Let's do this.

README.md

@@ -0,0 +1,25 @@
+# Transcoorder
+
+Convert SAM/BAM files with transcript coordinates to SAM files with genomic coordinates
+
+```
+$ transcoord -h
+usage: transcoord [-h] [-o OUT] [-t TAG_NAME] [--debug] [--version] gtf bam fasta
+
+positional arguments:
+  gtf                   GTF file containing transcripts
+  bam                   SAM or BAM files aligned to transcriptome
+  fasta                 FASTA format assembly coresponding to GTF
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -o OUT, --out OUT     output file for genomic SAM (default: stdout)
+  -t TAG_NAME, --tag-name TAG_NAME
+                        SAM tag name for storing transcript identifier. default: ZT
+  --debug               enable debugging
+  --version             display version number
+```
+
+Note: This is an incomplete work in progress script and you shouldn't rely on its output. I 
+made this as a proof of concept, and never had time to finish. It currently runs very slowly 
+and only handles reads that are mapped entirely within an exon.

setup.py

@@ -33,7 +33,6 @@ def get_version(string):
     install_requires=install_requires,
     entry_points={'console_scripts': ['transcoord = transcoorder.cli:main']},
     classifiers=[
-        "Development Status :: 5 - Production/Stable",
         "License :: OSI Approved :: BSD License", "Environment :: Console",
         "Intended Audience :: Science/Research", "Natural Language :: English",
         "Operating System :: Unix", "Programming Language :: Python :: 3.5",

transcoorder/__init__.py

@@ -53,6 +53,6 @@ def transcript_sam_to_genomic_sam(sam, transcript, genome_offset,
     for coord in transcript_coords:
         if sam.pos <= coord[1] and sam.pos >= coord[0]:
             # if read falls entirely within exon
-            if coord[1] - sam.pos > len(sam):
+            if coord[1] - sam.pos > len(sam.seq):
                 sam.pos += coord[0] + genome_offset
                 return sam

transcoorder/cli.py

@@ -75,7 +75,7 @@ def main(ext_args=None):
                     transcript, genome_offset, transcript_coords = features
                     read = transcript_sam_to_genomic_sam(
                         read, transcript, genome_offset, transcript_coords)
-                    if read:
+                    if read is not None:
                         outfile.write(read)
                 pbar.update(1)