--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_genomic_dna.py	Tue Jan 19 09:34:23 2016 -0500
@@ -0,0 +1,207 @@
+#!/usr/bin/env python
+import argparse
+import os
+
+import extract_genomic_dna_utils as egdu
+import bx.seq.nib
+import bx.seq.twobit
+from bx.intervals.io import Header, Comment
+
+
+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('--output', dest='output', help="Output dataset")
+args = parser.parse_args()
+
+input_is_gff = args.input_format == 'gff'
+interpret_features = input_is_gff and args.interpret_features == "yes"
+if len(args.columns.split(',')) == 5:
+    # Bed file.
+    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)
+    name_col = False
+
+if args.reference_genome_source == "history":
+    seq_path = egdu.convert_to_twobit(args.reference_genome)
+else:
+    seq_path = args.reference_genome
+seq_dir = os.path.split(seq_path)[0]
+
+includes_strand_col = strand_col >= 0
+strand = None
+nibs = {}
+skipped_lines = 0
+first_invalid_line = 0
+invalid_lines = []
+warnings = []
+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')
+
+for feature in file_iterator:
+    # Ignore comments, headers.
+    if isinstance(feature, (Header, Comment)):
+        line_count += 1
+        continue
+    name = ""
+    if interpret_features:
+        # Processing features.
+        egdu.convert_gff_coords_to_bed(feature)
+        chrom = feature.chrom
+        start = feature.start
+        end = feature.end
+        strand = feature.strand
+    else:
+        # Processing lines, either interval or GFF format.
+        line = feature.rstrip('\r\n')
+        if line and not line.startswith("#"):
+            fields = line.split('\t')
+            try:
+                chrom = fields[chrom_col]
+                start = int(fields[start_col])
+                end = int(fields[end_col])
+                if name_col:
+                    name = fields[name_col]
+                if input_is_gff:
+                    start, end = egdu.convert_gff_coords_to_bed([start, end])
+                if includes_strand_col:
+                    strand = fields[strand_col]
+            except:
+                warning = "Invalid chrom, start or end column values. "
+                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 start > end:
+                warning = "Invalid interval, start '%d' > end '%d'.  " % (start, end)
+                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 strand not in ['+', '-']:
+                strand = '+'
+            sequence = ''
+        else:
+            continue
+    # Open sequence file and get sequence for feature/interval.
+    if os.path.exists("%s/%s.nib" % (seq_dir, chrom)):
+        if chrom in nibs:
+            nib = nibs[chrom]
+        else:
+            nibs[chrom] = nib = bx.seq.nib.NibFile(open("%s/%s.nib" % (seq_path, chrom)))
+        try:
+            sequence = nib.get(start, end - start)
+        except Exception, e:
+            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)
+                first_invalid_line = line_count
+            skipped_lines += len(invalid_lines)
+            continue
+    elif os.path.isfile(seq_path):
+        if not(twobitfile):
+            twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
+        try:
+            if interpret_features:
+                # Create sequence from intervals within a feature.
+                sequence = ''
+                for interval in feature.intervals:
+                    sequence += twobitfile[interval.chrom][interval.start:interval.end]
+            else:
+                sequence = twobitfile[chrom][start:end]
+        except:
+            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)
+                first_invalid_line = line_count
+            skipped_lines += len(invalid_lines)
+            continue
+    else:
+        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)
+        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 includes_strand_col and strand == "-":
+        sequence = egdu.reverse_complement(sequence)
+    if args.output_format == "fasta":
+        l = len(sequence)
+        c = 0
+        if input_is_gff:
+            start, end = egdu.convert_bed_coords_to_gff([start, end])
+        fields = [args.genome, str(chrom), str(start), str(end), strand]
+        meta_data = "_".join(fields)
+        if name.strip():
+            out.write(">%s %s\n" % (meta_data, name))
+        else:
+            out.write(">%s\n" % meta_data)
+        while c < l:
+            b = min(c + 50, l)
+            out.write("%s\n" % str(sequence[c:b]))
+            c = b
+    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")])
+        else:
+            # Where is fields being set here?
+            meta_data = "\t".join(fields)
+        if input_is_gff:
+            format_str = "%s seq \"%s\";\n"
+        else:
+            format_str = "%s\t%s\n"
+        out.write(format_str % (meta_data, str(sequence)))
+    # Update line count.
+    if isinstance(feature, egdu.GFFFeature):
+        line_count += len(feature.intervals)
+    else:
+        line_count += 1
+out.close()
+
+if warnings:
+    warn_msg = "%d warnings, 1st is: " % len(warnings)
+    warn_msg += warnings[0]
+    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]))
+
+if args.reference_genome_source == "history":
+    os.remove(seq_path)