peterjc

#Copyright 2011 Peter Cock, released under GPL v3 licence
#
#Hack script to extract files in selected directories in one git
#repository and apply them to another repository using a potentially
#different directory structure.
#
#This written in Python and needs the git library, I used 0.3.2 RC1
#https://github.com/gitpython-developers/GitPython
#
#I assume when run both repositories are clean (no untracked files,

peterjc

from Bio import SeqIO
import sys
ids = set(x[:-1] for x in open(sys.argv[1]))
wanted = (rec for rec in SeqIO.parse(sys.stdin, "fastq") if rec.id in ids)
SeqIO.write(wanted, sys.stdout, "fastq")

peterjc

from Bio.SeqIO.QualityIO import FastqGeneralIterator
import sys
ids = set(x[:-1] for x in open(sys.argv[1]))
for title, seq, quals in FastqGeneralIterator(sys.stdin):
    if title.split(None,1)[0] in ids:
        print "@%s\n%s\n+\n%s\n" % (title, seq, quals)

peterjc

import zlib
import time

def decompress(comp_data):
    d = zlib.decompressobj(-15) #Negative window size means no headers
    uncomp_data = d.decompress(comp_data) + d.flush()
    del d
    return uncomp_data, zlib.crc32(uncomp_data)

def compress(orig_data):

peterjc

>ref
AGCATGTTAGATAA**GATAGCTGTGCTAGTAGGCAGTCAGCGCCAT

peterjc

#!/usr/bin/env python
#Example usage:
#
#    $ python ace_to_contig_stats.py < example.ace > example_stats.tsv
#
import sys
from Bio.Sequencing import Ace

sys.stdout.write("#Contig\tPadded length\tUnpadded length\tReads\n")
for contig in Ace.parse(sys.stdin):

peterjc

#!/usr/bin/env python 
#Copyright 2013, Peter Cock. All rights reserved.
#Released under the MIT License.
"""Python scipt to decode Roomba IR codes via the Linux mode2 tool.

Tested under Python 2.7 and Python 3.3, example usage:

$ mode2 -d /dev/lirc0 | python decode_roomba_ir.py
10101100 - 172 - 0xAC
10101100 - 172 - 0xAC

peterjc

#!/usr/bin/env python
#Copyright 2013, Peter Cock. All rights reserved.
#Released under the MIT License.
"""Python scipt to generate Roomba IR codes for LIRC.
 
Tested under Python 2.7 and Python 3.3, example usage:

$ python make_roomba_lirc.py > roomba.conf

See also:

peterjc

from reportlab.pdfgen import canvas
from reportlab.lib.pagesizes import letter
from reportlab.lib.units import inch
from reportlab.lib import colors
from reportlab.pdfbase.pdfmetrics import stringWidth

from reportlab.graphics.shapes import Drawing, String, Line, Rect, Wedge, ArcPath
from reportlab.graphics import renderPDF, renderPS
from reportlab.graphics.widgetbase import Widget

peterjc

#!/usr/bin/env python
"""Galaxy Tool Shed diff command."""

import sys
import os
import subprocess
import tempfile
from optparse import OptionParser

VERSION = "v0.0.1"