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def _index_bfast(ref_file):
    """Indexes bfast in color and nucleotide space for longer reads.

    This preps for 40+bp sized reads, which is bfast's strength.
    """
    dir_name = "bfast"
    window_size = 14
    bfast_nt_masks = [
   "1111111111111111111111",
   "1111101110111010100101011011111",

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(use '[clojure.java.io])
(use '[clojure.contrib.str-utils2 :only (join)])

(defn fasta-lengths [in-file]
   "Generate collection of FASTA record lengths, splitting at '>' delimiters"
  (->> (line-seq (reader in-file))
    (partition-by #(.startsWith ^String % ">"))
    (filter #(not (.startsWith ^String (first %) ">")))
    (map #(join "" %))
    (map #(.length ^String %))))

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with open ("dna.txt", "r") as myfile:
    data=myfile.readlines()
    mRNA=data[1]

def next_transcript(mRNA, cur_pos):
    initial=mRNA.find("AUG", cur_pos)
    for i in range(initial, len(mRNA),3):
        if mRNA[i:i+3] == "UAG":
            return initial, i

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(comment "
  Retrieve UniProt FASTA files for provided input identifiers using REST API.
    http://www.uniprot.org/faq/28

  Usage:
    cljr run fetch_uniprot_fasta.clj [Any number of Uniprot IDs]
")

(ns biostar.uniprot
  (:import [java.net URLEncoder])

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"""Retrieve sequences from a MAF file for a genomic coordinate.

Usage:
    maf_retrieve_region.py <maf file> <organism> <chromosome> <start> <end>
"""
import os
import sys
import subprocess

from bx.align import maf

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from Bio import Entrez

def fetch_gene_coordinates(search_term):
    handle = Entrez.esearch(db="gene", term=search_term)
    rec = Entrez.read(handle)
    gene_id = rec["IdList"][0] # assuming best match works
    
    handle = Entrez.efetch(db="gene", id=gene_id, retmode="xml")
    rec = Entrez.read(handle)[0]
    gene_locus = rec["Entrezgene_locus"][0]

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class ORFFinder:
    """Find the longest ORF in a given sequence
    "seq" is a string, if "start" is not provided any codon can be the start of
    and ORF. If muliple ORFs have the longest length the first one encountered
    is printed
    """
    def __init__(self, seq, start=[], stop=["TAG", "TAA", "TGA"]):
        self.seq = seq
        self.start = start
        self.stop = stop

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--- src/main/java/org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator.java.orig	2011-03-09 15:32:39.295875004 -0500
+++ src/main/java/org/biojava3/core/sequence/transcription/RNAToAminoAcidTranslator.java	2011-03-10 08:18:42.525875009 -0500
@@ -85,7 +85,6 @@
             codonL.add(codon);
             
         }
-
         unknownAminoAcidCompound = aminoAcids.getCompoundForString("X");
     }
 

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(ns distblast-cluster.vagrant
  (:require [pallet.compute :as compute]
            [pallet.phase :as phase]
            [pallet.core :as core]
            [pallet.utils :as utils]
            [pallet.compute.node-list :as node-list]
            [pallet.action.exec-script :as exec-script]))

(defn test-script [session]
  (-> session

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#!/bin/bash

#--- config

SERVICE_NAME=galaxy
RUN_AS=galaxy
RUN_IN=/your/galaxy/directory

#--- main actions