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html_lib.py
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import shutil
import os
modules = ["trimgalore", "fastqc", "kallisto", "star", "star-fusion", "picard", "picard_IS", "htseq-gene", "htseq-exon", "varscan", "gatk", 'jsplice']
module_names = {"trimgalore":"",
"fastqc":"",
"kallisto":"",
"star":"",
"star-fusion":"",
"picard":"",
"picard_IS":"",
"htseq-gene":"",
"htseq-exon":"",
"varscan":"",
"jsplice":"",
"gatk":""}
def get_menu(config, ns):
enabled = dict()
for module in modules:
if config.has_key(module):
if int(config[module][0].split("/")[0]) > 0:
enabled[module] = 1
menu = list()
menu.append('<h1><a #highlight="" href="./summary.html">Summary</a></h1>')
menu.append('<h1><a #highlight="" href="./hpc.html">HPC statistics</a></h1>')
if enabled.has_key("fastqc") or enabled.has_key("trimgalore"):
menu.append('<h1>Raw QC:</h1>')
if enabled.has_key("trimgalore"):
menu.append('<h2><a #highlight="" href="./trim.html">- TrimGalore/Cutadapt</a></h2>')
if enabled.has_key("fastqc"):
menu.append('<h2><a #highlight="" href="./fastqc.html">- FastQC</a></h2>')
if enabled.has_key("star") or enabled.has_key("picard") or enabled.has_key("htseq-gene") or enabled.has_key("htseq-exon"):
menu.append('<h1>Alignment QC:</h1>')
if enabled.has_key("picard"):
menu.append('<h2><a #highlight="" href="./picard.html">- Picard</a></h2>')
if enabled.has_key("picard_IS"):
menu.append('<h2><a #highlight="" href="./picard-is.html">- Picard Insert Size</a></h2>')
if enabled.has_key("star"):
menu.append('<h2><a #highlight="" href="./star.html">- STAR</a></h2>')
if enabled.has_key("kallisto"):
menu.append('<h2><a #highlight="" href="./kallisto.html">- KALLISTO</a></h2>')
if enabled.has_key("htseq-gene"):
menu.append('<h2><a #highlight="" href="./htseq-gene.html">- HTseq-Gene</a></h2>')
if enabled.has_key("htseq-exon"):
menu.append('<h2><a #highlight="" href="./htseq-exon.html">- HTseq-Exon</a></h2>')
if ns > 1:
if enabled.has_key("star") or enabled.has_key("htseq-gene") or enabled.has_key("htseq-exon") or enabled.has_key("kallisto"):
menu.append('<h1>Count statistics:</h1>')
menu.append('<h2><a #highlight="" href="./downloads.html">- DOWNLOADS</a></h2>')
if enabled.has_key("star"):
menu.append('<h2><a #highlight="" href="./star2.html">- STAR</a></h2>')
if enabled.has_key("kallisto"):
menu.append('<h2><a #highlight="" href="./kallisto2.html">- KALLISTO</a></h2>')
if enabled.has_key("htseq-gene"):
menu.append('<h2><a href="./htseq-gene2.html">- HTseq-Gene</a></h2>')
if enabled.has_key("htseq-exon"):
menu.append('<h2><a #highlight="" href="./htseq-exon2.html">- HTseq-Exon</a></h2>')
if enabled.has_key("gatk") or enabled.has_key("varscan"):
menu.append('<h1>Variant calling:</h1>')
if enabled.has_key("varscan"):
menu.append('<h2><a #highlight="" href="./varscan.html">- VARSCAN</a></h2>')
if enabled.has_key("gatk"):
menu.append('<h2><a #highlight="" href="./gatk.html">- GATK</a></h2>')
if enabled.has_key("star-fusion"):
menu.append('<h1>Gene fusions:</h1>')
menu.append('<h2><a #highlight="" href="./star-fusion.html">- Star-Fusion</a></h2>')
if enabled.has_key("jsplice"):
menu.append('<h1>Alternative splicing:</h1>')
menu.append('<h2><a #highlight="" href="./jsplice.html">- jSplice</a></h2>')
menu = "\n".join(menu)
return menu
def print_samples(path,config):
analysis = ['trimgalore', 'fastqc', 'kallisto', 'star', 'star-fusion', 'picard', "htseq-gene", "htseq-exon", "picard_IS", "varscan", 'gatk', 'jsplice']
sta= {"trimgalore":"TrimGalore", "fastqc":"FastQC","star":"STAR","star-fusion":"STAR-Fusion","picard":"PicardQC","kallisto":"Kallisto","htseq-gene":"HTseq-gene",
"htseq-exon":"HTseq-exon", "picard_IS":"Picard-InsertSize", "varscan":"VARSCAN", "gatk":"GATK", "jsplice":"jSplice"}
# SAMPLES LIST
samples = dict()
f = open(path + "/samples.list",'r')
hss = f.readline().strip("\n").split("\t")
idx = []
for i, ix in enumerate(hss):
if ix.startswith('FASTQ'):
idx.append(i)
hs = [hss[0]] + [hss[i] for i in idx]
for i in f:
i = i.strip("\n").split("\t")
if i[0] != "":
samples[i[0]] = [i[j] for j in idx]
f.close()
# scan
results = dict()
for i in analysis:
if config.has_key(i):
sok = dict()
if os.path.exists(path + "/results_" + i + "/samples_ok.txt"):
f = open(path + "/results_" + i + "/samples_ok.txt", 'r')
for j in f:
sok[j.strip("\n")] = 1
f.close()
results[i] = dict()
if i == "trimgalore":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
filess = y
for f in filess:
f = f.split("/")[-1]
link = "../results_trimgalore/" + f + "_trimming_report.txt"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["trimgalore"][x] = " / ".join(res)
elif i=="fastqc":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
filess = y
for f in filess:
f = f.split("/")[-1]
link = "../results_fastqc/"+f.replace(".fastq","").replace(".gz","")+"_fastqc/fastqc_report.html"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK",link)
res.append(link)
else:
res.append("FAIL")
results["fastqc"][x] = " / ".join(res)
elif i=="star":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_star/" + x + "_Aligned.out.sam"
link = '<a href="LINK" target="_blank">BAM-OK</a>'.replace("LINK", link)
res.append(link)
link = "../results_star/" + x + "_ReadsPerGene.out.tab"
link = '<a href="LINK" target="_blank">COUNTS-OK</a>'.replace("LINK", link)
res.append(link)
link = "../results_star/" + x + "_SJ.out.tab"
link = '<a href="LINK" target="_blank">SJ-OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("BAM-FAIL")
res.append("COUNTS-FAIL")
res.append("COUNTS-FAIL")
results["star"][x] = " / ".join(res)
elif i=="kallisto":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_kallisto/" + x + "/abundance.tsv"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["kallisto"][x] = " / ".join(res)
elif i=="star-fusion":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_star-fusion/" + x + "/star-fusion.fusion_candidates.final.abridged"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["star-fusion"][x] = " / ".join(res)
elif i=="picard_IS":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x) and os.path.exists(path + '/results_picard_IS/' + x + '.txt'):
link = "../results_picard_IS/" + x + ".txt"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["picard_IS"][x] = " / ".join(res)
elif i=="jsplice":
for x, y in sorted(samples.iteritems()):
res = []
if os.path.exists(path + '/results_jsplice/jSplice_results.html'):
link = '../results_jsplice/jSplice_results.html'
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["jsplice"][x] = " / ".join(res)
elif i=="picard":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_picard/" + x + ".general.qc"
link = '<a href="LINK" target="_blank">GENERAL-OK</a>'.replace("LINK", link)
res.append(link)
link = "../results_picard/" + x + ".protein_coding.qc"
link = '<a href="LINK" target="_blank">PC-OK</a>'.replace("LINK", link)
res.append(link)
link = "../results_picard/" + x + ".ribosomal.qc"
link = '<a href="LINK" target="_blank">RB-OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("GENERAL-FAIL")
res.append("PC-FAIL")
res.append("RB-FAIL")
results["picard"][x] = " / ".join(res)
elif i=="htseq-gene":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_htseq-gene/" + x + ".tab"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["htseq-gene"][x] = " / ".join(res)
elif i=="htseq-exon":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_htseq-exon/" + x + ".tab"
link = '<a href="LINK" target="_blank">OK</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["htseq-exon"][x] = " / ".join(res)
elif i=="varscan":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link = "../results_varscan/" + x + ".vcf"
link = '<a href="LINK" target="_blank">VCF</a>'.replace("LINK", link)
res.append(link)
else:
res.append("FAIL")
results["varscan"][x] = " / ".join(res)
elif i=="gatk":
for x, y in sorted(samples.iteritems()):
res = []
if sok.has_key(x):
link1 = "../results_gatk/" + x + ".vcf"
link1 = '<a href="LINK" target="_blank">VCF</a>'.replace("LINK", link1)
link2 = "../results_gatk/" + x + ".filt.vcf"
link2 = '<a href="LINK" target="_blank">VCF_FILT</a>'.replace("LINK", link2)
res.append(link1 + "/" + link2)
else:
res.append("FAIL")
results["gatk"][x] = " / ".join(res)
n = "<th bgcolor='#A8A8A8'>Sample</th>"
for i in hs[1:]:
n = n + "<th bgcolor='#A8A8A8'> Size "+i+" (Gb)</th>"
for i in range(len(analysis)):
if results.has_key(analysis[i]):
n = n +"<th bgcolor='#A8A8A8'>"+sta[analysis[i]]+"</th>"
thead = "<thead><tr>"+n+"</tr></thead>"
tab = list()
for i in sorted(samples.keys()):
n = ["<td bgcolor='#A8A8A8'>"+i+"</td>"]
for j in range(len(hs[1:])):
try:
n.append("<td bgcolor='#A8A8A8'>" + str(round(os.stat(samples[i][j]).st_size/1000000000.0, 2)) + "</td>")
except:
n.append("<td bgcolor='#A8A8A8'>NA</td>")
for a in analysis:
if results.has_key(a):
cl = "#00CC66"
if "FAIL" in results[a][i]:
cl = "#CC3300"
n.append("<td bgcolor='"+cl+"'>"+results[a][i]+"</td>")
tab.append("<tr>"+"".join(n)+"</tr>")
return '<table id="DT" class="display">' + thead + "<tbody>" + "\n".join(tab) + "</tbody></table>"
def config_file(path, fname):
f = open(path + "/" + fname,'r')
n = list()
for i in f:
i = i.strip("\n").split("\t")
if len(i) >= 2:
g = "<tr><td bgcolor='#00CC66'>"+i[0]+"</td><td bgcolor='#00CC66'>"+i[1]+"</td></tr>"
else:
g = "<tr><td colspan='2' bgcolor='#C0C0C0'>" + i[0] + "</td></tr>"
n.append(g)
f.close()
tab = "<table>"+"".join(n)+"</table>"
return tab
def print_table_default(datafile, index, select):
palette = ["#00FA9A", "#AFEEEE", "#D8BFD8", "#DEB887", "#D3D3D3", "#EEE8AA"]
if not os.path.exists(datafile):
return ""
f = open(datafile, 'r')
h = f.readline().strip("\n").split("\t")
if len(select) == 0:
select = range(len(h))
n = ""
for i in select:
n = n + "<th align='center' bgcolor='#A8A8A8'>" + h[i] + "</th>"
if index < 0:
n = '<table id="DT" class="display"><thead><tr>' + n + '</tr></thead><tbody>'
else:
n = '<table><thead><tr>' + n + '</tr></thead><tbody>'
M = dict()
r = 0
for i in f:
i = i.strip("\n").split("\t")
if len(i) > 0:
temp = ""
if index > -1:
if not M.has_key(i[index]):
M[i[index]] = palette[r % len(palette)]
r += 1
for k in select:
j = i[k]
if (j == "-1") or (j.startswith("NA ") or j.endswith(" NA") or j == "NA"):
temp = temp + "<td align='center' bgcolor='#CC3300'>" + j + "</td>"
else:
if index < 0:
temp = temp + "<td align='center' bgcolor='#00CC66'>" + j + "</td>"
else:
temp = temp + "<td align='center' bgcolor='" + M[i[index]] + "'>" + j + "</td>"
n = n + "<tr>" + temp + "</tr>"
n += "</tbody></table>"
return n
def check_project(path):
print "> Checking project path..."
if path == "":
exit("Parameter -p is required.")
if not os.path.exists(path):
exit("Path to project folder not found.")
if path.endswith("/"):
path = path[0:(len(path)-1)]
if not os.path.exists(path + "/config.txt"):
exit("Project configuration file not found: " + path + "/config.txt")
if not os.path.exists(path + "/samples.list"):
exit("Project samples file not found: " + path + "/samples.list")
project = path.split("/")
project = project[len(project)-1] # project id
return project, path
def stats_picard(path,samples,config):
n = os.listdir(path)
hh = "\t".join(["sample_id","mRNA-Coding", "mRNA-Ribosomal", "mRNA-Others","Intron","Intergenic","Unmapped","Med-CVcov","Med-5bias","Med-3bias","Med-5/3bias"])
if config.has_key("picard") and ("results_picard" in n):
files = os.listdir(path+"/results_picard")
n = [".general.qc",".protein_coding.qc",".ribosomal.qc"]
names = ["Sample","BASES (N)","ALIGN (N)","ALIGN (%)","INTRON (N)","INTRON (%)",
"INTERGEN (N)","INTERGEN (%)","MRNA (N)","MRNA (%)","Protein coding (%)",
"Ribosomal (%)","Others (%)","Coding (%)","UTR (%)","MEDIAN CV COVERAGE","MEDIAN 5' BIAS","MEDIAN 3' BIAS","MEDIAN 5'-3' BIAS"]
g = ["MEDIAN_CV_COVERAGE","MEDIAN_5PRIME_BIAS","MEDIAN_3PRIME_BIAS","MEDIAN_5PRIME_TO_3PRIME_BIAS"]
out = open(path + "/outputs/stats_picard.txt",'w')
table = ['<tr><th align="center" colspan="2" bgcolor="#A8A8A8"></th><th align="center" colspan="2" bgcolor="#A8A8A8">ALIGNED BASES</th><th align="center" colspan="6" bgcolor="#A8A8A8">GENOME LOCATION</th><th align="center" colspan="3" bgcolor="#A8A8A8">MRNA TYPE</th><th align="center" colspan="2" bgcolor="#A8A8A8">MRNA LOCATION</th><th align="center" colspan="4" bgcolor="#A8A8A8">OTHERS</th></tr>']
header = ""
for i in names:
header = header+"<th bgcolor='#A8A8A8'>"+i+"</th>"
print >> out, hh
header = "<tr>"+header+"</tr>"
table.append(header)
for i in sorted(samples.keys()):
stats = [{},{},{}]
heads = list()
ex = 0
for k in range(3):
if i+n[k] in files:
f = open(path+"/results_picard"+"/"+i+n[k],'r')
nx = 0
kdiff0 = 0
for ii in f:
if ii.startswith("PF_BASES"):
head = ii.rstrip().split("\t")
nx = 1
for kk in head:
if not (kk in heads):
heads.append(kk)
elif nx == 1:
vals = ii.strip("\n").split("\t")
for kk in range(len(head)):
stats[k][head[kk]] = vals[kk]
if (vals[kk] != "") and (vals[kk] != "?"):
if float(vals[kk]) > 0:
kdiff0 += 1
nx = 0
if kdiff0 == 0:
ex = 1
break
f.close()
else:
ex = 1
break
if ex ==1:
tr = "<td bgcolor='#CC3300'>"+i+"</td>"
o = i
for ii in range(18):
tr += "<td bgcolor='#CC3300'>NA</td>"
o += "\tNA"
tr = "<tr>"+tr+"</tr>"
table.append(tr)
s = ["NA" for ii in range(10)]
else:
align = int(stats[0]["PF_ALIGNED_BASES"])
cod = int(stats[0]["CODING_BASES"])
utr = int(stats[0]["UTR_BASES"])
intr = int(stats[0]["INTRONIC_BASES"])
inter = int(stats[0]["INTERGENIC_BASES"])
mrna = cod + utr
pc = int(stats[1]["CODING_BASES"])+int(stats[1]["UTR_BASES"])
rb = int(stats[2]["CODING_BASES"])+int(stats[2]["UTR_BASES"])
ot = mrna - pc - rb
pc = str(round(100*float(pc)/align,3))
rb = str(round(100*float(rb)/align,3))
ot = str(round(100*float(ot)/align,3))
tr = "<td bgcolor='#B8B8B8'>"+i+"</td>"
tr +="<td bgcolor='#00CC66'>"+stats[0]["PF_BASES"]+"</td>"
tr +="<td bgcolor='#00CC66'>"+str(align)+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(align)/float(stats[0]["PF_BASES"]),2))+"</td>"
tr +="<td bgcolor='#00CC66'>"+str(intr)+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(intr)/align,2))+"</td>"
tr +="<td bgcolor='#00CC66'>"+str(inter)+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(inter)/align,2))+"</td>"
tr +="<td bgcolor='#00CC66'>"+str(mrna)+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(mrna)/align,2))+"</td>"
tr +="<td bgcolor='#99CC66'>"+pc+"</td>"
tr +="<td bgcolor='#99CC66'>"+rb+"</td>"
tr +="<td bgcolor='#99CC66'>"+ot+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(cod)/align,2))+"</td>"
tr +="<td bgcolor='#99CC66'>"+str(round(100*float(utr)/align,2))+"</td>"
o = i + "\t" + stats[0]["PF_BASES"] + "\t" + str(align) + "\t" + str(round(100*float(align)/float(stats[0]["PF_BASES"]),2)) + "\t" + str(intr) + "\t" + str(round(100*float(intr)/align,2)) + "\t" + str(inter) + "\t" + str(round(100*float(inter)/align,2)) + "\t" + str(mrna) + "\t" + str(round(100*float(mrna)/align,2)) + "\t" +pc+ "\t" +rb+ "\t" +ot+ "\t" +str(round(100*float(cod)/align,2))+ "\t" + str(round(100*float(utr)/align,2))
for ix in g:
if stats[0][ix]!="?":
tr +="<td bgcolor='#99CC66'>"+str(round(float(stats[0][ix]),3))+"</td>"
o += "\t" + str(round(float(stats[0][ix]),3))
else:
tr +="<td bgcolor='#99CC66'>0</td>"
o += "\t0"
tr = "<tr>"+tr+"</tr>"
table.append(tr)
o = o.split("\t")
st= 0
s = []
for ind in [10, 11, 12, 5, 7, 3]:
s.append(str(round(float(o[ind]) * float(o[2])/float(o[1]),3)))
if ind != 3:
st += float(o[ind]) * float(o[2])/float(o[1])
for ind in [15,16,17,18]:
if o[ind] != "0":
s.append(str(round(float(o[ind]) * 100,3)))
else:
s.append("0")
s[5] = str(round(100 - st,3))
print >> out, i + "\t" + "\t".join(s)
out.close()
return "<table>"+"\n".join(table)+"</table>"
else:
return ""
def stats_picard_2(path,samples,config):
n = os.listdir(path)
H= ['sample_id','MEDIAN_INSERT_SIZE','MEDIAN_ABSOLUTE_DEVIATION','MIN_INSERT_SIZE',
'MAX_INSERT_SIZE','MEAN_INSERT_SIZE','STANDARD_DEVIATION','READ_PAIRS', 'LINK_TXT', 'LINK_PDF']
hh = "\t".join(H)
if config.has_key("picard_IS") and ("results_picard_IS" in n):
files = os.listdir(path+"/results_picard_IS")
out = open(path + "/outputs/stats_picard2.txt",'w')
print >> out, hh
for i in sorted(samples.keys()):
if i + ".txt" in files:
f = open(path+"/results_picard_IS"+"/"+i+".txt",'r')
k = 0
while (1):
h = f.readline()
if h.startswith("MEDIAN_INSERT_SIZE"):
j = f.readline().strip("\n").split("\t")
h = h.strip("\n").split("\t")
break
k += 1
if k > 10 or len(h) == 0:
j = ['NA' for i in range(7)]
break
J = []
for k in range(len(h)):
if h[k] in H:
J.append(j[k])
print >> out, "\t".join([i] + J + ['<a href="../results_picard_IS/' + i + '.txt" target="_blank">+</a>', '<a href="../results_picard_IS/' + i + '.pdf" target="_blank">+</a>'])
f.close()
else:
print >> out, "\t".join([i] + ['NA' for i in range(9)])
out.close()
return 1
def skeleton(path, path2html):
print "> Building HTML and OUTPUT folders skeletons..."
print " - Path: " + path
print " - Libs: " + path2html
# Creates output directiories
if os.path.exists(path + "/outputs"):
os.system("rm -r " + path + "/outputs")
os.mkdir(path + "/outputs")
# Creates HTML directories
n = os.listdir(path)
if "HTML" in n:
os.system("rm -r " + path + "/HTML")
if not ("HTML" in os.listdir(path)):
os.mkdir(path + "/HTML")
os.mkdir(path + "/HTML/html")
# Copy lightbox and jquery
shutil.copy(path2html + "/html/style.css", path + "/HTML/html/style.css")
shutil.copy(path2html + "/html/lytebox.js", path + "/HTML/html/lytebox.js")
shutil.copy(path2html + "/html/lytebox.css", path + "/HTML/html/lytebox.css")
shutil.copy(path2html + "/html/jquery-1.12.0.js", path + "/HTML/html/jquery-1.12.0.js")
shutil.copy(path2html + "/html/jquery.dataTables.min.js", path + "/HTML/html/jquery.dataTables.min.js")
shutil.copy(path2html + "/html/jquery.dataTables.min.css", path + "/HTML/html/jquery.dataTables.min.css")
shutil.copy(path2html + "/html/dataTables.colReorder.min.js", path + "/HTML/html/dataTables.colReorder.min.js")
shutil.copy(path2html + "/html/amcharts.js", path + "/HTML/html/amcharts.js")
shutil.copy(path2html + "/html/serial.js", path + "/HTML/html/serial.js")
shutil.copy(path2html + "/html/xy.js", path + "/HTML/html/xy.js")
os.system("cp -r " + path2html + "/html/images " + path + "/HTML/html/")
# def check_samples(path):
# # Parses the samples file
# print "> Parsing samples file..."
# try:
# f = open(path + "/samples.list", 'r')
# i = f.readline().strip("\n").split("\t")
# index = [-1,-1,-1]
# if ("FASTQ_1" in i) and ("FASTQ_2" in i):
# k = "paired-end"
# for r in range(len(i)):
# if i[r]=="SampleID":
# index[0] = r
# if i[r]=="FASTQ_1":
# index[1] = r
# if i[r]=="FASTQ_2":
# index[2] = r
# else:
# k = "single-end"
# for r in range(len(i)):
# if i[r]=="SampleID":
# index[0] = r
# if i[r]=="FASTQ":
# index[1] = r
# samples = dict()
# for i in f:
# i = i.strip("\n").split("\t")
# if len(i)>1:
# if k=="paired-end":
# samples[i[index[0]]] = [[i[index[1]],i[index[2]]],["Type",k]]
# else:
# samples[i[index[0]]] = [[i[index[1]]],["Type",k]]
# f.close()
# return samples
# except:
# exit("Error checking samples file: " + path + "/samples.list")
def build_amcharts(input, output, prog, pname, path, html_table, project, lmenu):
out = open(output, 'w')
f = open(input, 'r')
it = ""
for i in f:
i = i.strip("\n")
if i.startswith("#ITERATOR"):
pattern = i.replace("#ITERATOR=","")
f2 = open(path + "/outputs/" + pname[1] + "_pca.txt", 'r')
h = f2.readline()
it = list()
for j in f2:
np = pattern
j = j.strip("\n").split("\t")
for k in range(len(j)):
np = np.replace("#VAR"+str(len(j)-k-1),j[len(j)-k-1])
it.append(np)
it = ", ".join(it)
f2.close()
else:
if prog + "2.html" in i:
i = i.replace("#HIGHLIGHT", 'style="color:#808080"')
print >> out, i.replace("#LATMENU",lmenu).replace("#PROG", pname[0]).replace("#PROJECT", project).replace("#SITERATOR", it).replace("#HIGHTLIGHT", "").replace("#TABLE", html_table)
f.close()
out.close()
def check_config(path):
# Parses the configuration file
print "> Parsing configuration file..."
try:
z = ["trimgalore", "fastqc", "star", "star-fusion", "picard", "htseq-gene", "htseq-exon", "kallisto", "picard_IS", "varscan", "gatk", 'jsplice']
f = open(path + "/config.txt", 'r')
analysis = dict()
analysis["cluster"] = dict()
analysis["programs"] = dict()
for i in f:
if not i.startswith("#"):
i = i.strip("\n").split("\t")
if len(i) > 1:
if i[0] in z:
if int(i[1].split("/")[0]) > 0:
analysis[i[0]] = [i[1], "results_" + i[0], dict()]
elif i[0] in ["wt", "q"]:
analysis["cluster"][i[0]] = i[1]
elif i[0] == "star_args_own":
if analysis["programs"]["star_args"] == "own":
analysis["programs"]["star_args"] = i[1]
elif i[0] == "starfusion_own":
if analysis["programs"]["starfusion"] == "own":
analysis["programs"]["starfusion"] = i[1]
elif i[0] == "genome_build":
analysis[i[0]] = i[1]
else:
analysis["programs"][i[0]] = i[1]
f.close()
return analysis
except:
exit("Error checking configuration file: " + path + "/config.txt")
# def print_config(config,path):
# table = list()
# table.append(["Analysis", "Processors", "Folder", "Timestamp",
# "TStart","TEnd","Success","CPU-Time","MaxMemo",
# "AveMemo","MaxSwap","Parameters"])
# for i in modules:
# if config.has_key(i):
# n = check_log_cluster(path, config[i][1])
# st = []
# if len(config[i][2]) > 0:
# for v,w in config[i][2].iteritems():
# st.append(v+": "+w)
# st = "<br>".join(st)
# for j in range(len(n)):
# tt = [module_names[i]]+[config[i][0],"./"+config[i][1]]+n[j]+[st]
# table.append(tt)
# n = ""
# for i in table[0]:
# n = n+"<th bgcolor='#A8A8A8'>"+i+"</th>"
# n = ["<tr>"+n+"</tr>"]
# for i in table[1:]:
# temp = ""
# for j in i:
# if "NA" in j:
# temp = temp+"<td bgcolor='#CC3300'>"+j+"</td>"
# else:
# temp = temp+"<td bgcolor='#00CC66'>"+j+"</td>"
# n.append("<tr>"+temp+"</tr>")
# return n
# def check_log_cluster(path, val):
# t = os.listdir(path)
# if not (val in t):
# return ["NA","NA","NA","NA","NA","NA","NA"]
# t = os.listdir(path + "/" + val)
# t2 = list()
# for i in t:
# if i.startswith("log_cluster_") and (("scheduler" in i) == False):
# if len(i.split("_")) >= 4 :
# t2.append(i)
# if len(t2) == 0:
# return [["NA","NA","NA","NA","NA","NA","NA","NA"]]
# n = list()
# for jv in sorted(t2):
# f = open(path + "/" + val + "/" + jv,'r')
# ts = ""
# te = ""
# suc= "No"
# cpu_time = ""
# max_memo = ""
# ave_memo = ""
# max_swap = ""
# pid = "_".join(jv.split("_")[2:4]).replace(".txt","")
# for i in f:
# if i.startswith("Started at"):
# ts = i.rstrip().replace("Started at ","")
# if i.startswith("Results reported on"):
# te = i.rstrip().replace("Results reported on ","")
# if i.startswith("Successfully completed."):
# suc = "Yes"
# if "CPU time :" in i:
# cpu_time = " ".join(i.rstrip().split()[3:5])
# if "Max Memory :" in i:
# max_memo = " ".join(i.rstrip().split()[3:5])
# if "Average Memory :" in i:
# ave_memo = " ".join(i.rstrip().split()[3:5])
# if "Max Swap :" in i:
# max_swap = " ".join(i.rstrip().split()[3:5])
# f.close()
# n.append([pid,ts,te,suc,cpu_time,max_memo,ave_memo,max_swap])
# return n
def bar_getdata (filename, head, cols_bar, cols_line):
# LOAD DATA
if not os.path.exists(filename):
return ""
f = open(filename, 'r')
h = f.readline().strip("\n").split("\t")
if (len(cols_bar)==0) and (len(cols_line)==0):
cols_bar = range(1, len(h))
D = list()
for i in f:
i = i.strip("\n").split("\t")
n = list()
for j in range(len(h)):
if j == head:
n.append('"' + h[j] + '": "' + i[j] + '"')
elif (j in cols_bar) or (j in cols_line):
if i[j] != "NA":
n.append('"' + h[j] + '": ' + i[j])
else:
n.append('"' + h[j] + '": 0')
D.append("{" + ", ".join(n) + "}")
D = "var chartData = [" + ", ".join(D) + "];"
return D
def build_from_template(prog, project, data, html_table, html_table2, output, template, lmenu):
out = open(output,'w')
f = open(template, 'r')
r = output.split("/")[-1]
for i in f:
i = i.strip("\n")
if r in i:
i = i.replace("#HIGHLIGHT", 'style="color:#808080"')
print >> out, i.replace("#LATMENU",lmenu).replace("#PROG", prog).replace("#PROJECT", project).replace("#DATA", data).replace("#HIGHTLIGHT", "").replace("#TABLE2", html_table2).replace("#TABLE", html_table)
f.close()
out.close()