--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fromgtfTobed12.py	Fri Nov 04 15:37:12 2022 +0000
@@ -0,0 +1,150 @@
+import argparse
+import sys
+import warnings
+
+import gffutils
+
+warnings.filterwarnings("ignore", message="It appears you have a gene feature"
+                        " in your GTF file. You may want to use the "
+                        "`disable_infer_genes` option to speed up database "
+                        "creation")
+warnings.filterwarnings("ignore", message="It appears you have a transcript "
+                        "feature in your GTF file. You may want to use the "
+                        "`disable_infer_transcripts` option to speed up "
+                        "database creation")
+# In gffutils v0.10 they changed the error message:
+warnings.filterwarnings("ignore", message="It appears you have a gene feature"
+                        " in your GTF file. You may want to use the "
+                        "`disable_infer_genes=True` option to speed up "
+                        "database creation")
+warnings.filterwarnings("ignore", message="It appears you have a transcript "
+                        "feature in your GTF file. You may want to use the "
+                        "`disable_infer_transcripts=True` option to speed up "
+                        "database creation")
+
+
+def convert_gtf_to_bed(fn, fo, useGene, mergeTranscripts,
+                       mergeTranscriptsAndOverlappingExons, ucsc):
+    db = gffutils.create_db(fn, ':memory:')
+    # For each transcript:
+    prefered_name = "transcript_name"
+    if useGene or mergeTranscripts or mergeTranscriptsAndOverlappingExons:
+        prefered_name = "gene_name"
+    if mergeTranscripts or mergeTranscriptsAndOverlappingExons:
+        all_items = db.features_of_type("gene", order_by='start')
+    else:
+        all_items = db.features_of_type("transcript", order_by='start')
+    for tr in all_items:
+        # The name would be the name of the transcript/gene if exists
+        try:
+            # First try to have it directly on the feature
+            trName = tr.attributes[prefered_name][0]
+        except KeyError:
+            # Else try to guess the name of the transcript/gene from exons:
+            try:
+                trName = set([e.attributes[prefered_name][0]
+                              for e in
+                              db.children(tr,
+                                          featuretype='exon',
+                                          order_by='start')]).pop()
+            except KeyError:
+                # Else take the transcript id
+                trName = tr.id
+        # If the cds is defined in the gtf,
+        # use it to define the thick start and end
+        # The gtf is 1-based closed intervalls and
+        # bed are 0-based half-open so:
+        # I need to remove one from each start
+        try:
+            # In case of multiple CDS (when there is one entry per gene)
+            # I use the first one to get the start
+            # and the last one to get the end (order_by=-start)
+            cds_start = next(db.children(tr,
+                                         featuretype='CDS',
+                                         order_by='start')).start - 1
+            cds_end = next(db.children(tr,
+                                       featuretype='CDS',
+                                       order_by='-start')).end
+        except StopIteration:
+            # If the CDS is not defined, then it is set to the start
+            # as proposed here:
+            # https://genome.ucsc.edu/FAQ/FAQformat.html#format1
+            cds_start = tr.start - 1
+            cds_end = tr.start - 1
+        # Get all exons starts and lengths
+        if mergeTranscriptsAndOverlappingExons:
+            # We merge overlapping exons:
+            exons_starts = []
+            exons_length = []
+            current_start = -1
+            current_end = None
+            for e in db.children(tr, featuretype='exon', order_by='start'):
+                if current_start == -1:
+                    current_start = e.start - 1
+                    current_end = e.end
+                else:
+                    if e.start > current_end:
+                        # This is a non-overlapping exon
+                        # We store the previous exon:
+                        exons_starts.append(current_start)
+                        exons_length.append(current_end - current_start)
+                        # We set the current:
+                        current_start = e.start - 1
+                        current_end = e.end
+                    else:
+                        # This is an overlapping exon
+                        # We update current_end if necessary
+                        current_end = max(current_end, e.end)
+            if current_start != -1:
+                # There is a last exon to store:
+                exons_starts.append(current_start)
+                exons_length.append(current_end - current_start)
+        else:
+            exons_starts = [e.start - 1
+                            for e in
+                            db.children(tr, featuretype='exon',
+                                        order_by='start')]
+            exons_length = [len(e)
+                            for e in
+                            db.children(tr, featuretype='exon',
+                                        order_by='start')]
+        # Rewrite the chromosome name if needed:
+        chrom = tr.chrom
+        if ucsc and chrom[0:3] != 'chr':
+            chrom = 'chr' + chrom
+        fo.write("%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\n" %
+                 (chrom, tr.start - 1, tr.end, trName, 0, tr.strand,
+                  cds_start, cds_end, "0", len(exons_starts),
+                  ",".join([str(ex_l) for ex_l in exons_length]),
+                  ",".join([str(s - (tr.start - 1)) for s in exons_starts])))
+
+
+argp = argparse.ArgumentParser(
+    description=("Convert a gtf to a bed12 with one entry"
+                 " per transcript/gene"))
+argp.add_argument('input', default=None,
+                  help="Input gtf file (can be gzip).")
+argp.add_argument('--output', default=sys.stdout,
+                  type=argparse.FileType('w'),
+                  help="Output bed12 file.")
+argp.add_argument('--useGene', action="store_true",
+                  help="Use the gene name instead of the "
+                       "transcript name.")
+argp.add_argument('--ucscformat', action="store_true",
+                  help="If you want that all chromosome names "
+                       "begin with 'chr'.")
+group = argp.add_mutually_exclusive_group()
+group.add_argument('--mergeTranscripts', action="store_true",
+                   help="Merge all transcripts into a single "
+                        "entry to have one line per gene.")
+group.add_argument('--mergeTranscriptsAndOverlappingExons',
+                   action="store_true",
+                   help="Merge all transcripts into a single "
+                        "entry to have one line per gene and merge"
+                        " overlapping exons.")
+
+args = argp.parse_args()
+convert_gtf_to_bed(args.input, args.output, args.useGene,
+                   args.mergeTranscripts,
+                   args.mergeTranscriptsAndOverlappingExons,
+                   args.ucscformat)