rbbt-util 5.17.30 → 5.17.31
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/rbbt/tsv/parallel/traverse.rb +5 -6
- data/lib/rbbt/util/misc/omics.rb +27 -3
- metadata +1 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: ec2769ac8dcfb78a8e3b33cdf905f2b0e53e9340
|
4
|
+
data.tar.gz: 9362e1f40b97de7451f0f4ed7467a7f386745128
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 5df33607c693b25c3a0ff547ef690be714f2fa568fb9fd2f8d39819cd6ab8166fbd69cc5f212f5514460693190f349c4c699215c786b9ddcf3d546805dff174b
|
7
|
+
data.tar.gz: 53fdcaded28ebccbe7f88335e3448046300698554deba0bcf3e44b478ea131229128c2b2460f8db18e0ad3f67d83c425020c89bb22013c707a2c377a281937f2
|
@@ -29,20 +29,19 @@ module TSV
|
|
29
29
|
when Array, Hash
|
30
30
|
obj.size
|
31
31
|
when File
|
32
|
-
return nil if
|
32
|
+
return nil if Open.gzip?(file) or Open.bgzip?(file)
|
33
33
|
CMD.cmd("wc -l '#{obj.filename}'").read.to_i
|
34
|
-
when Path
|
35
|
-
|
36
|
-
CMD.cmd("wc -l '#{obj.find}'").read.to_i
|
37
|
-
when String
|
34
|
+
when Path, String
|
35
|
+
obj = obj.find if Path === obj
|
38
36
|
if File.exists? obj
|
39
|
-
return nil if
|
37
|
+
return nil if Open.gzip?(obj) or Open.bgzip?(obj)
|
40
38
|
CMD.cmd("wc -l '#{obj}'").read.to_i
|
41
39
|
else
|
42
40
|
nil
|
43
41
|
end
|
44
42
|
end
|
45
43
|
rescue Exception
|
44
|
+
Log.exception $!
|
46
45
|
nil
|
47
46
|
end
|
48
47
|
end
|
data/lib/rbbt/util/misc/omics.rb
CHANGED
@@ -197,16 +197,35 @@ module Misc
|
|
197
197
|
line = io.gets.strip
|
198
198
|
parts = line.split(sep)
|
199
199
|
chr, start, eend, *rest = parts
|
200
|
-
|
200
|
+
start = start.to_i
|
201
|
+
if eend =~ /^\d+$/
|
202
|
+
eend = eend.to_i
|
203
|
+
else
|
204
|
+
eend = start.to_i
|
205
|
+
end
|
206
|
+
[line,chr, start, eend, rest]
|
207
|
+
end
|
208
|
+
|
209
|
+
def self.intersect_streams_cmp_chr(chr1, chr2)
|
210
|
+
return chr1 <=> chr2
|
211
|
+
if chr1 =~ /^\d+$/ and chr2 =~ /^\d+$/
|
212
|
+
chr1 <=> chr2
|
213
|
+
elsif chr1 =~ /^\d+$/
|
214
|
+
-1
|
215
|
+
elsif chr2 =~ /^\d+$/
|
216
|
+
1
|
217
|
+
else
|
218
|
+
chr1 <=> chr2
|
219
|
+
end
|
201
220
|
end
|
202
221
|
|
203
222
|
def self.intersect_streams(f1, f2, out, sep=":")
|
204
223
|
finish = false
|
205
224
|
line1, chr1, start1, eend1, rest1 = intersect_streams_read(f1,sep)
|
206
225
|
line2, chr2, start2, eend2, rest2 = intersect_streams_read(f2,sep)
|
207
|
-
Misc.profile do
|
208
226
|
while not finish
|
209
|
-
|
227
|
+
cmp = intersect_streams_cmp_chr(chr1,chr2)
|
228
|
+
case cmp
|
210
229
|
when -1
|
211
230
|
move = 1
|
212
231
|
when 1
|
@@ -249,6 +268,11 @@ module Misc
|
|
249
268
|
end
|
250
269
|
end
|
251
270
|
end
|
271
|
+
end
|
272
|
+
|
273
|
+
def self.select_ranges(stream1, stream2, sep = "\t")
|
274
|
+
Misc.open_pipe do |sin|
|
275
|
+
intersect_streams(stream1, stream2,sin, sep)
|
252
276
|
end
|
253
277
|
end
|
254
278
|
end
|