mylons

import matplotlib.pyplot as pyplot

def plot_list(xs, ys, clf=False, label=None):
    if clf:
        pyplot.clf()
    line = pyplot.plot(xs, ps, label=name)
    
def make_plots(lists_of_x, lists_of_y):
   #assumes they're equal length lists of lists [ [ ] ]
   for i in xrange(lists_of_x):

mylons

import re
cigar = "32M1I89M1D7M1D37M1D16M1I71M1I12M1I18M1I19M3S"
matches = re.findall("([0-9]+)([A-Z]+)", cigar)
for length, operation in matches:
   print operation, length

mylons

while ($md =~ /(\d+)(\^?)([ACGTN]+)/g) {
            if ($2) { # deletion
                $read_pos += $1; # increment the matching length
            } elsif ($3) { # mismatch
                $read_pos += $1 + 1; # increment the matching length, then 1 for the mismatch
                #print STDERR "MD: $1 $3 read_pos $read_pos md_map $md_map[$read_pos]\n"; ##-#
                if ($line[1] & 0x0010) { # reverse read
                    $errors[$read_len - $md_map[$read_pos] - 1]++; # = 1 unless $errors[$read_len - 
                    md_map[$read_pos] - 1]; ### 
                } else { # forward read

mylons

#include <stdio.h>
#include <stdlib.h>


typedef struct {
    int start;
    int end;
} range_t;

mylons

 if(end + 1 < sams->n) {
          if(sams->sams[end].strand == sams->sams[end+1].strand //same strand
             && sams->sams[end].seqid == sams->sams[end+1].seqid) {
              sam_start = sams->sams[end].pos;
              sam_end = sams->sams[end].pos + sams->sams[end].target_len;
              sam_next_start = sams->sams[end+1].pos;
              sam_next_end = sam_next_start + sams->sams[end+1].target_len;
              if ( (sam_next_end > sam_end) && ((sam_next_end - sam_end) <= opt->max_seed_band) ) {
                  end++;
                  keep_banding = 1;

mylons

import os

def super_split(absolute_path):
    fdir, fname = os.path.split(absolute_path)
    tokens = fname.split('.')
    ext = tokens[-1]
    fname_no_ext = '.'.join( [ x for x in tokens[:len(tokens)-1] ])
    return fdir, fname_no_ext, ext

mylons

//ifs can have a value
val configFile = new java.io.File("~/.myapprc")

val configFilePath = if (configFile.exists()) { 
   configFile.getAbsolutePath()
 }
 else { 
   configFile.createNewFile()
   configFile.getAbsolutePath() 
}

mylons

#!/usr/bin/env python
import sys
import itertools
import collections

def Kdiff(nums, k):
    return sum(1 for x, y in itertools.combinations(nums, 2) if (x-y) == k)
def ErrorAndExit():
    print "0"
    sys.exit()

mylons

class Singleton:
    __single = None
    def __init__( self ):
        if Singleton.__single:
            raise Singleton.__single
        #this line of code is never reached
        #if __single already exists
        Singleton.__single = self

mylons

		try {
			BufferedReader in = new BufferedReader(new FileReader(pwd + "Makefile"));
			String str;
			while((str = in.readLine()) != null)
			 System.out.println(str);
			
			
			in.close();
			 
		} catch (FileNotFoundException e) {