def report(params):
""" circos_report to markdown file and html file
Args: report input dict, key is `yaml`, value is yaml file path::
"xx": path of xx.
Returns:
dict : key is `yaml`,value is yaml file path
"""
# handle input
yamlin = params["yaml"]
indict = yaml.load(open(yamlin))
yamlfile = "circos_report.json"
paramstr = json.dumps(indict)
cmd1 = "echo '%s' > %s " % (paramstr, yamlfile)
tag1 = "make sure the existed yaml file"
log.run("tag1", cmd1, i=None, o=[yamlfile])
templ = get_template("circos_report")
out = "circos_report.md"
cmd = "%s -t %s -j %s -o %s -y" % (render, templ, yamlfile, out)
log.run("render circos_report template", cmd)
cmd = "%s %s" % (md2html, out)
log.run("md2html circos_report ", cmd)
outdict = {}
outdict["circos_report"] = out
yamlout = yamladd(yamlin, outdict)
yamlout["circos_report_outdir"] = os.getcwd()
return yamlout
def report(params):
""" enrichreport to markdown file and html file
Args: report input dict, key is `yaml`, value is yaml file path::
"xx": path of xx.
Returns:
dict : key is `yaml`,value is yaml file path
"""
# handle input
yamlin = params["yaml"]
indict = yaml.load(open(yamlin))
enrichreportl = get_template("enrichreport")
out = "enrichreport.md"
cmd = "%s -t %s -j %s -o %s -y" % (render, enrichreportl, yamlin, out)
log.run("render enrichreport template", cmd)
cmd = "%s %s" % (md2html, out)
log.run("md2html enrichreport ", cmd, o=["html.tgz"])
outdict = {}
outdict["enrichreport"] = out
yamlout = yamladd(yamlin, outdict)
yamlout["enrichreport_outdir"] = os.getcwd()
return yamlout
def main_multi(params):
'''params is an input dict including the following keys
Args:
params (dict) : key is `yaml`, value is a yaml file::
plotinfo:
{
karytotype : karytotype file of circos
chrom_unit : the basic number of unit(numeric)
species : data file including unit of all chromosomes used for bedtools
},
circos_report_template : the report template
cnvinp : the output of calling cnv
snvinp : the output of calling snv
svinp : the output of calling sv
circos_multi_tmp : the template of snv&cnv&sv's conf
Returns:
params (dict) : key is `yaml`, value is a yaml file::
plotinfo :
{
karytotype : karytotype file of circos
chrom_unit : the basic number of unit(numeric)
species : data file including unit of all chromosomes used for bedtools
snp_min : the min value of snp file
snp_max : the max value of snp file
indel_min : the min value of indel file
indel_max : the max value of indel file
cnv_min : the min value of the cnv file
cnv_max : the max value of the cnv file
outfile : the output name of circos file
snp_out : the file are used for the snp input of circos png
indel_out : the file are used for the indel input of circos png
cnv_out : the file are used as the cnv input of circos' png
sv_out : the file are used as the sv input of circos' png
}
outconf : name of the circos conf file
circos_multi_tmp : the template of snv&cnv&sv's conf
circos_report_template : the report template
snp : the snp file after separated from annotated file
indel : the indel file after separated from annotated file
snvinp : the output of calling snv
cnvinp : the output of calling cnv
svinp : the output of calling sv
'''
# handle input ...
yamlin = params["yaml"]
indict = yaml.load(open(yamlin).read())
cycle_param = parse_param(indict)
circos_res = data_cycle(cycle_param)
# handle output ...
outdict = {}
outdict["circos_res"] = circos_res
outdict["circos_text"] = "circos图由里到外依次为sv,cnv,snp和indel的结果"
yamlout = yamladd(yamlin, outdict)
return yamlout
def arrange(params):
""" circos_report arrange output files
Args:
params: indict , key is `yaml`, value in yaml file::
circos_res:
{
patient1: saved circos' info of the patient
{
conf: the conf file of the specific patient
png: the png file of the specific patient
}
}
Returns:
dict : key is `yaml`, value is the path of yaml file
"""
# handle input
yamlin = params["yaml"]
indict = yaml.load(open(yamlin).read())
pngs = data_cycle(indict)
# process cmd
log.move(pngs, "report/circos")
#handle out
outdict = {}
outdict["circos_pngs"] = pngs
yamlout = yamladd(yamlin, outdict)
return yamlout
def arrange(arr_dict, yamlfile):
func_pdfs_report = files_report(arr_dict['func_pdfs'])
go_dot_pdfs_report = files_report(arr_dict['go_dot_pdfs'])
go_net_pdfs_report = files_report(arr_dict['go_net_pdfs'])
kegg_pdfs_report = files_report(arr_dict['kegg_pdfs'])
func_xls_report = transfor(arr_dict['func_csvs'])
go_xls_report = transfor(arr_dict['go_csvs'])
go_xls_all = transfor(arr_dict['go_csvs_all'])
kegg_xls_report = transfor(arr_dict['kegg_csvs'])
kegg_xls_all = transfor(arr_dict['kegg_csvs_all'])
if len(kegg_pdfs_report) == 0:
kegg_pdf_report = ''
else:
kegg_pdf_report = kegg_pdfs_report[0]
out_dict = {"func_pdfs_report": func_pdfs_report, "go_dot_pdfs_report": go_dot_pdfs_report, "go_net_pdfs_report": go_net_pdfs_report, \
"kegg_pdf_report": kegg_pdf_report, "func_xls_report": func_xls_report, "go_xls_report": go_xls_report, "kegg_xls_report": kegg_xls_report}
# report paramters
#
res = yamladd(yamlfile, out_dict)
return res
def arrange(ymlfile):
""" {{projName}} arrange output files use log.run
"""
# handle input
indict = yaml.load(open(ymlfile).read())
# process cmd and user log.move to arrange files to report
pass
# handle output
#handle out
outdict = {}
yamladd(ymlfile, outdict)
return ymlfile
def main_cnv(params):
'''params is an input dict including the following keys
Args:
params (dict) : key is `yaml`, value is a yaml file::
plotinfo:
{
karytotype : karytotype file of circos
chrom_unit : the basic number of unit(numeric)
species : data file including unit of all chromosomes used for bedtools
},
circos_report_template : the report template
cnvinp : the output of calling cnv
circos_cnv_tmp : the template of cnv's conf
Returns:
params (dict) : key is `yaml`, value is a yaml file::
plotinfo :
{
karytotype : karytotype file of circos
chrom_unit : the basic number of unit(numeric)
species : data file including unit of all chromosomes used for bedtools
cnv_min : the min value of the cnv file
cnv_max : the max value of the cnv file
outfile : the output name of circos file
cnv_out : the file are used as the cnv input of circos' png
}
outconf : name of the circos conf file
circos_cnv_tmp : the template of cnv's conf
circos_report_template : the report template
cnvinp : the output of calling cnv
'''
# handle input ...
yamlin = params["yaml"]
indict = yaml.load(open(yamlin).read())
cycle_param = parse_param(indict)
circos_res = data_cycle(cycle_param)
# handle output ...
outdict = {}
outdict["circos_res"] = circos_res
outdict["circos_text"] = "circos图为cnv的结果"
yamlout = yamladd(yamlin, outdict)
return yamlout
def circmd(params):
'''params is an input dict which includes the following keys
Args:
params (dict) : key is `yaml`, value is a yaml file::
'outconf:': the name of the circos conf file
Returns:
str : out yaml file
'''
# handle input ...
yamlin = params["yaml"]
indict = yaml.load(open(yamlin).read())
data_cycle(indict)
# handle output ...
outdict = {}
yamlout = yamladd(yamlin, outdict)
return yamlout
def report(ymlfile):
""" {{projName}} to markdown file and html file
"""
# handle input
indict = yaml.load(open(ymlfile))
render_yml = "{{projName}}_render.yml"
cmd = "echo '%s' > %s" % (json.dumps(indict),render_yml)
log.run("get {{projName}} args to render",cmd)
templ = get_template("{{projName}}")
out = "{{projName}}.md"
cmd = "%s -t %s -j %s -o %s -y" % (render,templ,render_yml,out)
log.run("render {{projName}} template",cmd,docker="jbioi/report",singularity="report.img")
cmd = "%s %s" % (md2html,out)
log.run("md2html {{projName}} ",cmd,docker="jbioi/report",singularity="report.img")
outdict = {}
outdict["{{projName}}"] = out
yamlout = yamladd(yamlin,outdict)
yamlout["{{projName}}_outdir"] = os.getcwd()
return ymlfile
def enrich(parms):
'''Gene GO functional annotation, GO enrichment and KEGG enrichment
Args:
parms (dict) : which has the following keys::
{
yaml : a yaml file including parms for gene enrich analysis
}
Returns:
dict : ``{"yaml": yamlfile for arrange and report}``
'''
yaml_file = parms["yaml"]
fp = open(yaml_file)
enrich_dict = yaml.load(fp.read())
fp.close()
files = enrich_dict['enrichFiles']
func_pdfs, func_csvs, func_xls = [], [], []
go_dot_pdfs, go_net_pdfs, go_csvs, go_csvs_all, go_xls, go_xls_all = [], [], [], [], [], []
kegg_pdfs, kegg_csvs, kegg_csvs_all, kegg_xls, kegg_xls_all = [], [], [], [], []
id_files = []
for prefix, enrichFile in files.items():
# check file
#
with open(enrichFile, 'r') as f:
head = f.readline().split('\t')
try:
gidx = head.index("Gene")
except ValueError:
print("\n\nInput file: {} need the head include 'Gene'.\n\n".
format(enrichFile))
# functation annotation
#
cmd = "%s %s %s" % (funcAnnoGO, enrichFile, prefix)
log.run('func annotation', cmd, i=[enrichFile])
# GO enrich analysis
#
cmd = "%s %s %s" % (enrichGO, enrichFile, prefix)
log.run('GO enrich analysis', cmd)
# KEGG enrich analysis
#
cmd = "%s %s %s" % (enrichKEGG, enrichFile, prefix)
log.run('KEGG enrich analysis', cmd)
for item in ['CC', 'BP', 'MF']:
func_pdfs.append('{prefix}.go.{item}.bar.func.pdf'.format(
prefix=prefix, item=item))
func_csvs.append('{prefix}.go.{item}.func.csv'.format(
prefix=prefix, item=item))
func_xls.append('{prefix}.go.{item}.func.xls'.format(prefix=prefix,
item=item))
go_dot_pdfs.append('{prefix}.go.{item}.dot.enrich.pdf'.format(
prefix=prefix, item=item))
go_net_pdfs.append('{prefix}.go.{item}.net.enrich.pdf'.format(
prefix=prefix, item=item))
go_csvs.append('{prefix}.go.{item}.enrich.csv'.format(
prefix=prefix, item=item))
go_csvs_all.append('{prefix}.go.{item}.enrich.all.csv'.format(
prefix=prefix, item=item))
go_xls.append('{prefix}.go.{item}.enrich.xls'.format(prefix=prefix,
item=item))
go_xls_all.append('{prefix}.go.{item}.enrich.all.xls'.format(
prefix=prefix, item=item))
id_files.append("{}.gene_id.csv".format(prefix))
kegg_pdfs.append('{}.KEGG.enrich.pdf'.format(prefix))
kegg_csvs.append('{}.KEGG.enrich.csv'.format(prefix))
kegg_csvs_all.append('{}.KEGG.enrich.all.csv'.format(prefix))
kegg_xls.append('{}.KEGG.enrich.xls'.format(prefix))
kegg_xls_all.append('{}.KEGG.enrich.all.xls'.format(prefix))
out_dict = {'func_pdfs':func_pdfs, 'go_dot_pdfs':go_dot_pdfs, 'go_net_pdfs': go_net_pdfs, 'kegg_pdfs':kegg_pdfs, \
'func_csvs': func_csvs, 'func_xls': func_xls, 'go_csvs': go_csvs, 'go_xls': go_xls, 'go_csvs_all': go_csvs_all, 'go_xls_all': go_xls_all, 'kegg_csvs': kegg_csvs , \
'kegg_csvs_all': kegg_csvs_all, 'kegg_xls': kegg_xls, 'kegg_xls_all': kegg_xls_all}
res = yamladd(yaml_file, out_dict)
# csv2xls
#
cmd = "{csv2xls} {yamlfile}".format(csv2xls=csv2xls, yamlfile=yaml_file)
log.run('csv2xls', cmd)
return res