soh-i

class W3m < Formula
  desc "Pager/text based browser"
  homepage "http://w3m.sourceforge.net/"
  url "https://downloads.sourceforge.net/project/w3m/w3m/w3m-0.5.3/w3m-0.5.3.tar.gz"
  sha256 "e994d263f2fd2c22febfbe45103526e00145a7674a0fda79c822b97c2770a9e3"

  depends_on "bdw-gc"
  depends_on "openssl"

soh-i

import lxml.html
import re
import requests
import time
from ppi.utils import debug

def _to_sp(sp):
    if sp == "sce":
        return "S. cerevisiae (yeast)"
    elif sp == "hsa":

soh-i

import inspect
import os
import os.path
import datetime

def header_info(func):
    def _header(*args, **kwargs):
        exec_path = inspect.currentframe().f_back.f_code.co_filename
        print "# Run '%s' function in %s" % (func.__name__, os.path.abspath(exec_path))
        print "# Host: %s" % (os.uname()[1])

soh-i

from pyfasta import Fasta
import HTSeq
import argparse
import re

def __mk_rna(*seq):
    return re.sub(r"[tT]", "U", "".join(seq)).upper()

def __query_builder(rec):
    if not isinstance(rec, HTSeq.GenomicFeature):

soh-i

/**
 * Created by yukke on 15/06/06.
 */

import htsjdk.samtools._
import java.io.File
import htsjdk.samtools.reference.{ReferenceSequence, ReferenceSequenceFileFactory, ReferenceSequenceFile}
import htsjdk.samtools.util.SamLocusIterator

import scala.collection.JavaConversions._

soh-i

diff --git a/build.xml b/build.xml
index 974d7c8..5fb82b9 100755
--- a/build.xml
+++ b/build.xml
@@ -188,6 +188,7 @@

     <target name="javadoc" depends="init" description="Generates the project javadoc.">
         <javadoc
+                additionalparam="-locale en_US -encoding utf-8 -charset utf-8"
                 sourcepath="${src}"

soh-i

def parse_dot_bracket_format(dot):
    binding_dict = {}
    for i, j in enumerate(dot):
        binding_dict[i] = None

    stack = []
    for i, j in enumerate(dot):
        if j == "(":
            stack.append(i)
        elif j == ")":

soh-i

def link_mature_and_pre(pre_dic, mature_dic):
    """
    miR-XXX-3p, miR-XXX-5p (mature) are derives from mir-XXX (pre),
    then it can be linked following:
    {pre: {3p: XXX, 5p: XXX}}
    """

    def matID_to_name(q, mature_HTSeq):
        # MIRAMTXXXX (transcript_id) to miR-XXX-Xp
        matures = []

soh-i

import java.io.File
import htsjdk.samtools._
import scala.compat.Platform
import scala.collection.JavaConversions._
import scala.util.control.Breaks.break


/**
 * Created by yukke on 15/05/23.
 */

soh-i

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

KSEQ_INIT(FILE*, read)

int main(int argc, char** argv)
{
  FILE* fp = fopen(argv[1], "r");
  if (fp == 0)