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"

peterjc

# Walks specified folders looking for .shed.yml files,
# with at least owner and name given.
#
# Matches the owner/name with the remote Tool Shed, and
# takes any missing meta-data from the remote Tool Shed.
#
# Pre-existing local data otherwise should be preserved.
#
# Does the yaml dump with some hackery because I couldn't
# work out how to make the library use the layout I wanted.

peterjc

from Bio import SeqIO
with open("CP008802.txt", "w") as output:
    output.write("Seqname\tSource\tfeature\tStart\tEnd\tScore\tStrand\tFrame\tAttributes\n")
    for record in SeqIO.parse("CP008802.gbk", "genbank"):
        print("Converting %s" % record.name)
        for f in record.features:
            if f.type != "gene":
                continue
            locus_tag = f.qualifiers["locus_tag"][0]
            if len(f.location.parts) > 1:

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

#
# A hack, loosly based on Eric Rasche's disgusting.py
# https://gist.github.com/erasche/4ac3448b036f09979e14
#
# Intended as a one-off use script to help with syncing local
# .shed.yml files with a Galaxy Tool Shed. See also:
# https://gist.github.com/peterjc/5ebbf446d799f3aaa639

import yaml
import os

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):