def buildWorkSpace(outfile, workspace):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
intronic
introns (requires annotator_regions to be set)
exonic
exonic (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
job_options = "-l mem_free=4000M"
workspace = workspace.lower()
if workspace == "genomic":
P.checkParameter("genome")
statement = '''
cgat index2bed
--genome=%(genome)s
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace in ("intergenic", "intronic", "cds"):
P.checkParameter("enrichment_regions")
workspace_upper = workspace.upper()
statement = '''
gunzip < %(enrichment_regions)s
| awk 'BEGIN {printf("track name=%(workspace)s\\n"); }
($3 == "%(workspace)s"
|| $3 == "%(workspace_upper)s")
&& !( $1 ~ /%(enrichment_remove_pattern)s/)
{ printf("%%s\\t%%i\\t%%i\\n", $1, $4-1, $5); }'
> %(outfile)s
'''
elif workspace == "unknown":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(enrichment_regions)s
| cgat gff2enrichment
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "known":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(enrichment_regions)s
| cgat gff2enrichment
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "alignable":
P.checkParameter("enrichment_alignment")
statement = '''gunzip
< %(enrichment_alignment)s
| sort -k10,10
| awk '$10 !~ /%(enrichment_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(outfile)s
'''
elif workspace == "gene-territories":
P.checkParameter("enrichment_geneterritories")
statement = '''
cgat gff2enrichment \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(enrichment_remove_pattern)s'
< %(enrichment_geneterritories)s > %(outfile)s
'''
elif workspace == "mappable":
P.checkParameter("enrichment_mappability")
statement = '''
cgat bed2gff < %(enrichment_mappability)s
| cgat gff2enrichment
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
else:
raise ValueError("unknown workspace '%s'" % workspace)
P.run()
def buildWorkSpace(outfile, workspace):
'''write genomic workspace.
Available workspaces are:
genomic
the full genome
intronic
introns (requires annotator_regions to be set)
exonic
exonic (requires annotator_regions to be set)
intergenic
introns (requires annotator_regions to be set)
geneterritories
introns (requires annotator_geneterritories to be set)
mappable
mappable part of genome (requires annotator_mappability to be set )
alignable
only the alignable part of a genome (requires annotator_alignment to be set)
If ``gc_control`` is True, the chromosomes will be divided into isochores
(requiers the paramater ``annotator_gc_workspace`` to be set).
'''
job_options = "-l mem_free=4000M"
workspace = workspace.lower()
if workspace == "genomic":
P.checkParameter("genome")
statement = '''
python %(scriptsdir)s/index2bed.py
--genome=%(genome)s
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace in ("intergenic", "intronic", "cds"):
P.checkParameter("enrichment_regions")
workspace_upper = workspace.upper()
statement = '''
gunzip < %(enrichment_regions)s
| awk 'BEGIN {printf("track name=%(workspace)s\\n"); }
($3 == "%(workspace)s"
|| $3 == "%(workspace_upper)s")
&& !( $1 ~ /%(enrichment_remove_pattern)s/)
{ printf("%%s\\t%%i\\t%%i\\n", $1, $4-1, $5); }'
> %(outfile)s
'''
elif workspace == "unknown":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "intronic" || $3 == "intergenic" )'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "known":
P.checkParameter("enrichment_regions")
statement = '''
awk '($3 == "CDS" || $3 ~ /UTR/ || $3 ~ /flank/)'
< %(enrichment_regions)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
elif workspace == "alignable":
P.checkParameter("enrichment_alignment")
statement = '''gunzip
< %(enrichment_alignment)s
| sort -k10,10
| awk '$10 !~ /%(enrichment_remove_pattern)s/ \
{if ($10!=l) {printf("\\n##Work\\t%%s", $10); l=$10;} \
printf("\\t(%%i,%%i)", $12,$13); }; \
END {printf ("\\n");}'\
> %(outfile)s
'''
elif workspace == "gene-territories":
P.checkParameter("enrichment_geneterritories")
statement = '''
python %(scriptsdir)s/gff2enrichment.py \
--section=workspace \
--max-length=0 \
--log=%(outfile)s.log \
--remove-regex='%(enrichment_remove_pattern)s'
< %(enrichment_geneterritories)s > %(outfile)s
'''
elif workspace == "mappable":
P.checkParameter("enrichment_mappability")
statement = '''
python %(scriptsdir)s/bed2gff.py < %(enrichment_mappability)s
| python %(scriptsdir)s/gff2enrichment.py
--section=workspace
--max-length=0
--log=%(outfile)s.log
--remove-regex='%(enrichment_remove_pattern)s'
> %(outfile)s
'''
else:
raise P.PipelineError("unknown workspace '%s'" % workspace)
P.run()
