more ws tests

ws-tests/entrez_webquery.py

@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Oct 23 09:49:13 2018
+
+@author: Martha Kandziora
+"""
+
+
+### Error message
+#  File "/home/mkandziora/physcrape_web_dev/physcraper/physcraper/wrappers.py", line 560, in filter_data_run
+#    filteredScrape.run_blast(delay=14)
+#  File "/home/mkandziora/physcrape_web_dev/physcraper/physcraper/__init__.py", line 1930, in run_blast
+#    self.run_web_blast_query(query, equery, fn_path)
+#  File "/home/mkandziora/physcrape_web_dev/physcraper/physcraper/__init__.py", line 1831, in run_web_blast_query
+#    hitlist_size=self.config.hitlist_size)
+#  File "/home/mkandziora/physcrape_web_dev/physcraper/physcraper/AWSWWW.py", line 142, in qblast
+#    handle = _urlopen(request)
+#  File "/usr/lib64/python2.7/urllib2.py", line 154, in urlopen
+#    return opener.open(url, data, timeout)
+#  File "/usr/lib64/python2.7/urllib2.py", line 431, in open
+#    response = self._open(req, data)
+#  File "/usr/lib64/python2.7/urllib2.py", line 449, in _open
+#    '_open', req)
+#  File "/usr/lib64/python2.7/urllib2.py", line 409, in _call_chain
+#    result = func(*args)
+#  File "/usr/lib64/python2.7/urllib2.py", line 1258, in https_open
+#    context=self._context, check_hostname=self._check_hostname)
+#  File "/usr/lib64/python2.7/urllib2.py", line 1214, in do_open
+#    raise URLError(err)
+#urllib2.URLError: <urlopen error [Errno -2] Name or service not known>
+
+## from printing statements
+#use BLAST webservice
+#TCGAAACCTGCATAGCAGAACGACCCGTGAACATGTAACAACAACCGGGTGTCCTTGGTATCGGACTCTTGTCTGATTCTTTGGATGCCTCGTCGATGTGCGTCTTTGGCCTGCCCCTTGGGTTCCAATTACGTCACGTTGGCACAACAACAACCCCCCGGCACGGCATGTGCCAAGGAAATTTAAACATAAGAAGGGCTCGTACCATGCATCCCCGTTCGCGGGGTTTGCGTGGGATGTGGCTTCTTTATAATCACAAACGACTCTCGGCAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTTTGGTCGAGGGCACGTCTGTCTGGGCGTCACACATCGCGTCGCCCCCACCATTCCTCTCTGATCGGGATGATGGGAAGGGGGCGGATATTGGTCTCCCGTTCCTACGGTGCGGTTGGCTAAAATAGGAGTCCCCTTCGACGGACGCACGACTAGTGGTGGTTGACAAGACCCTCTTATCGAGTCGTGCGTTCTAAGGAGTAAGGAAGATCTCTTAAAAAACCC
+#txid102812[orgn] AND 1900/01/01:2018/10/23[mdat]
+#5000
+
+import physcraper.AWSWWW as AWSWWW
+
+
+query = "TCGAAACCTGCATAGCAGAACGACCCGTGAACATGTAACAACAACCGGGTGTCCTTGGTATCGGACTCTTGTCTGATTCTTTGGATGCCTCGTCGATGTGCGTCTTTGGCCTGCCCCTTGGGTTCCAATTACGTCACGTTGGCACAACAACAACCCCCCGGCACGGCATGTGCCAAGGAAATTTAAACATAAGAAGGGCTCGTACCATGCATCCCCGTTCGCGGGGTTTGCGTGGGATGTGGCTTCTTTATAATCACAAACGACTCTCGGCAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTTTGGTCGAGGGCACGTCTGTCTGGGCGTCACACATCGCGTCGCCCCCACCATTCCTCTCTGATCGGGATGATGGGAAGGGGGCGGATATTGGTCTCCCGTTCCTACGGTGCGGTTGGCTAAAATAGGAGTCCCCTTCGACGGACGCACGACTAGTGGTGGTTGACAAGACCCTCTTATCGAGTCGTGCGTTCTAAGGAGTAAGGAAGATCTCTTAAAAAACCC"
+equery = "txid102812[orgn]"
+
+result_handle = AWSWWW.qblast("blastn",
+                              "nt",
+                              query,
+                              entrez_query=equery,
+                              hitlist_size=50)
+
+
+tmp = result_handle.read()
+result_handle.close()
+
+

ws-tests/textncbiblast.py

@@ -0,0 +1,32 @@
+import sys
+import physcraper.AWSWWW as AWSWWW
+import datetime
+
+start = datetime.datetime.now()
+sys.stderr.write("running a blast query against NCBI START {}".format(start))
+
+
+query="ATATCAATAAGCGGAGGAAAAGAAACCAACAGGGATTGCCTCAGTAACGGCGAGTGAAGCGGCAACAGCTCAAATTTGAAATCTGGCCCTAGGCCCGAGTTGTAATTTGCAGAGGATGCTTCCGGTGCGGCGCCGTCCAAGTCCCCTGGAACGGGGTGCCACAGAGGGTGAGAGCCCCGTCGGGTCGGCCGCCAAGCCTATGTGAAGCTCCTTCGACGAGTCGAGTAGTTTGGGAATGCTGCTCTAAATGGGAGGTAGACCCCTTCTAAAGCTAAATATTGGCCAGAGACCGATAGCGCACAAGTAGAGTGATCGAAAGATGAAAAGCACTTTGAAAAGAGGGTTAAACAGTACGTGAAATTGTTGAAAGGGAAGCGCTTGTGACCAGACGTGCGCCGGGTGTTCAGCGGGCGTTCTCGCCCGTCTACTCGCCCTGGCGCAGGCCAGCGTCGGTTCGGATGGGTGGACAAAGGTACCAGGAACGTGGCTCCCTCGGGAGTGTTATAGCCTGGTGCGTCATGCCCCCGTCCGGACCGAGGTTCGCGCTCTGCAAGGACGCTGGCGTAATGGTCCCCAGCGGCCCGTCTTGAAACACGGACCAAGGAGTCGAGGTTTTGTGCGAGTGTCTGGGTGTCAAACCCGCACGCGTAATGAAAGTGAACGCAGGTGGGAGCTTCGGCGCACCACCGACCGATCCTGAAGTTTTCGGATGGATTTGAGTAAGAGCATAGGGCCTCGGACCCGAAAGATGGTGAACTATACTTGGATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGCAGCGGTTCTGACGTGCAAATCGATCGTCAAATCTGAGTATGGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTACCGCCGAAGTTTCCCTCAGGATAG"
+result_handle = AWSWWW.qblast("blastn",
+                               "nt",
+                               query,
+                               hitlist_size=2)
+
+
+end = datetime.datetime.now()
+sys.stderr.write("END time {}".format(end))
+result_handle.close()
+
+
+ncbi_id = 147538
+equery = equery + "txid{}[orgn]) ".format(ncbi_id)
+
+
+
+result_handle = AWSWWW.qblast("blastn",
+                            "nt",
+                            query,
+                            url_base=self.config.url_base,
+                            entrez_query=equery,
+                            hitlist_size=self.config.hitlist_size,
+                            num_threads=self.config.num_threads)