# HG changeset patch # User rlegendre # Date 1506502750 14400 # Node ID 01b945ba3697ce1814692164b5ad3d674f54d2fd Uploaded diff -r 000000000000 -r 01b945ba3697 ribo_tools/get_codon_frequency.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/get_codon_frequency.py Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,736 @@ +#!/usr/bin/env python2.7 +# -*- coding: utf-8 -*- + +''' + Created on sep. 2013 + @author: rachel legendre + @copyright: rachel.legendre@igmors.u-psud.fr + @license: GPL v3 +''' + +from __future__ import division +import os, sys, optparse, tempfile, subprocess, re, shutil, commands, urllib, time +import itertools +from math import log10 +from decimal import Decimal +from Bio import SeqIO +from Bio.Seq import Seq +from numpy import arange, std, array, linspace, average +#from matplotlib import pyplot as pl +import matplotlib +matplotlib.use('Agg') +import matplotlib.pyplot as pl +from matplotlib import font_manager +from matplotlib import colors +import csv +from scipy import stats, errstate +from collections import OrderedDict +import ribo_functions +import HTSeq +# #libraries for debugg +#import pdb +import cPickle + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.stderr.write("Programme aborted at %s\n" % time.asctime(time.localtime(time.time()))) + sys.exit() + + +def init_codon_dict(): + + Codon_dict = OrderedDict([('AAA', 0), ('AAC', 0), ('AAG', 0), ('AAT', 0), ('ACA', 0), ('ACC', 0), ('ACG', 0), ('ACT', 0), ('AGA', 0), ('AGC', 0), ('AGG', 0), ('AGT', 0), ('ATA', 0), ('ATC', 0), ('ATG', 0), ('ATT', 0), ('CAA', 0), ('CAC', 0), ('CAG', 0), ('CAT', 0), ('CCA', 0), ('CCC', 0), ('CCG', 0), ('CCT', 0), ('CGA', 0), ('CGC', 0), ('CGG', 0), ('CGT', 0), ('CTA', 0), ('CTC', 0), ('CTG', 0), ('CTT', 0), ('GAA', 0), ('GAC', 0), ('GAG', 0), ('GAT', 0), ('GCA', 0), ('GCC', 0), ('GCG', 0), ('GCT', 0), ('GGA', 0), ('GGC', 0), ('GGG', 0), ('GGT', 0), ('GTA', 0), ('GTC', 0), ('GTG', 0), ('GTT', 0), ('TAA', 0), ('TAC', 0), ('TAG', 0), ('TAT', 0), ('TCA', 0), ('TCC', 0), ('TCG', 0), ('TCT', 0), ('TGA', 0), ('TGC', 0), ('TGG', 0), ('TGT', 0), ('TTA', 0), ('TTC', 0), ('TTG', 0), ('TTT', 0)]) + return Codon_dict + + + +def get_codon_usage(bamfile, GFF, site, kmer, a_pos): + ''' + Read GFF dict and get gene codon usage. + Return dict of codons usage + ''' + try: + codon = init_codon_dict() + multi_tag = "XS:i:" ## bowtie Tag + tag = "IH:i:1" ## RUM tag + + for feature in GFF : + if feature.type == 'gene' : + codon_dict = init_codon_dict() + chrom = feature.iv.chrom + start = feature.iv.start + stop = feature.iv.end + if start+50 < stop-50 : + region = chrom + ':' + str(start+50) + '-' + str(stop-50) + # #get all reads in this gene + reads = subprocess.check_output(["samtools", "view", bamfile, region]) + head = subprocess.check_output(["samtools", "view", "-H", bamfile]) + read_tab = reads.split('\n') + for read in read_tab: + # # search mapper for eliminate multiple alignements + if 'bowtie' in head: + multi_tag = "XS:i:" + elif 'bwa' in head: + multi_tag = "XT:A:R" + elif 'TopHat' in head: + tag = "NH:i:1" + else : + stop_err("No PG tag find in "+samfile+". Please use bowtie, bwa or Tophat for mapping") + + if len(read) == 0: + continue + len_read = len(read.split('\t')[9]) + # if it's read of good length + if len_read == kmer and (tag in read or multi_tag not in read): + feat = read.split('\t') + seq = feat[9] + # if it's a reverse read + if feat[1] == '16' : + if site == "A" : + # #get A-site + cod = str(Seq(seq[a_pos-5:a_pos-2]).reverse_complement()) + elif site == "P" : + # #get P-site + cod = str(Seq(seq[a_pos-2:a_pos+1]).reverse_complement()) + else : + # #get site-E + cod = str(Seq(seq[a_pos+1:a_pos+4]).reverse_complement()) + # # test if it's a true codon not a CNG codon for example + if codon_dict.has_key(cod) : + codon_dict[cod] += 1 + # if it's a forward read + elif feat[1] == '0' : + if site == "A" : + # #get A-site + cod = seq[a_pos:a_pos+3] + elif site == "P" : + # #get P-site + cod = seq[a_pos-3:a_pos] + else : + # #get site-E + cod = seq[a_pos-6:a_pos-3] + if codon_dict.has_key(cod) : + codon_dict[cod] += 1 + del(read) + # # add in global dict + for cod, count in codon_dict.iteritems() : + codon[cod] += count + if sum(codon.values()) == 0 : + stop_err('There are no reads aligning on annotated genes in your GFF file') + else : + return codon + + except Exception, e: + stop_err('Error during codon usage calcul: ' + str(e)) + + + + +''' +http://pyinsci.blogspot.fr/2009/09/violin-plot-with-matplotlib.html +''' +def violin_plot(ax, data, pos, bp=False): + ''' + create violin plots on an axis + ''' + dist = max(pos) - min(pos) + w = min(0.15 * max(dist, 1.0), 0.5) + for d, p in zip(data, pos): + k = stats.gaussian_kde(d) # calculates the kernel density + m = k.dataset.min() # lower bound of violin + M = k.dataset.max() # upper bound of violin + x = arange(m, M, (M - m) / 100.) # support for violin + v = k.evaluate(x) # violin profile (density curve) + v = v / v.max() * w # scaling the violin to the available space + ax.fill_betweenx(x, p, v + p, facecolor=color1, alpha=0.3) + ax.fill_betweenx(x, p, -v + p, facecolor=color2, alpha=0.3) + if bp: + ax.boxplot(data, notch=1, positions=pos, vert=1) + + + +''' +http://log.ooz.ie/2013/02/matplotlib-comparative-histogram-recipe.html +''' +def comphist(x1, x2, orientation='vertical', **kwargs): + """Draw a comparative histogram.""" + # Split keyword args: + kwargs1 = {} + kwargs2 = {} + kwcommon = {} + for arg in kwargs: + tgt_arg = arg[:-1] + if arg.endswith('1'): + arg_dict = kwargs1 + elif arg.endswith('2'): + arg_dict = kwargs2 + else: + arg_dict = kwcommon + tgt_arg = arg + arg_dict[tgt_arg] = kwargs[arg] + kwargs1.update(kwcommon) + kwargs2.update(kwcommon) + + fig = pl.figure() + + # Have both histograms share one axis. + if orientation == 'vertical': + ax1 = pl.subplot(211) + ax2 = pl.subplot(212, sharex=ax1) + # Flip the ax2 histogram horizontally. + ax2.set_ylim(ax1.get_ylim()[::-1]) + pl.setp(ax1.get_xticklabels(), visible=False) + legend_loc = (1, 4) + else: + ax1 = pl.subplot(122) + ax2 = pl.subplot(121, sharey=ax1) + # Flip the ax2 histogram vertically. + ax2.set_xlim(ax2.get_xlim()[::-1]) + pl.setp(ax1.get_yticklabels(), visible=False) + legend_loc = (1, 2) + + ax1.hist(x1, orientation=orientation, **kwargs1) + ax2.hist(x2, orientation=orientation, **kwargs2) + ax2.set_ylim(ax1.get_ylim()[::-1]) + ax1.legend(loc=legend_loc[0]) + ax2.legend(loc=legend_loc[1]) + # Tighten up the layout. + pl.subplots_adjust(wspace=0.0, hspace=0.0) + return fig + + +def compute_FC_plot(cond1_norm, cond2_norm, cod_name, codon_to_test, dirout): + + FC_tab = [] + for z, y in zip(cond1_norm.itervalues(), cond2_norm.itervalues()): + fc = z - y + FC_tab.append(fc) + # #codon_to_test = ['TGA','TAG','TAA'] + + a = [] + b = [] + cod = [] + for codon in cond1_norm.iterkeys(): + if codon in codon_to_test : + fc = cond1_norm[codon] - cond2_norm[codon] + b.append(fc) + cod.append(codon) + else : + fc = cond1_norm[codon] - cond2_norm[codon] + a.append(fc) + + + fig = pl.figure(num=1) + comphist(array(a), array(b), label1='All codon', label2=cod_name, color2='green', bins=30, rwidth=1) + # pl.show() + pl.savefig(dirout + '/hist_codon_fc.png', format="png", dpi=340) + pl.clf() + + + # #violin plot + pos = range(2) + dat = array([array(a), array(b)]) + fig = pl.figure() + pl.title("Distribution of codons FoldChange between two conditions") + ax = fig.add_subplot(1, 1, 1) + lab = array(['All codons', cod_name]) + violin_plot(ax, dat, pos, bp=1) + for x, z in zip(dat, pos): + ax.plot(z, average(x), color='r', marker='*', markeredgecolor='r') + xtickNames = pl.setp(ax, xticklabels=lab) + pl.savefig(dirout + '/violinplot_codon.png', format="png", dpi=340) + pl.clf() + + # (Fval,pval) = stats.ttest_ind(a, b, axis=0, equal_var=True) + (Fval, pval) = stats.mannwhitneyu(a, b) + return pval + + +def get_aa_dict(cond1_norm, cond2_norm): + + # ## create amino acid dictionnary: + AA = OrderedDict({}) + AA['Phe'] = [cond1_norm['TTT'] + cond1_norm['TTC'], cond2_norm['TTT'] + cond2_norm['TTC']] + AA['Leu'] = [cond1_norm['TTA'] + cond1_norm['TTG'] + cond1_norm['CTT'] + cond1_norm['CTC'] + cond1_norm['CTA'] + cond1_norm['CTG'], cond2_norm['TTA'] + cond2_norm['TTG'] + cond2_norm['CTT'] + cond2_norm['CTC'] + cond2_norm['CTA'] + cond2_norm['CTG']] + AA['Ile'] = [cond1_norm['ATT'] + cond1_norm['ATC'] + cond1_norm['ATA'], cond2_norm['ATT'] + cond2_norm['ATC'] + cond2_norm['ATA']] + AA['Met'] = [cond1_norm['ATG'], cond2_norm['ATG']] + AA['Val'] = [cond1_norm['GTT'] + cond1_norm['GTC'] + cond1_norm['GTA'] + cond1_norm['GTG'] + cond1_norm['AGT'] + cond1_norm['AGC'], cond2_norm['GTT'] + cond2_norm['GTC'] + cond2_norm['GTA'] + cond2_norm['GTG'] + cond2_norm['AGT'] + cond2_norm['AGC']] + AA['Ser'] = [cond1_norm['TCT'] + cond1_norm['TCC'] + cond1_norm['TCA'] + cond1_norm['TCG'], cond2_norm['TCT'] + cond2_norm['TCC'] + cond2_norm['TCA'] + cond2_norm['TCG']] + AA['Pro'] = [cond1_norm['CCT'] + cond1_norm['CCC'] + cond1_norm['CCA'] + cond1_norm['CCG'], cond2_norm['CCT'] + cond2_norm['CCC'] + cond2_norm['CCA'] + cond2_norm['CCG']] + AA['Thr'] = [cond1_norm['ACT'] + cond1_norm['ACC'] + cond1_norm['ACA'] + cond1_norm['ACG'], cond2_norm['ACT'] + cond2_norm['ACC'] + cond2_norm['ACA'] + cond2_norm['ACG']] + AA['Ala'] = [cond1_norm['GCT'] + cond1_norm['GCC'] + cond1_norm['GCA'] + cond1_norm['GCG'], cond2_norm['GCT'] + cond2_norm['GCC'] + cond2_norm['GCA'] + cond2_norm['GCG']] + AA['Tyr'] = [cond1_norm['TAT'] + cond1_norm['TAC'], cond2_norm['TAT'] + cond2_norm['TAC']] + AA['Stop'] = [cond1_norm['TAA'] + cond1_norm['TAG'] + cond1_norm['TGA'], cond2_norm['TAA'] + cond2_norm['TAG'] + cond2_norm['TGA']] + AA['His'] = [cond1_norm['CAT'] + cond1_norm['CAC'], cond2_norm['CAT'] + cond2_norm['CAC']] + AA['Gln'] = [cond1_norm['CAA'] + cond1_norm['CAG'], cond2_norm['CAA'] + cond2_norm['CAG']] + AA['Asn'] = [cond1_norm['AAT'] + cond1_norm['AAC'], cond2_norm['AAT'] + cond2_norm['AAC']] + AA['Lys'] = [cond1_norm['AAA'] + cond1_norm['AAG'], cond2_norm['AAA'] + cond2_norm['AAG']] + AA['Asp'] = [cond1_norm['GAT'] + cond1_norm['GAC'], cond2_norm['GAT'] + cond2_norm['GAC']] + AA['Glu'] = [cond1_norm['GAA'] + cond1_norm['GAG'], cond2_norm['GAA'] + cond2_norm['GAG']] + AA['Cys'] = [cond1_norm['TGT'] + cond1_norm['TGC'], cond2_norm['TGT'] + cond2_norm['TGC']] + AA['Trp'] = [cond1_norm['TGG'], cond2_norm['TGG']] + AA['Arg'] = [cond1_norm['CGT'] + cond1_norm['CGC'] + cond1_norm['CGA'] + cond1_norm['CGG'] + cond1_norm['AGA'] + cond1_norm['AGG'], cond2_norm['CGT'] + cond2_norm['CGC'] + cond2_norm['CGA'] + cond2_norm['CGG'] + cond2_norm['AGA'] + cond2_norm['AGG']] + AA['Gly'] = [cond1_norm['GGT'] + cond1_norm['GGC'] + cond1_norm['GGA'] + cond1_norm['GGG'], cond2_norm['GGT'] + cond2_norm['GGC'] + cond2_norm['GGA'] + cond2_norm['GGG']] + + + return AA + + + +def plot_codon_usage(result, dirout, c1, c2, outfile, color1, color2): + ''' + Take list of dict of codon usage and use matplotlib for do graph + ''' + + # #if there are replicat + if len(result) == 4 : + # store each dict in variables to make code more readable + cond1_1 = result[0].copy() + cond1_2 = result[1].copy() + cond2_1 = result[2].copy() + cond2_2 = result[3].copy() + # get codon order in one of list + codon_sorted = sorted(cond1_1.iterkeys(), reverse=False) + try: + # get max of each list + sum11 = sum(list(cond1_1.itervalues())) + sum12 = sum(list(cond1_2.itervalues())) + sum21 = sum(list(cond2_1.itervalues())) + sum22 = sum(list(cond2_2.itervalues())) + # for each codon, get values and sd in each condition + cond1_val = {} + cond1 = {} + cond2_val = {} + cond2 = {} + std_cond1 = [] + std_cond2 = [] + max_val = [] # # max value for graph + for i in codon_sorted: + # # cond1 = mean of replicats cond1 divided by max + cond1_val[i] = ((cond1_1[i] / sum11 + cond1_2[i] / sum12) / 2) + cond1[i] = ((cond1_1[i] + cond1_2[i]) / 2) + # # standard deviation = absolute value of difference between replicats of cond1 + std_cond1.append(std(array([(cond1_1[i] * 100 / sum11), (cond1_2[i] * 100 / sum12)]))) + # # cond2 = mean of replicats cond1divided by max + cond2_val[i] = ((cond2_1[i] / sum21 + cond2_2[i] / sum22) / 2) + cond2[i] = ((cond2_1[i] + cond2_2[i]) / 2) + # # standard deviation = absolute value of difference between replicats of cond2 + std_cond2.append(std(array([((cond2_1[i]) * 100 / sum21), ((cond2_2[i]) * 100 / sum22)]))) + # # max value for each codon + max_val.append(max((cond1_1[i] / sum11 + cond1_2[i] / sum12) / 2, (cond2_1[i] / sum21 + cond2_2[i] / sum22) / 2)) + + # for graph design + cond1_norm = OrderedDict(sorted(cond1_val.items(), key=lambda t: t[0])) + cond1_norm.update ((x, y * 100) for x, y in cond1_norm.items()) + cond2_norm = OrderedDict(sorted(cond2_val.items(), key=lambda t: t[0])) + cond2_norm.update ((x, y * 100) for x, y in cond2_norm.items()) + max_val = [x * 100 for x in max_val] + except ZeroDivisionError: + stop_err("Not enough reads to compute the codon occupancy") + + AA = get_aa_dict(cond1_norm, cond2_norm) + max_valaa = [] + cond1_aa = [] + cond2_aa = [] + aa_name = list(AA.iterkeys()) + for z in AA.itervalues(): + cond1_aa.append(z[0]) + cond2_aa.append(z[1]) + max_valaa.append(max(z)) + # # plot amino acid profile : + fig = pl.figure(figsize=(15,10), num=1) + width = .50 + ax = fig.add_subplot(111) + ax.xaxis.set_ticks([]) + ind = arange(21) + pl.xlim(0, 21) + ax.bar(ind, cond1_aa, width, facecolor=color1, label=c1) + ax.bar(ind + width, cond2_aa, width, facecolor=color2, label=c2) + for x, y, z in zip(ind, max_valaa, aa_name): + ax.text(x + width, y + 0.2, '%s' % z, ha='center', va='bottom', fontsize=14) + ax.set_ylabel('Ribosome Occupancy (percent of normalized reads)') + ax.set_xlabel('Amino Acid') + handles, labels = ax.get_legend_handles_labels() + ax.legend(handles, labels) + pl.savefig(dirout + '/hist_amino_acid.png', format="png", dpi=340) + pl.clf() + + + # # compute theorical count in COND2 + sum2 = (sum21 + sum22) / 2 + cond2_count = [] + for z in cond1_norm.itervalues() : + count = int(z * sum2 / 100) + cond2_count.append(count) + + expected = array(cond2_count) + observed = array(list(cond2.itervalues())) + + # write result + with open(outfile, 'w') as out : + out.write('Codon,Raw_' + c1 + ',Raw_' + c2 + ',Norm_' + c1 + ',Norm_' + c2 + ',FC(Mut/WT)\n') + for i in codon_sorted: + ## if global foldchange is equal to zero + if cond1_norm[i] == 0 and cond2_norm[i] == 0: + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',1.0\n') + elif cond1_norm[i] == 0 : + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',0.0\n') + else: + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',' + str(cond2_norm[i] / cond1_norm[i]) + '\n') + with errstate(all='ignore'): + chi = stats.chisquare(observed, expected) + out.write('Khi2 test\n') + out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') + + + + # plot result + fig = pl.figure(figsize=(20,10), num=1) + width = .40 + ind = arange(len(codon_sorted)) + ax = fig.add_subplot(111) + pl.xlim(0, len(codon_sorted) + 1) + ax.spines['right'].set_color('none') + ax.spines['top'].set_color('none') + ax.xaxis.set_ticks([]) + ax.spines['left'].set_smart_bounds(True) + ax.yaxis.set_ticks_position('left') + ax.bar(ind, list(cond1_norm.itervalues()), width, facecolor=color1, yerr=std_cond1, error_kw={'elinewidth':1, 'ecolor':'black'}, label=c1) + ax.bar(ind + width, list(cond2_norm.itervalues()), width, yerr=std_cond2, facecolor=color2, error_kw={'elinewidth':1, 'ecolor':'black'}, label=c2) + for x, y, z in zip(ind, max_val, codon_sorted): + ax.text(x + width, y + 0.2, '%s' % z, ha='center', va='bottom', fontsize=8) + ax.set_ylabel('Ribosome Occupancy (percent of normalized reads)') + ax.set_xlabel('Codons') + handles, labels = ax.get_legend_handles_labels() + ax.legend(handles, labels) + pl.savefig(dirout + '/hist_codons.png', format="png", dpi=340) + pl.clf() + + + elif len(result) == 2 : + + # store each dict in OrderedDict sorted by key to make code more readable + cond1 = result[0] + cond2 = result[1] + cond1_norm = result[0].copy() + cond2_norm = result[1].copy() + # pdb.set_trace() + # get codon order in one of list + codon_sorted = sorted(cond1.iterkeys(), reverse=False) + try: + # get sum of each list + sum1 = sum(list(cond1.itervalues())) + sum2 = sum(list(cond2.itervalues())) + # #Normalize values by sum of each libraries + cond1_norm.update ((x, (y / sum1) * 100.0) for x, y in cond1_norm.items()) + cond2_norm.update((x, (y / sum2) * 100.0) for x, y in cond2_norm.items()) + except ZeroDivisionError: + stop_err("Not enough reads to compute the codon occupancy. "+str(sum1)+" and "+str(sum2)+" reads are used for each condition, respectively.\n") + + # # compute theorical count in COND2 + cond2_count = [] + for z in cond1_norm.itervalues() : + count = int(z * sum2 / 100.0) + cond2_count.append(count) + + expected = array(cond2_count) + observed = array(list(cond2.itervalues())) + + AA = get_aa_dict(cond1_norm, cond2_norm) + + max_val = [] + cond1_aa = [] + cond2_aa = [] + aa_name = list(AA.iterkeys()) + for z in AA.itervalues(): + cond1_aa.append(z[0]) + cond2_aa.append(z[1]) + max_val.append(max(z)) + + # # plot amino acid profile : + fig = pl.figure(figsize=(15,10), num=1) + width = .45 + ax = fig.add_subplot(111) + ind = arange(21) + pl.xlim(0, 21) + #kwargs = {"hatch":'x'} + #ax.bar(ind, cond1_aa, width, facecolor=color1, label=c1, **kwargs) + #kwargs = {"hatch":'.'} + #ax.bar(ind + width, cond2_aa, width, facecolor=color2, label=c2, **kwargs) + ax.bar(ind, cond1_aa, width, facecolor=color1, label=c1) + ax.bar(ind + width, cond2_aa, width, facecolor=color2, label=c2) + #for x, y, z in zip(ind, max_val, aa_name): + # ax.text(x + width, y + 0.2, '%s' % z, ha='center', va='bottom', fontsize=14) + axis_font = {'size':'10'} + pl.xticks(ind + width, aa_name,**axis_font) + ax.spines['right'].set_visible(False) + ax.spines['top'].set_visible(False) + ax.yaxis.set_ticks_position('left') + ax.xaxis.set_ticks_position('bottom') + #ax.xaxis.set_ticks([]) + ax.set_ylabel('Ribosome Occupancy (percent of normalized reads)',**axis_font) + ax.set_xlabel('Amino Acids', **axis_font) + handles, labels = ax.get_legend_handles_labels() + font_prop = font_manager.FontProperties(size=8) + ax.legend(handles, labels, prop=font_prop) + pl.savefig(dirout + '/hist_amino_acid.png', format="png", dpi=340) + pl.clf() + + # write result + with open(outfile, 'w') as out : + out.write('Codon,Raw_' + c1 + ',Raw_' + c2 + ',Norm_' + c1 + ',Norm_' + c2 + ',FC(Mut/WT)\n') + for i in codon_sorted: + if cond1_norm[i] == 0 and cond2_norm[i] == 0: + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',1.0\n') + elif cond1_norm[i] == 0 : + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',0.0\n') + else: + out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',' + str(cond2_norm[i] / cond1_norm[i]) + '\n') + out.write('Khi2 test\n') + with errstate(all='ignore'): + chi = stats.chisquare(observed, expected) + out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') + + # # get max value for each codon for histogram + max_val = [] # # max value for graph + for i in cond1: + # # max value for each codon + max_val.append(max(cond1_norm[i], cond2_norm[i])) + + # plot result + fig = pl.figure(figsize=(20,10), num=1) + #fig = pl.figure(num=1) + width = .40 + ind = arange(len(codon_sorted)) + ax = fig.add_subplot(111) + pl.xlim(0, len(codon_sorted) + 1) + ax.spines['right'].set_color('none') + ax.spines['top'].set_color('none') + ax.xaxis.set_ticks([]) + ax.spines['left'].set_smart_bounds(True) + ax.yaxis.set_ticks_position('left') + ax.bar(ind, list(cond1_norm.itervalues()), width, facecolor=color1, label=c1) + ax.bar(ind + width, list(cond2_norm.itervalues()), width, facecolor=color2, label=c2) + for x, y, z in zip(ind, max_val, codon_sorted): + ax.text(x + width, y + 0.2, '%s' % z, ha='center', va='bottom', fontsize=8) + ax.set_ylabel('Ribosome Occupancy (percent of normalized reads)') + ax.set_xlabel('Codons') + handles, labels = ax.get_legend_handles_labels() + ax.legend(handles, labels) + pl.savefig(dirout + '/hist_codons.png', format="png", dpi=340) + pl.clf() + + + else : + stop_err('Error running codon usage plotting : ' + str(e)) + + + return (cond1_norm, cond2_norm, chi[1]) + +def write_html_file(html, chi_pval, cond1, cond2): + try : + + + html_str = """ + + + + + + + + +

Global visualization

+

+

Visualization of density footprint in each codon.

If user has selected "Yes" for the replicate option the standard deviation between each replicate is plotted as an error bar in histogram.
+ +

+

+

Test for homogeneity distribution between each condition

+ H0 : %s and %s are same distribution
+ Khi2 test p-value: %s

+ If p-value less than 0.05, we can reject homogeneity distribution so we can hypothesize that distributions are not the same. Otherwise, we accept H0
+ +

+

+

Visualization of density footprint in each codon groupe by amino acid

+ +

+ + """ % (cond1,cond2,chi_pval) + + + html_file = open(html, "w") + html_file.write(html_str) + html_file.close() + + except Exception, e : + stop_err('Error during html page creation : ' + str(e)) + + + + +def check_codons_list (codons) : + + for codon in codons : + if codon not in init_codon_dict().iterkeys() : + stop_err('Please to enter a valid codon : ' + codon + ' is not find\n') + + +def check_index_bam (bamfile) : + # #testing indexed bam file + if os.path.isfile(bamfile + ".bai") : + pass + else : + cmd = "samtools index %s " % (bamfile) + proc = subprocess.Popen(args=cmd, shell=True, stderr=subprocess.PIPE) + returncode = proc.wait() + # if returncode != 0: + # raise Exception + +def plot_fc (cond1, cond2, site, dirout): + + fc = cond1.copy() + + for key, value in fc.iteritems(): + if cond1[key] == 0: + fc[key] = 1 + else: + fc[key] = cond2[key]/cond1[key] + + index = arange(len(fc.keys())) + label = fc.keys() + label = [w.replace('T','U') for w in label] + pl.figure(figsize=(15,10), num=1) + ax = pl.subplot(1,1,1) + pl.xticks([]) + pl.scatter(index, fc.values(), color='b') + pl.axhline(y=1,color='r') + pl.xticks(index, label, rotation=90) + pl.ylabel('Foldchange of codon occupancy') + ax.yaxis.set_ticks_position('left') + ax.xaxis.set_ticks_position('bottom') + pl.ylim(-1,3) + pl.title(site+" site") + pl.savefig(dirout + '/fc_codons.png', format="png", dpi=340) + + +def __main__(): + + + # Parse command line options + parser = optparse.OptionParser() + parser.add_option("-g", "--gff", dest="gff", type="string", + help="gff file", metavar="FILE") + + parser.add_option("-1", "--file1", dest="file1", type="string", + help="Bam Ribo-Seq alignments cond 1, if rep option, separate files by commas ", metavar="FILE") + + parser.add_option("-2", "--file2", dest="file2", type="string", + help="Bam Ribo-Seq alignments cond 2, if rep option, separate files by commas", metavar="FILE") + + parser.add_option("-c", "--cond1", dest="c1", type="string", + help="Name for first condition", metavar="STR") + + parser.add_option("-C", "--cond2", dest="c2", type="string", + help="Name of second condition", metavar="STR") + + parser.add_option("-k", "--kmer", dest="kmer", type="int", default = 28 , + help="Length of your phasing reads", metavar="INT") + +# parser.add_option("-l", "--list", dest="list_cod", type= "string", +# help="list of codons to compare to other", metavar="STR") + + parser.add_option("-o", "--out", dest="outfile", type="string", + help="write report to FILE", metavar="FILE") + + parser.add_option("-d", "--dirout", dest="dirout", type="string", + help="write report to PNG files", metavar="FILE") + + parser.add_option("-a", "--asite", dest="asite", type="int", default = 15 , + help="Off-set from the 5'end of the footprint to the A-site (default is 15)", metavar="INT") + + parser.add_option("-s", "--site", dest="site", type="string", default = "A" , + help="Script can compute in site A, P or E (default is A-site)", metavar="A|P|E") + + parser.add_option("-r", "--rep", dest="rep", type="string", default = "no" , + help="if replicate or not", metavar="yes|no") + + parser.add_option("-x", "--hex_col1", dest="color1", type= "string", default = "SkyBlue" , + help="Color for first condition", metavar="STR") + + parser.add_option("-X", "--hex_col2", dest="color2", type= "string", default = "Plum" , + help="Color for second condition", metavar="STR") + + parser.add_option("-q", "--quiet", + action="store_false", dest="verbose", default=True, + help="don't print status messages to stdout") + + (options, args) = parser.parse_args() + print "Begin codon frequency analysis at", time.asctime(time.localtime(time.time())) + + try: + authorized_site = ["A", "P", "E"] + if options.site not in authorized_site : + stop_err(options.site + ' is not a authorized ribosome site') + + ## Check if colors exist + if not colors.is_color_like(options.color1) : + stop_err( options.color1+' is not a proper color' ) + if not colors.is_color_like(options.color2) : + stop_err( options.color2+' is not a proper color' ) + + + #### NOT USE IN FINAL VERSION + # # get codon list + # codons = options.list_cod.upper().split(',') + # check_codons_list(codons) + GFF = HTSeq.GFF_Reader(options.gff) + # # get html file and directory : + (html, html_dir) = options.dirout.split(',') + if not os.path.exists(html_dir): + try: + os.mkdir(html_dir) + except Exception, e : + stop_err('Error running make directory : ' + str(e)) + # #RUN analysis + # #If there are replicats + if options.rep == "yes" : + result = [] + # split name of each file options by "," + cond1 = options.file1.split(',') + cond2 = options.file2.split(',') + # # calcul for each file + for fh in itertools.chain(cond1, cond2): + check_index_bam (fh) + result.append(get_codon_usage(fh, GFF, options.site, options.kmer, options.asite)) + (cond1, cond2, chi_pval) = plot_codon_usage(result, html_dir, options.c1, options.c2, options.outfile,options.color1, options.color2) + # t_pval = compute_FC_plot(cond1,cond2,codons,html_dir) + plot_fc (cond1, cond2, options.site, html_dir) + + # #If there are no replicat + elif options.rep == "no" : + result = [] + # #calcul for each cond + for fh in (options.file1, options.file2): + check_index_bam (fh) + result.append(get_codon_usage(fh, GFF, options.site, options.kmer,options.asite)) + (cond1, cond2, chi_pval) = plot_codon_usage(result, html_dir, options.c1, options.c2, options.outfile,options.color1, options.color2) + + # t_pval = compute_FC_plot(cond1,cond2,codons,html_dir) + plot_fc (cond1, cond2, options.site, html_dir) + else : + sys.stderr.write("Please enter yes or no for --rep option. Programme aborted at %s" % time.asctime(time.localtime(time.time()))) + sys.exit() + + # write_html_file(html,chi_pval,t_pval,codons,options.c1, options.c2) + write_html_file(html, chi_pval, options.c1, options.c2) + + print "Finish codon frequency analysis at", time.asctime(time.localtime(time.time())) + except Exception, e: + stop_err('Error running codon frequency analysis (main program) : ' + str(e)) + + +if __name__=="__main__": + __main__() diff -r 000000000000 -r 01b945ba3697 ribo_tools/get_codon_frequency.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/get_codon_frequency.xml Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,101 @@ + + To compare Ribo-seq alignments between two sets of conditions, to determine codon occupancy + + samtools + matplotlib + numpy + scipy + Bio + + + get_codon_frequency.py + --gff=$annot + --rep=$replicat_opt['rep'] + --cond1 $cond1 + --cond2 $cond2 + --kmer=$kmer + --asite=$asite + --out $out + --site $site + --hex_col1 $color1 + --hex_col2 $color2 + --dirout $html_file,$html_file.files_path + #if str( $replicat_opt['rep'] ) == 'yes': + --file1=$file1,$file11 + --file2=$file2,$file22 + #else + --file1=$file1 + --file2=$file2 + #end if + + + + + + + + + + + + + ## Use conditional balise : if rep =yes : 4 files, else 2 files + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Summary +------- +This tool uses Ribo-seq (BAM file) to determine whether codon occupancy differs between two sets of conditions. For each footprint, the codons at the chosen site are recorded and a histogram displaying all the normalised codon numbers is plotted for both sets of conditions. A second histogram groups together all the codons corresponding to a given amino acid. A chi-squared test is then carried out to determine whether the distribution of the codons used is the same in both sets of conditions. + + +Output +------- +This tool provides an html file containing graphs and a statistical test result. An additional csv file with codon numbers is provided. + + +Dependances +------------ + +.. class:: warningmark + +This tool depends on Python (>=2.7) and following packages : numpy 1.8.0, Biopython 1.58, scipy 0.12.0 and matplotlib 1.3.1. Samtools is used for bam manipulation. + + + + + + + + + + + diff -r 000000000000 -r 01b945ba3697 ribo_tools/kmer_analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/kmer_analysis.py Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,464 @@ +#!/usr/bin/env python2.7.3 +#-*- coding: utf-8 -*- +''' + Created on Jun. 2014 + @author: rachel legendre + @copyright: rachel.legendre@igmors.u-psud.fr + @license: GPL v3 +''' + +import os, sys, time, optparse, re, urllib, subprocess, tempfile, commands +import pysam +#from matplotlib import pyplot as pl +import matplotlib +matplotlib.use('Agg') +import matplotlib.pyplot as pl +from numpy import arange +from collections import OrderedDict +import ribo_functions +#import cPickle +## suppress matplotlib warnings +import warnings +warnings.filterwarnings('ignore') + + +total_mapped_read = 0 + + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.stderr.write( "Programme aborted at %s\n" % time.asctime( time.localtime( time.time() ) ) ) + sys.exit() + + +def split_bam(bamfile,tmpdir): + ''' + split bam by chromosome and write sam file in tmpdir + ''' + try: + #get header + results = subprocess.check_output(['samtools', 'view', '-H',bamfile]) + header = results.split('\n') + + #define genome size + genome = [] + for line in header: + result = re.search('SN', line) + if result : + #print line + feat = line.split('\t') + chrom = re.split(":", feat[1]) + #print feat[1] + genome.append(chrom[1]) + + #split sam by chrom + n = 0 + for chrm in genome: + with open(tmpdir+'/'+chrm+'.sam', 'w') as f : + #write header correctly for each chromosome + f.write(header[0]+'\n') + expr = re.compile(chrm+'\t') + el =[elem for elem in header if expr.search(elem)][0] + f.write(el+'\n') + f.write(header[-2]+'\n') + #write all reads for each chromosome + reads = subprocess.check_output(["samtools", "view", bamfile, chrm]) + f.write(reads) + # calculate number of reads + n += reads.count(chrm) + + sys.stdout.write("%d reads are presents in your bam file\n" % n) + + except Exception, e: + stop_err( 'Error during bam file splitting : ' + str( e ) ) + + + +def get_first_base(tmpdir, kmer): + ''' + write footprint coverage file for each sam file in tmpdir and get kmer distribution + ''' + global total_mapped_read + + ## tags by default + multi_tag = "XS:i:" + tag = "IH:i:1" + + ## init kmer dict + KMER = OrderedDict({}) + + try: + file_array = (commands.getoutput('ls '+tmpdir)).split('\n') + ##write coverage for each sam file in tmpdir + for samfile in file_array: + with open(tmpdir+'/'+samfile, 'r') as sam : + ##get chromosome name + chrom = samfile.split(".sam")[0] + + for line in sam: + #initialize dictionnary + if '@SQ\tSN:' in line : + size = int(line.split('LN:')[1]) + genomeF = [0]*size + genomeR = [0]*size + # define multiple reads keys from mapper + elif '@PG\tID' in line : + if 'bowtie' in line: + multi_tag = "XS:i:" + elif 'bwa' in line: + multi_tag = "XT:A:R" + elif 'TopHat' in line: + tag = "NH:i:1" + else : + stop_err("No PG tag find in "+samfile+". Please use bowtie, bwa or Tophat for mapping") + + # get footprint + elif re.search('^[^@].+', line) : + len_read = len(line.split('\t')[9]) + ##full kmer dict + if KMER.has_key(len_read): + KMER[len_read] += 1 + else : + KMER[len_read] = 1 + + #print line.rstrip() + read_pos = int(line.split('\t')[3]) + read_sens = int(line.split('\t')[1]) + #len_read = len(line.split('\t')[9]) + if len_read == kmer and (tag in line or multi_tag not in line): + ###if line.split('\t')[5] == '28M' : + total_mapped_read +=1 + #if it's a forward read + if read_sens == 0 : + #get 5' base + genomeF[read_pos] += 1 + #if it's a reverse read + elif read_sens == 16 : + #get 5' base + read_pos += (len_read-1) + genomeR[read_pos] += 1 + + #try: + #write coverage in files + with open(tmpdir+'/assoCov_'+chrom+'.txt', 'w') as cov : + for i in range(0,size): + cov.write(str(genomeF[i])+'\t-'+str(genomeR[i])+'\n') + #except Exception,e: + # stop_err( 'Error during coverage file writting : ' + str( e ) ) + + #sys.stdout.write("%d reads are in your bam file\n" % total_mapped_read) + + return KMER + + except Exception, e: + stop_err( 'Error during footprinting : ' + str( e ) ) + + +def __percent__(prop): + + if sum(prop) != 0 : + perc = [0,0,0] + if prop[0] != 0 : + perc[0] = int("{0:.0f}".format((prop[0]*100.0)/sum(prop))) + if prop[1] != 0 : + perc[1] = int("{0:.0f}".format((prop[1]*100.0)/sum(prop))) + if prop[2] != 0 : + perc[2] = int("{0:.0f}".format((prop[2]*100.0)/sum(prop))) + return perc + else : + return prop + + +def frame_analysis(tmpdir,GFF): + ''' + This function take footprint and annotation (gff) for analyse reading frame in each gene + ''' + global total_mapped_read + try: + chrom = "" # initializing chromosome + nb_gene = 0 # number of analysed genes + whole_phasing = [0,0,0] + for gene in GFF['order']: + ## maybe no start position in GTF file so we must to check and replace + exon_number = GFF[gene]['exon_number'] + try : GFF[gene]['start'] + except : + if GFF[gene]['strand'] == '+' : + GFF[gene]['start'] = GFF[gene]['exon'][1]['start'] + else : + GFF[gene]['start'] = GFF[gene]['exon'][exon_number]['stop'] + ## also for stop coordinates + try : GFF[gene]['stop'] + except : + if GFF[gene]['strand'] == '+' : + GFF[gene]['stop'] = GFF[gene]['exon'][exon_number]['stop'] + + else : + GFF[gene]['stop'] = GFF[gene]['exon'][1]['start'] + cov = [] + ##first chromosome : we open corresponding file + try: + if chrom == "" : + chrom = GFF[gene]['chrom'] + with open(tmpdir+"/assoCov_"+chrom+".txt") as f : + data = f.readlines() + ##if we change chromosome + elif chrom != GFF[gene]['chrom'] : + chrom = GFF[gene]['chrom'] + with open(tmpdir+"/assoCov_"+chrom+".txt") as f : + data = f.readlines() + except IOError : + print tmpdir+"/assoCov_"+chrom+".txt doesn't exist" + + try: + ## if a gene without intron : + if GFF[gene]['exon_number'] == 1: + + ## get coverage for each gene + if GFF[gene]['strand'] == "+": + for i in range(GFF[gene]['exon'][1]['start'],GFF[gene]['exon'][1]['stop']+1): + cov.append(int((data[i].rstrip()).split("\t")[0])) + else : + for i in range(GFF[gene]['exon'][1]['start'],GFF[gene]['exon'][1]['stop']+1): + cov.append(int(((data[i].rstrip()).split("\t")[1]).replace("-",""))) + cov.reverse() + else : + ## For each gene, get coverage and sum of exon size + if GFF[gene]['strand'] == "+": + + for exon in range(1,GFF[gene]['exon_number']+1) : + for i in range(GFF[gene]['exon'][exon]['start'],GFF[gene]['exon'][exon]['stop']+1): + #if i <= GFF[gene]['stop'] : + cov.append(int((data[i].rstrip()).split("\t")[0])) + else : + + for exon in range(1,GFF[gene]['exon_number']+1) : + for i in range(GFF[gene]['exon'][exon]['start'],GFF[gene]['exon'][exon]['stop']+1): + #if i <= GFF[gene]['start'] : + cov.append(int(((data[i].rstrip()).split("\t")[1]).replace("-",""))) + cov.reverse() + except : + #print gene+" could not be analysed." + #del GFF[gene] + continue + len_cov = len(cov) + prop = [0,0,0] + for nuc in range(0,len_cov-2,3) : + ## Calculate proportion + prop[0] += cov[nuc] + prop[1] += cov[nuc+1] + prop[2] += cov[nuc+2] + whole_phasing = (map(lambda (x, y): x + y, zip(whole_phasing, prop))) + + whole_phasing = __percent__(whole_phasing) + #sys.stdout.write("Proportion of reads in each frame :\n%s\n" % whole_phasing) + return whole_phasing + + except Exception, e: + stop_err( 'Error during frame analysis : ' + str( e ) ) + + + +def make_report(html_file, dirout, kmer, results) : + + array = sorted(kmer.items(), key=lambda x: x[0]) + values = [] + label = [] + for x,y in array : + values.append(y) + label.append(x) + index = arange(len(label)) + bar_width = 0.35 + axis_font = {'size':'10'} + fig, ax = pl.subplots() + pl.bar(index ,values, color='LightsteelBlue') + pl.xlabel('kmer value', **axis_font) + pl.ylabel('Number of reads', **axis_font) + pl.title('Number of reads for each k-mer') + pl.xticks(index + bar_width, label, **axis_font) + #pl.show() + fig.subplots_adjust() + pl.savefig(dirout+"/kmer_proportion.png", format='png', dpi=640) + pl.clf() + + for key, phase in results.iteritems() : + fig = pl.figure(num=1) + frame = phase + index = arange(3) + bar_width = 0.5 + pl.bar(index,frame,color=['RoyalBlue','LightSkyBlue','LightBlue']) + pl.xlabel('Frame in gene', **axis_font) + pl.ylabel('Percent of read', **axis_font) + pl.title('Proportion of reads in each frame for '+str(key)+'-mer') + pl.xticks(index+bar_width, ('1', '2', '3'), **axis_font) + #pl.tight_layout() + pl.ylim(0,100) + fig.subplots_adjust() + pl.draw() + pl.show() + pl.savefig(dirout+"/"+str(key)+"_phasing.png", format='png', dpi=300) + pl.clf() + + kmer_summary = '' + kmer_sorted = OrderedDict(sorted(kmer.iteritems(), key=lambda x: x[0])) + for key, number in kmer_sorted.iteritems() : + if number > 100 : + kmer_summary += '
  • ' + kmer_summary += 'Analysis of '+str(key)+'-mer :
    ' + kmer_summary += 'You have '+str(number)+' '+str(key)+'-mer :
    ' + kmer_summary += 'Phasing of '+str(key)+'-mer is : '+str(results[key])+'
    ' + kmer_summary += '
    ' + kmer_summary += '
    • ' + else : + kmer_summary += '
  • ' + kmer_summary += 'Analysis of '+str(key)+'-mer :
    ' + kmer_summary += 'You have '+str(number)+' '+str(key)+'-mer :
    ' + kmer_summary += '
    • ' + + html_str = """ + + + + + + + kmer analysis + + +

    k-mer analysis results

    +

    +

    +

    + + +""" + all = html_str % kmer_summary + + html = open(html_file,"w") + html.write(all) + html.close() + +def __main__(): + + #Parse command line options + parser = optparse.OptionParser() + parser.add_option("-g", "--gff", dest="gff", type= "string", + help="GFF annotation file", metavar="FILE") + + parser.add_option("-b", "--bam", dest="bamfile", type= "string", + help="Bam Ribo-Seq alignments ", metavar="FILE") + + parser.add_option("-o", "--out", dest="html_file", type= "string", + help="write report to FILE", metavar="FILE") + + parser.add_option("-d", "--dirout", dest="dirout", type= "string", + help="write report to PNG files", metavar="FILE") + + parser.add_option("-q", "--quiet", + action="store_false", dest="verbose", default=True, + help="don't print status messages to stdout") + + (options, args) = parser.parse_args() + sys.stdout.write("Begin kmer and phasing analysis at %s\n" % time.asctime( time.localtime( time.time() ) ) ) + + try: + + if not os.path.exists(options.dirout): + try: + os.mkdir(options.dirout) + except Exception, e : + stop_err('Error running make directory : ' + str(e)) + + ##testing indexed bam file + if os.path.isfile(options.bamfile+".bai") : + pass + else : + cmd = "samtools index %s " % (options.bamfile) + proc = subprocess.Popen( args=cmd, shell=True, stderr = subprocess.PIPE) + returncode = proc.wait() + + tmpdir = tempfile.mkdtemp() + ## identify GFF or GTF format from 9th column + with open (options.gff,"r") as gffile : + for line in gffile : + if '#' in line : + ## skip header + gffile.next() + elif 'gene_id' in line : + ## launch gtf reader : + GFF = ribo_functions.store_gtf(options.gff) + break + elif 'ID=' in line : + ## launch gff reader + GFF = ribo_functions.store_gff(options.gff) + break + else : + stop_err( 'Please check your annotation file is in correct format, GFF or GTF' ) + #GFF = store_gff(options.gff) + #GFF = ribo_functions.store_gtf(options.gff) + ## check gff reading + if not GFF['order'] : + stop_err( 'Incorrect GFF file' ) + for gene in GFF['order']: + if not GFF[gene]['exon'] : + del GFF[gene] + GFF['order'].remove(gene) + ## split bam + split_bam(options.bamfile,tmpdir) + ################################### + ## First analysis with 28mer : + ################################### + ## compute coverage and distribution kmer + kmer = get_first_base(tmpdir, 28) + ## compute phasing + whole_phasing = frame_analysis(tmpdir,GFF) + ## save phasing + results = {} + results[28] = whole_phasing + ## compute analysis with other kmer + for keys in kmer.iterkeys() : + if keys != 28 : + + ## If not enought reads in this kmer : + if kmer[keys] > 100 : + ## remove all txt files in tmp directory + if os.system("rm "+tmpdir+"/*.txt") != 0 : + stop_err( 'Error during tmp directory cleaning') + ## compute coverage and distribution kmer + tmp = get_first_base(tmpdir, keys) + ## compute phasing + whole_phasing = frame_analysis(tmpdir,GFF) + + results[keys] = whole_phasing + ## get report + make_report(options.html_file, options.dirout, kmer, results) + #======================================================================= + # ############ + # # tests + # ############ + # with open("kmer_dict",'rb') as km: + # kmer = cPickle.load(km) + # with open("results_dict",'rb') as res: + # results = cPickle.load(res) + # with open("kmer_dict",'wb') as km: + # cPickle.dump(kmer,km) + # with open("results_dict",'wb') as res: + # cPickle.dump(results,res) + # make_report(options.html_file, options.dirout, kmer, results) + #======================================================================= + + sys.stdout.write("Finish kmer and phasing analysis at %s\n" % time.asctime( time.localtime( time.time() ) ) ) + + except Exception, e: + stop_err( 'Error running kmer and phasing analysis : ' + str( e ) ) + + +if __name__=="__main__": + __main__() \ No newline at end of file diff -r 000000000000 -r 01b945ba3697 ribo_tools/kmer_analysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/kmer_analysis.xml Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,46 @@ + + To calculate the proportion and phasing of each kmer + + samtools + numpy + matplotlib + pysam + + + kmer_analysis.py --gff $gff --bam $bamfile --dirout $output.files_path --out $output + + + + + + + + + + + + + + + +Summary +------- +The kmer tool computes the distribution of footprints length from Bam file and determines the proportion of footprints beginning in each frame, for all annotated genes in the `GFF3`_ file. + + +.. _GFF3: http://gmod.org/wiki/GFF3 + +Output +------- +This tool provides an html report detailing the proportions and phasing of the kmers. + + +Dependances +------------ + +.. class:: warningmark + +This tool depends on Python (>=2.7) and following packages : numpy 1.8.0 and matplotlib 1.3.1. Samtools and pysam are used for bam manipulation. + + + \ No newline at end of file diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/README.markdown --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/lightbox/README.markdown Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,15 @@ +## Lightbox2 +by Lokesh Dhakar | [lokeshdhakar.com](http://www.lokeshdhakar.com) | [twitter.com/lokesh](http://twitter.com/lokesh) + +### Information and support +For examples, downloads, and information on using Lightbox, visit the Lightbox2 homepage: +[http://lokeshdhakar.com/projects/lightbox2/](http://lokeshdhakar.com/projects/lightbox2/) + +For personal support issues and feature requests, visit the Lightbox forums: +[http://lokeshdhakar.com/forums/](http://lokeshdhakar.com/forums/) + +### License +Licensed under the Creative Commons Attribution 2.5 License - http://creativecommons.org/licenses/by/2.5/ + +* Free for use in both personal and commercial projects. +* Attribution requires leaving author name, author homepage link, and the license info intact. diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/css/lightbox.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/lightbox/css/lightbox.css Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,202 @@ +/* line 7, ../sass/lightbox.sass */ +body:after { + content: url(../img/close.png) url(../img/loading.gif) url(../img/prev.png) url(../img/next.png); + display: none; +} + +/* line 11, ../sass/lightbox.sass */ +.lightboxOverlay { + position: absolute; + top: 0; + left: 0; + z-index: 9999; + background-color: black; + filter: progid:DXImageTransform.Microsoft.Alpha(Opacity=80); + opacity: 0.8; + display: none; +} + +/* line 20, ../sass/lightbox.sass */ +.lightbox { + position: absolute; + left: 0; + width: 100%; + z-index: 10000; + text-align: center; + line-height: 0; + font-weight: normal; +} +/* line 28, ../sass/lightbox.sass */ +.lightbox .lb-image { + display: block; + height: auto; + -webkit-border-radius: 3px; + -moz-border-radius: 3px; + -ms-border-radius: 3px; + -o-border-radius: 3px; + border-radius: 3px; +} +/* line 32, ../sass/lightbox.sass */ +.lightbox a img { + border: none; +} + +/* line 35, ../sass/lightbox.sass */ +.lb-outerContainer { + position: relative; + background-color: white; + *zoom: 1; + width: 250px; + height: 250px; + margin: 0 auto; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + -ms-border-radius: 4px; + -o-border-radius: 4px; + border-radius: 4px; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.lb-outerContainer:after { + content: ""; + display: table; + clear: both; +} + +/* line 44, ../sass/lightbox.sass */ +.lb-container { + padding: 4px; +} + +/* line 47, ../sass/lightbox.sass */ +.lb-loader { + position: absolute; + top: 43%; + left: 0%; + height: 25%; + width: 100%; + text-align: center; + line-height: 0; +} + +/* line 56, ../sass/lightbox.sass */ +.lb-cancel { + display: block; + width: 32px; + height: 32px; + margin: 0 auto; + background: url(../img/loading.gif) no-repeat; +} + +/* line 63, ../sass/lightbox.sass */ +.lb-nav { + position: absolute; + top: 0; + left: 0; + height: 100%; + width: 100%; + z-index: 10; +} + +/* line 71, ../sass/lightbox.sass */ +.lb-container > .nav { + left: 0; +} + +/* line 74, ../sass/lightbox.sass */ +.lb-nav a { + outline: none; +} + +/* line 77, ../sass/lightbox.sass */ +.lb-prev, .lb-next { + width: 49%; + height: 100%; + cursor: pointer; + /* Trick IE into showing hover */ + display: block; +} + +/* line 84, ../sass/lightbox.sass */ +.lb-prev { + left: 0; + float: left; +} +/* line 87, ../sass/lightbox.sass */ +.lb-prev:hover { + background: url(../img/prev.png) left 48% no-repeat; +} + +/* line 90, ../sass/lightbox.sass */ +.lb-next { + right: 0; + float: right; +} +/* line 93, ../sass/lightbox.sass */ +.lb-next:hover { + background: url(../img/next.png) right 48% no-repeat; +} + +/* line 96, ../sass/lightbox.sass */ +.lb-dataContainer { + margin: 0 auto; + padding-top: 5px; + *zoom: 1; + width: 100%; + -moz-border-radius-bottomleft: 4px; + -webkit-border-bottom-left-radius: 4px; + border-bottom-left-radius: 4px; + -moz-border-radius-bottomright: 4px; + -webkit-border-bottom-right-radius: 4px; + border-bottom-right-radius: 4px; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.lb-dataContainer:after { + content: ""; + display: table; + clear: both; +} + +/* line 103, ../sass/lightbox.sass */ +.lb-data { + padding: 0 4px; + color: #bbbbbb; +} +/* line 106, ../sass/lightbox.sass */ +.lb-data .lb-details { + width: 85%; + float: left; + text-align: left; + line-height: 1.1em; +} +/* line 111, ../sass/lightbox.sass */ +.lb-data .lb-caption { + font-size: 13px; + font-weight: bold; + line-height: 1em; +} +/* line 115, ../sass/lightbox.sass */ +.lb-data .lb-number { + display: block; + clear: left; + padding-bottom: 1em; + font-size: 12px; + color: #999999; +} +/* line 121, ../sass/lightbox.sass */ +.lb-data .lb-close { + display: block; + float: right; + width: 30px; + height: 30px; + background: url(../img/close.png) top right no-repeat; + text-align: right; + outline: none; + filter: progid:DXImageTransform.Microsoft.Alpha(Opacity=70); + opacity: 0.7; +} +/* line 130, ../sass/lightbox.sass */ +.lb-data .lb-close:hover { + cursor: pointer; + filter: progid:DXImageTransform.Microsoft.Alpha(Opacity=100); + opacity: 1; +} diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/css/screen.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/lightbox/css/screen.css Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,522 @@ +/* line 17, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +html, body, div, span, applet, object, iframe, +h1, h2, h3, h4, h5, h6, p, blockquote, pre, +a, abbr, acronym, address, big, cite, code, +del, dfn, em, img, ins, kbd, q, s, samp, +small, strike, strong, sub, sup, tt, var, +b, u, i, center, +dl, dt, dd, ol, ul, li, +fieldset, form, label, legend, +table, caption, tbody, tfoot, thead, tr, th, td, +article, aside, canvas, details, embed, +figure, figcaption, footer, header, hgroup, +menu, nav, output, ruby, section, summary, +time, mark, audio, video { + margin: 0; + padding: 0; + border: 0; + font: inherit; + font-size: 100%; + vertical-align: baseline; +} + +/* line 22, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +html { + line-height: 1; +} + +/* line 24, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +ol, ul { + list-style: none; +} + +/* line 26, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +table { + border-collapse: collapse; + border-spacing: 0; +} + +/* line 28, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +caption, th, td { + text-align: left; + font-weight: normal; + vertical-align: middle; +} + +/* line 30, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +q, blockquote { + quotes: none; +} +/* line 103, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +q:before, q:after, blockquote:before, blockquote:after { + content: ""; + content: none; +} + +/* line 32, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +a img { + border: none; +} + +/* line 116, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/reset/_utilities.scss */ +article, aside, details, figcaption, figure, footer, header, hgroup, menu, nav, section, summary { + display: block; +} + +/* Typography + *----------------------------------------------- */ +/* line 10, ../sass/screen.sass */ +body, +input, +textarea { + color: #cccccc; + font-size: 18px; + font-family: "Karla", "lucida grande", sans-serif; +} + +/* line 17, ../sass/screen.sass */ +h1, +h2, +h3, +h4, +h5, +h6 { + line-height: 1.2em; + color: #fdf485; +} + +/* line 26, ../sass/screen.sass */ +h1 { + font-size: 72px; + line-height: 1em; +} + +/* line 30, ../sass/screen.sass */ +h2 { + font-size: 48px; + line-height: 1.2em; + margin-bottom: 0.3em; +} + +/* line 35, ../sass/screen.sass */ +h3 { + font-size: 18px; + text-transform: uppercase; + letter-spacing: 0.1em; + color: #e5d404; + margin-bottom: 0.3em; +} + +/* line 42, ../sass/screen.sass */ +h4 { + font-size: 18px; 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+ font-size: 14px; +} +/* line 117, ../sass/screen.sass */ +.sub-point code { + font-size: 12px; + padding: 2px; +} + +/* -- Layout ------------------------------------------------------------------ */ +/* line 124, ../sass/screen.sass */ +body { + margin: 40px 40px 80px 40px; + background: #444444; +} + +/* line 128, ../sass/screen.sass */ +.wrapper { + max-width: 740px; + margin: 0 auto; +} + +/* line 132, ../sass/screen.sass */ +.section { + padding: 0 0 40px 0; + margin-bottom: 40px; + *zoom: 1; + border-bottom: 4px solid #373737; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.section:after { + content: ""; + display: table; + clear: both; +} +/* line 137, ../sass/screen.sass */ +.section.last { + border-bottom: none; +} + +/* line 140, ../sass/screen.sass */ +.section-header { + text-align: center; +} + +/* line 143, ../sass/screen.sass */ +.section-subheader { + margin-top: -0.6em; + margin-bottom: 1em; + text-align: center; + font-size: 24px; +} + +/* line 149, ../sass/screen.sass */ +.row { + *zoom: 1; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.row:after { + content: ""; + display: table; + clear: both; +} + +/* -- Sections ------------------------------------------------------------------ */ +/* -- Intro -- */ +/* line 156, ../sass/screen.sass */ +.intro-section { + text-align: center; +} + +/* line 159, ../sass/screen.sass */ +.logo { + color: white; + margin-bottom: 0.05em; +} +/* line 162, ../sass/screen.sass */ +.logo .version { + color: #fdf485; +} + +/* line 165, ../sass/screen.sass */ +.author { + margin-top: -9px; + padding-left: 23px; + line-height: 1.2em; +} + +/* line 170, ../sass/screen.sass */ +.author-links { + font-size: 16px; +} + +/* line 173, ../sass/screen.sass */ +.lead { + font-size: 22px; +} + +/* -- Examples -- */ +/* line 177, ../sass/screen.sass */ +.examples-section { + text-align: center; +} + +/* line 180, ../sass/screen.sass */ +.image-row { + *zoom: 1; + margin-bottom: 20px; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.image-row:after { + content: ""; + display: table; + clear: both; +} + +/* line 184, ../sass/screen.sass */ +.example-image-link { + display: inline-block; + margin: 0 10px 20px 10px; + line-height: 0; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + -ms-border-radius: 4px; + -o-border-radius: 4px; + border-radius: 4px; + border: 4px solid #5e5e5e; + -webkit-transition: all 0.1s ease-out; + -moz-transition: all 0.1s ease-out; + -o-transition: all 0.1s ease-out; + transition: all 0.1s ease-out; +} +/* line 191, ../sass/screen.sass */ +.example-image-link:hover { + border: 4px solid #00bfa8; +} + +/* line 194, ../sass/screen.sass */ +.example-image { + -webkit-border-radius: 2px; + -moz-border-radius: 2px; + -ms-border-radius: 2px; + -o-border-radius: 2px; + border-radius: 2px; +} + +/* -- Download -- */ +/* line 199, ../sass/screen.sass */ +.download-section { + text-align: center; +} + +/* line 202, ../sass/screen.sass */ +.download-button { + display: block; + max-width: 300px; + margin: 0 auto 20px auto; + padding-top: 20px; + padding-bottom: 10px; + background-color: #2b2b2b; + border: 4px solid #444444; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + -ms-border-radius: 4px; + -o-border-radius: 4px; + border-radius: 4px; + -webkit-transition: all 0.1s ease-out; + -moz-transition: all 0.1s ease-out; + -o-transition: all 0.1s ease-out; + transition: all 0.1s ease-out; + *zoom: 1; +} +/* line 38, ../../../../.rvm/gems/ruby-1.9.3-p392/gems/compass-0.12.2/frameworks/compass/stylesheets/compass/utilities/general/_clearfix.scss */ +.download-button:after { + content: ""; + display: table; + clear: both; +} +/* line 213, ../sass/screen.sass */ +.download-button:hover { + border-color: #00bfa8; + background-color: #444444; +} +/* line 216, ../sass/screen.sass */ +.download-button .file { + font-size: 36px; + color: white; + line-height: 1em; +} +/* line 220, ../sass/screen.sass */ +.download-button .version { + font-size: 24px; + color: #00bfa8; +} + +/* -- Sharing -- */ +/* line 226, ../sass/screen.sass */ +.sharing { + position: fixed; + top: 20px; + right: 0; +} + +/* -- Donate -- */ +/* line 233, ../sass/screen.sass */ +.donate-button-form { + text-align: center; +} + +/* line 235, ../sass/screen.sass */ +.donate-button { + border: 4px solid rgba(0, 0, 0, 0); + -webkit-border-radius: 4px; + -moz-border-radius: 4px; + -ms-border-radius: 4px; + -o-border-radius: 4px; + border-radius: 4px; + -webkit-transition: all 0.1s ease-out; + -moz-transition: all 0.1s ease-out; + -o-transition: all 0.1s ease-out; + transition: all 0.1s ease-out; +} +/* line 239, ../sass/screen.sass */ +.donate-button:hover { + background-color: #444444; + border-color: #00bfa8; +} + +/* -- Responsive design -------------------------------------------------------------- */ +@media only screen and (max-width: 640px) { + /* line 247, ../sass/screen.sass */ + body { + margin: 80px 10px 40px 10px; + font-size: 14px; + } + + /* line 250, ../sass/screen.sass */ + h1 { + font-size: 48px; + } + + /* line 252, ../sass/screen.sass */ + h2 { + font-size: 26px; + } + + /* line 254, ../sass/screen.sass */ + h3 { + font-size: 16px; + } + + /* line 256, ../sass/screen.sass */ + ol { + list-style-position: inside; + } + + /* line 258, ../sass/screen.sass */ + code, + kbd, + pre, + pre code { + font-size: 11px; + } + + /* line 263, ../sass/screen.sass */ + .sub-point { + font-size: 12px; + } + /* line 265, ../sass/screen.sass */ + .sub-point code { + font-size: 9px; + } + + /* line 267, ../sass/screen.sass */ + .lead { + font-size: 16px; + } + + /* line 269, ../sass/screen.sass */ + .section { + padding-bottom: 20px; + margin-bottom: 20px; + } + + /* line 272, ../sass/screen.sass */ + .author { + margin-top: -5px; + padding-left: 30px; + } + + /* line 275, ../sass/screen.sass */ + .author-links { + font-size: 12px; + } +} diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/close.png Binary file ribo_tools/lightbox/img/close.png has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/donate.png Binary file ribo_tools/lightbox/img/demopage/donate.png has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/favicon.ico Binary file ribo_tools/lightbox/img/demopage/favicon.ico has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-1.jpg Binary file ribo_tools/lightbox/img/demopage/image-1.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-2.jpg Binary file ribo_tools/lightbox/img/demopage/image-2.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-3.jpg Binary file ribo_tools/lightbox/img/demopage/image-3.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-4.jpg Binary file ribo_tools/lightbox/img/demopage/image-4.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-5.jpg Binary file ribo_tools/lightbox/img/demopage/image-5.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/image-6.jpg Binary file ribo_tools/lightbox/img/demopage/image-6.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-1.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-1.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-2.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-2.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-3.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-3.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-4.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-4.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-5.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-5.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/demopage/thumb-6.jpg Binary file ribo_tools/lightbox/img/demopage/thumb-6.jpg has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/loading.gif Binary file ribo_tools/lightbox/img/loading.gif has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/next.png Binary file ribo_tools/lightbox/img/next.png has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/img/prev.png Binary file ribo_tools/lightbox/img/prev.png has changed diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/index.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/lightbox/index.html Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,179 @@ + + + + + + Lightbox 2 + + + + + + + + + + + + + + +
    + +
    +
    +

    Lightbox2

    +
    +

    + by Lokesh Dhakar
    + + Follow me on Twitter + +

    +

    + Lightbox is small javascript library used to overlay images on top of the current page. It's a snap to setup and works on all modern browsers. +

    +
    + +
    +
    +

    Examples

    +
    + +

    Single images

    +
    + thumb-1 + thumb-1 +
    + +

    An image set

    + +
    +
    + Plants: image 1 0f 4 thumb + Plants: image 2 0f 4 thumb + Plants: image 3 0f 4 thumb + Plants: image 4 0f 4 thumb +
    +
    +
    + +
    +
    +

    Download

    +
    + + +
    + Lightbox +
    + v2.6 +
    +
    +     + +

    + Lightbox2 is open-source.
    View and fork the code on Github. +

    +
    + +
    +
    +

    How to use

    +

    Step-by-step instructions

    +
    +

    Part 1 - Get setup

    +
      +
    1. Download and unzip the latest version of Lightbox from above.
      2. +
    2. Look inside the js folder to find jquery-1.10.2.min.js and lightbox-2.6.min.js and load both of these files from your html page. Load jQuery first: +
      <script src="js/jquery-1.10.2.min.js"></script>
+<script src="js/lightbox-2.6.min.js"></script>
+
      3. +
    3. Look inside the css folder to find lightbox.css and load it from your html page: +
      <link href="css/lightbox.css" rel="stylesheet" />
+
      +
      4. +
    4. Look inside the img folder to find close.png, loading.gif, prev.png, and next.png. These files are used in lightbox.css. By default, lightbox.css will look for these images in a folder called img.
      5. +
    +

    Part 2 - Turn it on

    + +
    + + +
    +
    +

    Help

    +
    +

    Bugs

    +

    If you find a bug, create an issue on Github. Include your operating system and browser version along with detailed steps to reproduce the bug.

    + +

    Feature requests

    +

    If you want a feature added, please create an issue on Github. Someone else or I might be able to help out. No guarantees.

    + +

    Support questions

    +

    If you have a question that is not a bug or a feature request, your best chance of getting an answer is by following these steps:

    +
      +
    1. Search the Lightbox forums.
      You will not be able to post new questions in the forum as posting has been disabled. The forum is having spam problems and the forum will eventually be phased out.
      2. +
    2. Search Stackoverflow.
      3. +
    3. Create a new question on Stackoverflow.
      4. +
    +
    + + + +
    + + +
    + + + + + + + +
    + + + diff -r 000000000000 -r 01b945ba3697 ribo_tools/lightbox/js/jquery-1.10.2.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ribo_tools/lightbox/js/jquery-1.10.2.min.js Wed Sep 27 04:59:10 2017 -0400 @@ -0,0 +1,6 @@ +/*! jQuery v1.10.2 | (c) 2005, 2013 jQuery Foundation, Inc. | jquery.org/license +//@ sourceMappingURL=jquery-1.10.2.min.map +*/ +(function(e,t){var n,r,i=typeof t,o=e.location,a=e.document,s=a.documentElement,l=e.jQuery,u=e.$,c={},p=[],f="1.10.2",d=p.concat,h=p.push,g=p.slice,m=p.indexOf,y=c.toString,v=c.hasOwnProperty,b=f.trim,x=function(e,t){return new x.fn.init(e,t,r)},w=/[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/.source,T=/\S+/g,C=/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,N=/^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]*))$/,k=/^<(\w+)\s*\/?>(?:<\/\1>|)$/,E=/^[\],:{}\s]*$/,S=/(?:^|:|,)(?:\s*\[)+/g,A=/\\(?:["\\\/bfnrt]|u[\da-fA-F]{4})/g,j=/"[^"\\\r\n]*"|true|false|null|-?(?:\d+\.|)\d+(?:[eE][+-]?\d+|)/g,D=/^-ms-/,L=/-([\da-z])/gi,H=function(e,t){return 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