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##gff-version   3
##sequence-region   seq01 1 900
##sequence-region   seq02 1 900
##sequence-region   seq03 1 900
##sequence-region   seq04 1 900
##sequence-region   seq05 1 900
##sequence-region   seq06 1 900
##sequence-region   seq07 1 2000
##sequence-region   seq08 1 2000
##sequence-region   seq09 1 2000

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PdomSCFr1.1-0001	Cufflinks	transcript	2872997	2880927	500	.	.	gene_id "CUFF.181"; transcript_id "CUFF.181.1"; FPKM "0.5000000000"; frac "0.000000"; conf_lo "0.500000"; conf_hi "0.500000"; cov "0.225344";
PdomSCFr1.1-0001	Cufflinks	exon	2872997	2880927	500	.	.	gene_id "CUFF.181"; transcript_id "CUFF.181.1"; exon_number "1"; FPKM "0.5000000000"; frac "0.000000"; conf_lo "0.500000"; conf_hi "0.500000"; cov "0.225344";
PdomSCFr1.1-0001	Cufflinks	transcript	2873500	2875236	1000	.	.	gene_id "CUFF.181"; transcript_id "CUFF.181.2"; FPKM "1.0000000000"; frac "0.000000"; conf_lo "1.000000"; conf_hi "1.000000"; cov "0.450687";
PdomSCFr1.1-0001	Cufflinks	exon	2873500	2875236	1000	.	.	gene_id "CUFF.181"; transcript_id "CUFF.181.2"; exon_number "1"; FPKM "1.0000000000"; frac "0.000000"; conf_lo "1.000000"; conf_hi "1.000000"; cov "0.450687";
PdomSCFr1.1-0001	Cufflinks	transcript	2875367	2880803	1000	.	.	gene_id "CUFF.181"; transcript_id "CUFF.181.3"; FPKM "1.0000000000"; frac "0.000000"; conf_lo "1.000000"; conf_hi "1.0000

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[create obj/gt_config.h]
[compile sqlite3.o]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]
[compile array2dim_sparse.o]
[compile array3dim.o]
[compile basename.o]
[compile bioseq.o]
[compile bioseq_col.o]

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#!/usr/bin/env python
import re, sys

# Usage: gsq2gff3 < in.gsq > out.gff3

print "##gff-version   3"
for line in sys.stdin:
  line = line.rstrip()
  matches = re.search("hqPGS_(.+)[+-]_(.+)([+-])\s\((.+)\)", line)
  if not matches:

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#!/usr/bin/env python
import getopt, os, re, sys

class Seq:
  def __init__(self, defline, seq):
    self.defline = defline
    self.seq = seq
    match = re.match("^>(\S+)", defline)
    self.id = match.group(1)

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#!/usr/bin/env python
import getopt, os, subprocess, sys

def print_usage(outstream):
  usage = ("Usage: tdc-driver [options] cufflinks.gtf refseq.fasta\n"
           "  Options:\n"
           "    -h|--help:            print this help message and exit\n"
           "    -o|--out-dir: PATH    output directory; default is 'tdc.$pid'\n"
           "    -T|--tdc-dir: PATH    TransDecoder directory; default is '/usr/local/src/transdecoder'\n")
  print >> outstream, usage

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#!/usr/bin/env python
import getopt, os, re, sys

class Seq:
  def __init__(self, defline, seq):
    self.defline = defline
    self.seq = seq
    match = re.match("^>(\S+)", defline)
    self.id = match.group(1)

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#!/usr/bin/env python
import re, sys

# vrlpr.py: find overlapping genes in a GTF file
# Usage: python vrlpr.py < genes.gtf > overlaps.txt

def overlap(range1, range2):
  return range1[0] == range2[0] and range1[2] >= range2[1] and \
         range1[1] <= range2[2]

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==> Downloading http://genometools.org/pub/genometools-1.5.2.tar.gz
Already downloaded: /Library/Caches/Homebrew/genometools-1.5.2.tar.gz
==> Verifying genometools-1.5.2.tar.gz checksum
tar xf /Library/Caches/Homebrew/genometools-1.5.2.tar.gz
==> make prefix=/usr/local/Cellar/genometools/1.5.2 64bit=yes
[create obj/gt_config.h]
[compile sqlite3.o]
[compile alphabet.o]
[compile array.o]
[compile array2dim.o]

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/*

Copyright (c) 2014, Daniel S. Standage <daniel.standage@gmail.com>

Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF