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Added both inclusive and exclusive filters 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-06-11 18:40:41 +00:00
parent e6d8faf293
commit c0370f4d0a
1 changed files with 21 additions and 6 deletions
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27
python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py
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@ -26,7 +26,8 @@ parser.add_option("-R", "--reference", metavar="PATH", dest="reference", help="S
parser.add_option("-n", "--gene-name-columns", dest="gene_name_columns", metavar="GENE_NAMES", help="Comma-separated list of column names that contain gene names. This arg is passed through to the GenomicAnnotator. The GenomicAnnotator docs have more details on this.")
parser.add_option("-q", "--queue", dest="queue", metavar="QUEUE", help="Specifies the LSF queue to use.", default="solexa")
parser.add_option("-s", "--num-parallel-processes", dest="num_parallel_processes", metavar="SLOTS", help="How many processes to launch simultaneously. This is only used when the -l option is set.", default="1")
parser.add_option("-w", "--filter-out-chromosomes", dest="filter", metavar="FILTER", help="Skips these chromosomes - specified by a python expression which must evaluate to a list (eg. ['chr1', 'chr2', 'chr3'] or ['chr'+x for x in range(1, 10)].")
parser.add_option("-v", "--filter-in-chromosomes", dest="filterin", metavar="FILTER", help="Only process these chromosomes - specified by a python expression which must evaluate to a list (eg. ['chr1', 'chr2', 'chr3'] or ['chr'+x for x in range(1, 10)].")
parser.add_option("-w", "--filter-out-chromosomes", dest="filterout", metavar="FILTER", help="Skip these chromosomes - specified by a python expression which must evaluate to a list (eg. ['chr1', 'chr2', 'chr3'] or ['chr'+x for x in range(1, 10)].")
(options, args) = parser.parse_args()
@ -61,15 +62,26 @@ if not os.access(reference, os.R_OK):
queue = options.queue
num_parallel_processes = int(options.num_parallel_processes)
chr_filter = options.filter
if options.filterout and options.filterin:
error("Either -v or -w filters can be specified, but not both")
elif options.filterout:
filter_out = True
chr_filter = options.filterout
elif options.filterin:
filter_out = False
chr_filter = options.filterin
else:
chr_filter = None
if chr_filter:
try:
chr_filter = eval(chr_filter)
except Exception, e:
error("Invalid -f filter string: " + chr_filter + " " + str(e))
error("Invalid filter string: " + chr_filter + " " + str(e))
if type(chr_filter) != type([]):
error(" -f filter string doesn't evaluate to a list: " + chr_filter)
error("Filter string doesn't evaluate to a list: " + chr_filter)
@ -86,10 +98,13 @@ contigs += [ "chr" + str(x) for x in contig_chars ]
contigs += [ "chr" + str(x) + "_random" for x in set( contig_chars ).difference(set(['M',12,14,20,'X','Y'])) ] # There are no "_random" chromosomes for chrM,12,14,20,Y
if chr_filter:
contigs = [ x for x in set( contigs ).difference(set(chr_filter)) ] # Filter out contigs
if filter_out:
contigs = [ x for x in contigs if x in set( contigs ).difference(set(chr_filter)) ] # Filter out contigs
else:
contigs = chr_filter # Only process these contigs
while True:
input_str = raw_input("Filtered out: " + str(chr_filter) + "\nWill process: " + str(contigs) + ".\n Proceed [Y/N]? ")
input_str = raw_input("Filter applied: " + str(chr_filter) + "\nWill process: " + str(contigs) + ".\n Proceed [Y/N]? ")
if input_str.upper() == "Y":
break
elif input_str.upper() == "N":