="package" version="377">ucsc-fatotwobit</requirement>
     </requirements>
+    <required_files>
+        <include path="extract_genomic_dna_utils.py" />
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
 #set genome = $input.metadata.dbkey
 #set datatype = $input.datatype
@@ -104,7 +107,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9" ftype="fasta"/>
             <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="tilde"/>
@@ -114,7 +117,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="bedtools_getfasta_default"/>
             <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
@@ -123,7 +126,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <param name="output_format" value="interval"/>
             <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
         </test>
@@ -131,7 +134,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <param name="output_format" value="interval"/>
             <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
         </test>
diff -r 5cc8e93ee98f -r 80414c33a59a extract_genomic_dna_utils.py
--- a/extract_genomic_dna_utils.py	Fri Dec 06 15:24:00 2019 -0500
+++ b/extract_genomic_dna_utils.py	Thu Nov 21 07:20:29 2024 +0000
@@ -178,7 +178,7 @@
             try:
                 interval = GenomicIntervalReader.next(self)
                 raw_size += len(self.current_line)
-            except StopIteration as e:
+            except StopIteration:
                 # No more intervals to read, but last feature needs to be
                 # returned.
                 interval = None