standage

#!/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)

standage

#!/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

standage

#!/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]

standage

==> 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

standage

# -q: output in Fastq format
# -Q: ignore BAM quality flags
# -P: paired-end data
bam2fastx -qQP -o clean.fq <(bwa mem contaminants.fasta reads.1.fq reads.2.fq | \
                             perl -ne '@v = split(/\t/); print if(m/^@/ or ($v[1] & 4 and $v[1] & 8))' | \
                             samtools view -bhS -)

standage

#!/usr/bin/env bash
for file in `ls -1 *.results`
do
  base_name=`basename $file .results`
  sed -i.bak -e "1 s/^/$base_name./" -e $"1 s/\t/\t$base_name./g" $file
done

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perl -ne 'next unless(/^PdomSCFr1.1/); @v = split(/\t/); if($v[3] eq "" or $v[4] eq ""){ $two = <STDIN>; @v2 = split(/\t/, $two); $v[3] = $v2[3]; $v[4] = $v2[4]; print join("\t", @v), $two; } else{ print }' \
  < pdom-annot-p1.2-prealign.gff3 \
  > pdom-annot-p1.2-prealign-fixed.gff3

standage

import re, sys

if __name__ == "__main__":
  """
  Input:  GFF3 file containing gene (mRNA and tRNA) annotations
  Output: text files with new IDs for genes (written to stdout) and RNAs (written to stderr)
  """
  prefix  = sys.argv[1]
  release = sys.argv[2]
  genecount = 0