# HG changeset patch
# User saket-choudhary
# Date 1412723951 14400
# Node ID 697e66764209fe37b8bfac1ef442e53b96464b5e
# Parent 5cc3210369ac73ec881091ae0aa4998e5aa45922
Uploaded
diff -r 5cc3210369ac -r 697e66764209 sift_web/sift_web.py
--- a/sift_web/sift_web.py Thu Sep 04 17:46:51 2014 -0400
+++ b/sift_web/sift_web.py Tue Oct 07 19:19:11 2014 -0400
@@ -15,26 +15,7 @@
def retry(ExceptionToCheck, tries=10, delay=3, backoff=2, logger=None):
- """Retry calling the decorated function using an exponential backoff.
-
- http://www.saltycrane.com/blog/2009/11/trying-out-retry-decorator-python/
- original from: http://wiki.python.org/moin/PythonDecoratorLibrary#Retry
-
- :param ExceptionToCheck: the exception to check. may be a tuple of
- exceptions to check
- :type ExceptionToCheck: Exception or tuple
- :param tries: number of times to try (not retry) before giving up
- :type tries: int
- :param delay: initial delay between retries in seconds
- :type delay: int
- :param backoff: backoff multiplier e.g. value of 2 will double the delay
- each retry
- :type backoff: int
- :param logger: logger to use. If None, print
- :type logger: logging.Logger instance
- """
def deco_retry(f):
-
@wraps(f)
def f_retry(*args, **kwargs):
mtries, mdelay = tries, delay
@@ -53,9 +34,7 @@
mtries -= 1
mdelay *= backoff
return f(*args, **kwargs)
-
return f_retry # true decorator
-
return deco_retry
@@ -68,6 +47,7 @@
self.url_dict = {'full': self.full_download_url,
'condensed': self.condensed_download_url,
'summary': self.summary_download_url}
+ self.job_id = None
def upload(self, inputpath):
payload = {'table': 'human37_66'}
@@ -77,19 +57,19 @@
return request.text
@retry(requests.exceptions.HTTPError)
- def get_full_data(self, job_id, full_output):
+ def get_full_data(self, full_output):
r = requests.request(
- 'GET', (self.full_download_url) % (job_id, job_id))
+ 'GET', (self.full_download_url) % (self.job_id, self.job_id))
if r.text != 'No file exists':
with open(full_output, 'wb') as f:
f.write(r.text)
else:
- return requests.HTTPError()
+ raise(requests.HTTPError())
@retry(requests.exceptions.HTTPError)
- def get_condensed_data(self, job_id, condensed_output):
+ def get_condensed_data(self, condensed_output):
r = requests.request(
- 'GET', (self.condensed_download_url) % (job_id, job_id))
+ 'GET', (self.condensed_download_url) % (self.job_id, self.job_id))
if r.text != 'No file exists':
with open(condensed_output, 'wb') as f:
f.write(r.text)
@@ -97,9 +77,9 @@
raise(requests.HTTPError())
@retry(requests.exceptions.HTTPError)
- def get_summary_data(self, job_id, summary_output):
+ def get_summary_data(self, summary_output):
r = requests.request(
- 'GET', (self.summary_download_url) % (job_id, job_id))
+ 'GET', (self.summary_download_url) % (self.job_id, self.job_id))
if r.text != 'No file exists':
with open(summary_output, 'wb') as f:
f.write(r.text)
@@ -119,9 +99,10 @@
soup = BeautifulSoup(content)
p = soup.findAll('p')
job_id = p[1].string.split(':')[-1].replace(' ', '').replace(').', '')
- sift_web.get_full_data(job_id, args.output1)
- sift_web.get_condensed_data(job_id, args.output2)
- sift_web.get_summary_data(job_id, args.output3)
+ sift_web.job_id = job_id
+ sift_web.get_full_data(args.output1)
+ sift_web.get_condensed_data(args.output2)
+ sift_web.get_summary_data(args.output3)
if __name__ == '__main__':
diff -r 5cc3210369ac -r 697e66764209 sift_web/sift_web.xml
--- a/sift_web/sift_web.xml Thu Sep 04 17:46:51 2014 -0400
+++ b/sift_web/sift_web.xml Tue Oct 07 19:19:11 2014 -0400
@@ -13,9 +13,17 @@
-
-
-
+
+
+
+
+
+
+
+
+
+
+
diff -r 5cc3210369ac -r 697e66764209 sift_web/test-data/sift_input.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sift_web/test-data/sift_input.txt Tue Oct 07 19:19:11 2014 -0400
@@ -0,0 +1,14 @@
+1,100382265,C,G,user comment 1
+1,100380997,A,G,user comment 2
+22,30163533,A,C
+X,12905093,A,T
+2,230633386,G,C
+1,100382265,C,A
+7,117199641,ATCA,.
+7,117199647,TTT,.
+10,50184923,TGG,.
+12,121438957,ACC,.
+1,43217995,G,GCCA
+10,102762472,G,GGCG
+9,117856130,T,G
+9,117856135,C,G
diff -r 5cc3210369ac -r 697e66764209 sift_web/test-data/sift_output_condensed.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sift_web/test-data/sift_output_condensed.tsv Tue Oct 07 19:19:11 2014 -0400
@@ -0,0 +1,15 @@
+#ROW_NO. INPUT PROTEIN_ID LENGTH STRAND CODON_CHANGE POS RESIDUE_REF RESIDUE_ALT TYPE SCORE PREDICTION (cutoff=-2.5) #SEQ #CLUSTER SCORE PREDICTION (cutoff=0.05) MEDIAN_INFO #SEQ dbSNP_ID
+1 1,100382265,C,G,user comment 1 ENSP00000294724 1532 1 TCC [C/G]GA CAT 1487 R G Single AA Change -1.75 Neutral 107 30 0.118 Tolerated 2.82 71 rs12118058
+2 1,100380997,A,G,user comment 2 ENSP00000294724 1532 1 GCA G[A/G]A AAA 1405 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.80 72 rs28730708
+3 22,30163533,A,C ENSP00000333278 132 1 ACG [A/C]GG GGA 49 R R Synonymous 0.00 Neutral 3 1 NA NA NA NA
+4 X,12905093,A,T ENSP00000370034 1049 1 AAT G[A/T]A AGC 489 E V Single AA Change -1.99 Neutral 265 30 0.044 Damaging 2.87 154
+5 2,230633386,G,C ENSP00000373696 2040 -1 GAG [C/G]AG CAG 1958 Q E Single AA Change 0.46 Neutral 127 30 0.602 Tolerated 2.89 136
+6 1,100382265,C,A ENSP00000294724 1532 1 TCC [C/A]GA CAT 1487 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.82 71
+7 7,117199641,ATCA,. ENSP00000003084 1480 1 Frameshift NA NA 273 30 NA NA NA NA
+8 7,117199647,TTT,. ENSP00000003084 1480 1 ATC [TTT/-] GGT 508 F . Deletion -13.79 Deleterious 273 30 NA NA NA NA rs121909001
+9 10,50184923,TGG,. ENSP00000320563 3184 1 GCC [TGG/-] GGC 3064 W . Deletion -6.39 Deleterious 101 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000443112 662 1 GAG [ACC/-] TTC 651 T . Deletion -3.66 Deleterious 158 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000236040 804 -1 CCA [-/TGG] CAT 506 P PW Insertion -9.11 Deleterious 157 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000359240 669 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.26 Deleterious 136 30 NA NA NA NA
+13 9,117856130,T,G record not found rs1513
+14 9,117856135,C,G record not found
diff -r 5cc3210369ac -r 697e66764209 sift_web/test-data/sift_output_full.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sift_web/test-data/sift_output_full.tsv Tue Oct 07 19:19:11 2014 -0400
@@ -0,0 +1,63 @@
+#ROW_NO. INPUT PROTEIN_ID LENGTH STRAND CODON_CHANGE POS RESIDUE_REF RESIDUE_ALT TYPE SCORE PREDICTION (cutoff=-2.5) #SEQ #CLUSTER SCORE PREDICTION (cutoff=0.05) MEDIAN_INFO #SEQ dbSNP_ID
+1 1,100382265,C,G,user comment 1 ENSP00000294724 1532 1 TCC [C/G]GA CAT 1487 R G Single AA Change -1.75 Neutral 107 30 0.118 Tolerated 2.82 71 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000354635 1515 1 TCC [C/G]GA CAT 1470 R G Single AA Change -1.75 Neutral 107 30 0.114 Tolerated 2.84 71 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000354971 1516 1 TCC [C/G]GA CAT 1471 R G Single AA Change -1.75 Neutral 107 30 0.108 Tolerated 2.83 73 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000355106 1532 1 TCC [C/G]GA CAT 1487 R G Single AA Change -1.75 Neutral 107 30 0.118 Tolerated 2.82 71 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000359180 1516 1 TCC [C/G]GA CAT 1471 R G Single AA Change -1.75 Neutral 107 30 0.108 Tolerated 2.83 73 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000359182 1532 1 TCC [C/G]GA CAT 1487 R G Single AA Change -1.75 Neutral 107 30 0.118 Tolerated 2.82 71 rs12118058
+1 1,100382265,C,G,user comment 1 ENSP00000359184 1532 1 TCC [C/G]GA CAT 1487 R G Single AA Change -1.75 Neutral 107 30 0.118 Tolerated 2.82 71 rs12118058
+2 1,100380997,A,G,user comment 2 ENSP00000294724 1532 1 GCA G[A/G]A AAA 1405 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.80 72 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000354635 1515 1 GCA G[A/G]A AAA 1388 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.82 72 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000354971 1516 1 GCA G[A/G]A AAA 1389 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.81 74 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000355106 1532 1 GCA G[A/G]A AAA 1405 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.80 72 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000359180 1516 1 GCA G[A/G]A AAA 1389 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.81 74 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000359182 1532 1 GCA G[A/G]A AAA 1405 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.80 72 rs28730708
+2 1,100380997,A,G,user comment 2 ENSP00000359184 1532 1 GCA G[A/G]A AAA 1405 E G Single AA Change -4.58 Deleterious 107 30 0.004 Damaging 2.80 72 rs28730708
+3 22,30163533,A,C ENSP00000332887 63 1 AAC G[A/C]G GGG 49 E A Single AA Change -3.11 Deleterious 87 30 0.020 Damaging 2.79 85
+3 22,30163533,A,C ENSP00000333278 132 1 ACG [A/C]GG GGA 49 R R Synonymous 0.00 Neutral 3 1 NA NA NA NA
+3 22,30163533,A,C ENSP00000384962 62 1 AAC G[A/C]G GGG 49 E A Single AA Change -3.05 Deleterious 85 30 0.057 Tolerated 3.02 57
+3 22,30163533,A,C ENSP00000385696 82 1 AAC G[A/C]G GGG 49 E A Single AA Change -3.00 Deleterious 88 30 0.036 Damaging 3.07 83
+4 X,12905093,A,T ENSP00000370034 1049 1 AAT G[A/T]A AGC 489 E V Single AA Change -1.99 Neutral 265 30 0.044 Damaging 2.87 154
+5 2,230633386,G,C ENSP00000283943 1992 -1 GAG [C/G]AG CAG 1910 Q E Single AA Change 0.46 Neutral 127 30 0.811 Tolerated 2.90 99
+5 2,230633386,G,C ENSP00000373696 2040 -1 GAG [C/G]AG CAG 1958 Q E Single AA Change 0.46 Neutral 127 30 0.602 Tolerated 2.89 136
+5 2,230633386,G,C ENSP00000373697 1722 -1 GAG [C/G]AG CAG 1640 Q E Single AA Change 0.33 Neutral 129 30 1.000 Tolerated 2.96 95
+5 2,230633386,G,C ENSP00000408330 187 -1 GAG [C/G]AG CAG 170 Q E Single AA Change 0.86 Neutral 120 30 1.000 Tolerated 2.82 62
+6 1,100382265,C,A ENSP00000294724 1532 1 TCC [C/A]GA CAT 1487 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.82 71
+6 1,100382265,C,A ENSP00000354635 1515 1 TCC [C/A]GA CAT 1470 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.84 71
+6 1,100382265,C,A ENSP00000354971 1516 1 TCC [C/A]GA CAT 1471 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.83 73
+6 1,100382265,C,A ENSP00000355106 1532 1 TCC [C/A]GA CAT 1487 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.82 71
+6 1,100382265,C,A ENSP00000359180 1516 1 TCC [C/A]GA CAT 1471 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.83 73
+6 1,100382265,C,A ENSP00000359182 1532 1 TCC [C/A]GA CAT 1487 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.82 71
+6 1,100382265,C,A ENSP00000359184 1532 1 TCC [C/A]GA CAT 1487 R R Synonymous 0.00 Neutral 107 30 1.000 Tolerated 2.82 71
+7 7,117199641,ATCA,. ENSP00000003084 1480 1 Frameshift NA NA 273 30 NA NA NA NA
+7 7,117199641,ATCA,. ENSP00000389119 1438 1 Frameshift NA NA 273 30 NA NA NA NA
+7 7,117199641,ATCA,. ENSP00000403677 1419 1 Frameshift NA NA 275 30 NA NA NA NA
+8 7,117199647,TTT,. ENSP00000003084 1480 1 ATC [TTT/-] GGT 508 F . Deletion -13.79 Deleterious 273 30 NA NA NA NA rs121909001
+8 7,117199647,TTT,. ENSP00000389119 1438 1 ATC [TTT/-] GGT 478 F . Deletion -13.79 Deleterious 273 30 NA NA NA NA rs121909001
+8 7,117199647,TTT,. ENSP00000403677 1419 1 ATC [TTT/-] GGT 447 F . Deletion -14.12 Deleterious 275 30 NA NA NA NA rs121909001
+9 10,50184923,TGG,. ENSP00000265453 1271 1 GCC [TGG/-] GGC 1151 W . Deletion -8.05 Deleterious 103 30 NA NA NA NA
+9 10,50184923,TGG,. ENSP00000309314 2267 1 GCC [TGG/-] GGC 2155 W . Deletion -7.09 Deleterious 103 30 NA NA NA NA
+9 10,50184923,TGG,. ENSP00000320563 3184 1 GCC [TGG/-] GGC 3064 W . Deletion -6.39 Deleterious 101 30 NA NA NA NA
+9 10,50184923,TGG,. ENSP00000409696 3176 1 GCC [TGG/-] GGC 3064 W . Deletion -6.39 Deleterious 101 30 NA NA NA NA
+9 10,50184923,TGG,. ENSP00000443499 624 1 GCC [TGG/-] GGC 527 W . Deletion -8.09 Deleterious 110 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000257555 631 1 GAG [ACC/-] TTC 620 T . Deletion -3.40 Deleterious 159 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000339938 572 1 GAG [ACC/-] TTC 561 T . Deletion -3.47 Deleterious 163 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000342683 521 1 GAG [ACC/-] TTC 510 T . Deletion -2.88 Deleterious 164 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000438300 523 1 GAG [ACC/-] TTC 512 T . Deletion -3.05 Deleterious 164 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000438531 452 1 GAG [ACC/-] TTC 441 T . Deletion -3.49 Deleterious 165 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000438804 638 1 GAG [ACC/-] TTC 627 T . Deletion -3.40 Deleterious 159 30 NA NA NA NA
+10 12,121438957,ACC,. ENSP00000443112 662 1 GAG [ACC/-] TTC 651 T . Deletion -3.66 Deleterious 158 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000236040 804 -1 CCA [-/TGG] CAT 506 P PW Insertion -9.11 Deleterious 157 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000296388 736 -1 CCA [-/TGG] CAT 506 P PW Insertion -9.11 Deleterious 158 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000380245 697 -1 CCA [-/TGG] CAT 506 P PW Insertion -9.14 Deleterious 160 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000394294 152 -1 CCA [-/TGG] CAT 98 P PW Insertion -9.13 Deleterious 153 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000408056 222 -1 CCA [-/TGG] CAT 114 P PW Insertion -9.17 Deleterious 153 30 NA NA NA NA
+11 1,43217995,G,GCCA ENSP00000437795 601 -1 CCA [-/TGG] CAT 371 P PW Insertion -8.74 Deleterious 162 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000314437 631 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.15 Deleterious 137 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000359240 669 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.26 Deleterious 136 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000359243 669 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.26 Deleterious 136 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000402042 199 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.83 Deleterious 101 27 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000407713 240 1 CAG [-/GCG] GAT 59 Q QA Insertion -3.24 Deleterious 113 30 NA NA NA NA
+12 10,102762472,G,GGCG ENSP00000416972 221 1 CAG [-/GCG] GAT 59 Q QA Insertion -4.09 Deleterious 97 26 NA NA NA NA
+13 9,117856130,T,G record not found rs1513
+14 9,117856135,C,G record not found
diff -r 5cc3210369ac -r 697e66764209 sift_web/test-data/sift_output_summary.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sift_web/test-data/sift_output_summary.tsv Tue Oct 07 19:19:11 2014 -0400
@@ -0,0 +1,13 @@
+#Type Total Found_in_dbSNP Not_found_in_dbSNP PROVEAN_neutral PROVEAN_deleterious PROVEAN_NA SIFT_tolerated SIFT_damaging SIFT_NA
+Protein_coding 12 3 9 5 6 1 3 2 7
+Single_AA_Change 4 2 2 3 1 0 2 2 0
+Synonymous 2 0 2 2 0 0 1 0 1
+Deletion 3 1 2 0 3 0 0 0 3
+Insertion 2 0 2 0 2 0 0 0 2
+Multiple_AA_Change 0 0 0 0 0 0 0 0 0
+Frameshift 1 0 1 0 0 1 0 0 1
+Nonsense 0 0 0 0 0 0 0 0 0
+Unknown 0 0 0 0 0 0 0 0 0
+Input_error 0 0 0 0 0 0 0 0 0
+Non_protein_coding 2 1 1 0 0 2 0 0 2
+Input_format_error 0 0 0 0 0 0 0 0 0