gregpinero

"""
Randomly insert genetic barcodes (and weighted randomly chosen quality values) as the first N bp of each read in a FASTQ file.

Greg Pinero 2012

"""

import sys
import argparse

gregpinero

def get_free_memory():
    """
    Try to figure out how much memory is free on a Unix system.
    Returns free memory in mB.
    """ 
    data = open("/proc/meminfo", 'rt').readlines()
    free = 0
    for line in data:
        if line.startswith("MemFree") or line.startswith("Buffers") or line.startswith("Cached"):
            items = line.split()

gregpinero

import re
infile = 'dsim-all-chromosome-r1.3.reassembly1.updated_wsu1.fasta'

ref_count = 0
for line in open(infile,'r'):
	if line.startswith('>'):
		ref_count += 1
		print '>' + re.sub(r'[^0-9a-zA-Z_]', '', line)[:50]
	else:
		print line,

gregpinero

"""Quick functions for reading and writing FASTQ"""

def read_fastq(filehandle):
    ''' Return dictionary with 'seq_id', 'seq', 'qual_id', and 'qual'  '''
    record_line = 0
    read_number = 0
    fastq_record = dict()
    for line in filehandle:
        record_line += 1

gregpinero

Perl syntax basics:

Perl ===
Start interactive interpreter:
perl -de 1
==== Syntax Basics ====
<pre><nowiki>
data types: $scalars, @lists, and %hashes
""my"" makes a variable be in the scope of its block and lower.  Use ""our"" for globals.
Put ""use strict"" at beginning of file to be required to declare variables.

gregpinero

--Log Insert
CREATE TRIGGER LogInsert ON [dbo].[CustomerProduct]
FOR INSERT
AS
INSERT changelog SELECT TOP 1 getdate(), 'Insert', 'CustomerProduct', CustomerID, ProductID, 'PaymenttypeID', '', Paymenttypeid FROM inserted
INSERT changelog SELECT TOP 1 getdate(), 'Insert', 'CustomerProduct', CustomerID, ProductID, 'ExpirationDate', '', convert(varchar(12), ExpirationDate, 110) FROM inserted
INSERT changelog SELECT TOP 1 getdate(), 'Insert', 'CustomerProduct', CustomerID, ProductID, 'Rate', '', Rate FROM inserted

gregpinero

""""""
Sample script using Lyons ABA web service methods

""""""

import httplib
import urllib
import xml.dom.minidom

#-------SETTINGS-------

gregpinero

import re
import datetime
import math

def format_timeinterval(start, end=None):
   if not end:
       end = datetime.now()
   return format_timedelta(end - start)

def format_secondsdelta(seconds):

gregpinero

/*
   name:

   mv:  

   app: 
  
   note:
*/

gregpinero

import re
import datetime
from time import time
import sys
import math
import zipfile
import pickle
from cStringIO import StringIO
from dateutil.relativedelta import relativedelta