annotate fetch_fasta_from_NCBI.py @ 3:8be88084f89c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
author artbio
date Wed, 08 Nov 2017 13:00:26 -0500
parents 50f5ef3313bb
children c667d0ee39f5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
1 #!/usr/bin/env python
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
2 # -*- coding: utf-8 -*-
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
3 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
4 From a taxonomy ID retrieves all the nucleotide sequences
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
5 It returns a multiFASTA nuc/prot file
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
6
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
7 Entrez Database UID common name E-utility Database Name
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
8 Nucleotide GI number nuccore
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
9 Protein GI number protein
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
10
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
11 Retrieve strategy:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
12
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
13 esearch to get total number of UIDs (count)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
14 esearch to get UIDs in batches
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
15 loop untile end of UIDs list:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
16 epost to put a batch of UIDs in the history server
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
17 efetch to retrieve info from previous post
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
18
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
19 retmax of efetch is 1/10 of declared value from NCBI
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
20
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
21 queries are 1 sec delayed, to satisfy NCBI guidelines
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
22 (more than what they request)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
23 """
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
24 import argparse
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
25 import httplib
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
26 import logging
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
27 import re
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
28 import sys
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
29 import time
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
30 import urllib
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
31 import urllib2
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
32
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
33
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
34 class QueryException(Exception):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
35 pass
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
36
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
37
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
38 class Eutils:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
39
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
40 def __init__(self, options, logger):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
41 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
42 Initialize retrieval parameters
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
43 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
44 self.logger = logger
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
45 self.base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
46 self.query_string = options.query_string
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
47 self.dbname = options.dbname
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
48 if options.outname:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
49 self.outname = options.outname
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
50 else:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
51 self.outname = 'NCBI_download' + '.' + self.dbname + '.fasta'
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
52 self.ids = []
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
53 self.retmax_esearch = 100000
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
54 self.retmax_efetch = 500
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
55 self.count = 0
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
56 self.webenv = ""
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
57 self.query_key = ""
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
58
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
59 def dry_run(self):
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
60 self.get_count_value()
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
61
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
62 def retrieve(self):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
63 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
64 Retrieve the fasta sequences corresponding to the query
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
65 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
66 self.get_count_value()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
67 # If no UIDs are found exit script
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
68 if self.count > 0:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
69 self.get_uids_list()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
70 try:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
71 self.get_sequences()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
72 except QueryException as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
73 self.logger.error("Exiting script.")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
74 raise e
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
75 else:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
76 self.logger.error("No UIDs were found. Exiting script.")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
77 raise Exception("")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
78
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
79 def get_count_value(self):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
80 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
81 just to retrieve Count (number of UIDs)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
82 Total number of UIDs from the retrieved set to be shown in the XML
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
83 output (default=20). By default, ESearch only includes the first 20
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
84 UIDs retrieved in the XML output. If usehistory is set to 'y',
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
85 the remainder of the retrieved set will be stored on the History server
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
86
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
87 http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
88 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
89 self.logger.info("retrieving data from %s" % self.base)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
90 self.logger.info("for Query: %s and database: %s" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
91 (self.query_string, self.dbname))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
92 querylog = self.esearch(self.dbname, self.query_string, '', '',
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
93 "count")
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
94 self.logger.debug("Query response:")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
95 for line in querylog:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
96 self.logger.debug(line.rstrip())
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
97 if '</Count>' in line:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
98 self.count = int(line[line.find('<Count>')+len('<Count>'):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
99 line.find('</Count>')])
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
100 self.logger.info("Found %d UIDs" % self.count)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
101
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
102 def get_uids_list(self):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
103 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
104 Increasing retmax allows more of the retrieved UIDs to be included in
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
105 the XML output, up to a maximum of 100,000 records.
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
106 from http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
107 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
108 retmax = self.retmax_esearch
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
109 if (self.count > retmax):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
110 num_batches = (self.count / retmax) + 1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
111 else:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
112 num_batches = 1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
113 self.logger.info("Batch size for esearch action: %d UIDs" % retmax)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
114 self.logger.info("Number of batches for esearch action: %d " %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
115 num_batches)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
116 for n in range(num_batches):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
117 querylog = self.esearch(self.dbname, self.query_string, n*retmax,
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
118 retmax, '')
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
119 for line in querylog:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
120 if '<Id>' in line and '</Id>' in line:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
121 uid = (line[line.find('<Id>')+len('<Id>'):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
122 line.find('</Id>')])
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
123 self.ids.append(uid)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
124 self.logger.info("Retrieved %d UIDs" % len(self.ids))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
125
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
126 def esearch(self, db, term, retstart, retmax, rettype):
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
127 url = self.base + "esearch.fcgi"
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
128 self.logger.debug("url: %s" % url)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
129 values = {'db': db,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
130 'term': term,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
131 'rettype': rettype,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
132 'retstart': retstart,
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
133 'retmax': retmax}
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
134 data = urllib.urlencode(values)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
135 self.logger.debug("data: %s" % str(data))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
136 req = urllib2.Request(url, data)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
137 response = urllib2.urlopen(req)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
138 querylog = response.readlines()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
139 response.close()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
140 time.sleep(1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
141 return querylog
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
142
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
143 def epost(self, db, ids):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
144 url = self.base + "epost.fcgi"
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
145 self.logger.debug("url_epost: %s" % url)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
146 values = {'db': db,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
147 'id': ids}
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
148 data = urllib.urlencode(values)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
149 req = urllib2.Request(url, data)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
150 serverResponse = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
151 nb_trials = 0
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
152 while not serverResponse:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
153 nb_trials += 1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
154 try:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
155 self.logger.debug("Try number %s for opening and readin URL %s"
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
156 % (nb_trials, url+data))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
157 response = urllib2.urlopen(req)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
158 querylog = response.readlines()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
159 response.close()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
160 serverResponse = True
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
161 except urllib2.HTTPError as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
162 self.logger.info("urlopen error:%s, %s" % (e.code, e.read()))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
163 self.logger.info("Retrying in 1 sec")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
164 serverResponse = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
165 time.sleep(1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
166 except urllib2.URLError as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
167 self.logger.info("urlopen error: Failed to reach a server")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
168 self.logger.info("Reason :%s" % (e.reason))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
169 self.logger.info("Retrying in 1 sec")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
170 serverResponse = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
171 time.sleep(1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
172 except httplib.IncompleteRead as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
173 self.logger.info("IncompleteRead error: %s" % (e.partial))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
174 self.logger.info("Retrying in 1 sec")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
175 serverResponse = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
176 time.sleep(1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
177 self.logger.debug("query response:")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
178 for line in querylog:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
179 self.logger.debug(line.rstrip())
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
180 if '</QueryKey>' in line:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
181 self.query_key = str(line[line.find('<QueryKey>') +
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
182 len('<QueryKey>'):line.find('</QueryKey>')
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
183 ])
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
184 if '</WebEnv>' in line:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
185 self.webenv = str(line[line.find('<WebEnv>')+len('<WebEnv>'):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
186 line.find('</WebEnv>')])
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
187 self.logger.debug("*** epost action ***")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
188 self.logger.debug("query_key: %s" % self.query_key)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
189 self.logger.debug("webenv: %s" % self.webenv)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
190 time.sleep(1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
191
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
192 def efetch(self, db, query_key, webenv):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
193 url = self.base + "efetch.fcgi"
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
194 self.logger.debug("url_efetch: %s" % url)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
195 values = {'db': db,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
196 'query_key': query_key,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
197 'webenv': webenv,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
198 'rettype': "fasta",
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
199 'retmode': "text"}
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
200 data = urllib.urlencode(values)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
201 req = urllib2.Request(url, data)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
202 self.logger.debug("data: %s" % str(data))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
203 serverTransaction = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
204 counter = 0
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
205 response_code = 0
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
206 while not serverTransaction:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
207 counter += 1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
208 self.logger.info("Server Transaction Trial: %s" % (counter))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
209 try:
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
210 self.logger.debug("Going to open")
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
211 response = urllib2.urlopen(req)
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
212 self.logger.debug("Going to get code")
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
213 response_code = response.getcode()
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
214 self.logger.debug("Going to read, de code was : %s",
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
215 str(response_code))
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
216 fasta = response.read()
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
217 self.logger.debug("Did all that")
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
218 response.close()
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
219 if((response_code != 200) or
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
220 ("Resource temporarily unavailable" in fasta) or
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
221 ("Error" in fasta) or (not fasta.startswith(">"))):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
222 serverTransaction = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
223 if (response_code != 200):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
224 self.logger.info("urlopen error: Response code is not\
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
225 200")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
226 elif ("Resource temporarily unavailable" in fasta):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
227 self.logger.info("Ressource temporarily unavailable")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
228 elif ("Error" in fasta):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
229 self.logger.info("Error in fasta")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
230 else:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
231 self.logger.info("Fasta doesn't start with '>'")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
232 else:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
233 serverTransaction = True
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
234 except urllib2.HTTPError as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
235 serverTransaction = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
236 self.logger.info("urlopen error:%s, %s" % (e.code, e.read()))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
237 except urllib2.URLError as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
238 serverTransaction = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
239 self.logger.info("urlopen error: Failed to reach a server")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
240 self.logger.info("Reason :%s" % (e.reason))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
241 except httplib.IncompleteRead as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
242 serverTransaction = False
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
243 self.logger.info("IncompleteRead error: %s" % (e.partial))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
244 if (counter > 500):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
245 serverTransaction = True
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
246 if (counter > 500):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
247 raise QueryException({"message":
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
248 "500 Server Transaction Trials attempted for\
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
249 this batch. Aborting."})
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
250 fasta = self.sanitiser(self.dbname, fasta)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
251 time.sleep(0.1)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
252 return fasta
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
253
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
254 def sanitiser(self, db, fastaseq):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
255 if(db not in "nuccore protein"):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
256 return fastaseq
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
257 regex = re.compile(r"[ACDEFGHIKLMNPQRSTVWYBZ]{49,}")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
258 sane_seqlist = []
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
259 seqlist = fastaseq.split("\n\n")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
260 for seq in seqlist[:-1]:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
261 fastalines = seq.split("\n")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
262 if len(fastalines) < 2:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
263 self.logger.info("Empty sequence for %s" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
264 ("|".join(fastalines[0].split("|")[:4])))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
265 self.logger.info("%s download is skipped" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
266 ("|".join(fastalines[0].split("|")[:4])))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
267 continue
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
268 if db == "nuccore":
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
269 badnuc = 0
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
270 for nucleotide in fastalines[1]:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
271 if nucleotide not in "ATGC":
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
272 badnuc += 1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
273 if float(badnuc)/len(fastalines[1]) > 0.4:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
274 self.logger.info("%s ambiguous nucleotides in %s\
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
275 or download interrupted at this offset\
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
276 | %s" % (float(badnuc)/len(fastalines[1]),
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
277 "|".join(fastalines[0].split("|")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
278 [:4]),
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
279 fastalines[1]))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
280 self.logger.info("%s download is skipped" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
281 (fastalines[0].split("|")[:4]))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
282 continue
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
283 """ remove spaces and trim the header to 100 chars """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
284 fastalines[0] = fastalines[0].replace(" ", "_")[:100]
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
285 cleanseq = "\n".join(fastalines)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
286 sane_seqlist.append(cleanseq)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
287 elif db == "protein":
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
288 fastalines[0] = fastalines[0][0:100]
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
289 fastalines[0] = fastalines[0].replace(" ", "_")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
290 fastalines[0] = fastalines[0].replace("[", "_")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
291 fastalines[0] = fastalines[0].replace("]", "_")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
292 fastalines[0] = fastalines[0].replace("=", "_")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
293 """ because blast makedb doesn't like it """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
294 fastalines[0] = fastalines[0].rstrip("_")
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
295 fastalines[0] = re.sub(regex, "_", fastalines[0])
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
296 cleanseq = "\n".join(fastalines)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
297 sane_seqlist.append(cleanseq)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
298 self.logger.info("clean sequences appended: %d" % (len(sane_seqlist)))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
299 return "\n".join(sane_seqlist)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
300
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
301 def get_sequences(self):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
302 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
303 Total number of records from the input set to be retrieved,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
304 up to a maximum of 10,000. Optionally, for a large set the value of
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
305 retstart can be iterated while holding retmax constant, thereby
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
306 downloading the entire set in batches of size retmax.
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
307 http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
308 """
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
309 batch_size = self.retmax_efetch
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
310 count = self.count
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
311 uids_list = self.ids
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
312 self.logger.info("Batch size for efetch action: %d" % batch_size)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
313 self.logger.info("Number of batches for efetch action: %d" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
314 ((count / batch_size) + 1))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
315 with open(self.outname, 'w') as out:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
316 for start in range(0, count, batch_size):
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
317 end = min(count, start+batch_size)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
318 batch = uids_list[start:end]
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
319 if self.epost(self.dbname, ",".join(batch)) != -1:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
320 mfasta = ''
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
321 while not mfasta:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
322 self.logger.info("retrieving batch %d" %
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
323 ((start / batch_size) + 1))
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
324 try:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
325 mfasta = self.efetch(self.dbname, self.query_key,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
326 self.webenv)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
327 out.write(mfasta + '\n')
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
328 except QueryException as e:
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
329 self.logger.error("%s" % e.message)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
330 raise e
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
331
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
332
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
333 LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
334 LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
335 LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
336
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
337
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
338 def command_parse():
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
339 parser = argparse.ArgumentParser(description='Retrieve data from NCBI')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
340 parser.add_argument('-i', dest='query_string', help='NCBI Query String',
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
341 required=True)
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
342 parser.add_argument('-o', dest='outname', help='output file name')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
343 parser.add_argument('-d', dest='dbname', help='database type')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
344 parser.add_argument('--count', '-c', dest='count_ids',
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
345 action='store_true', default=False,
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
346 help='dry run ouputing only the number of sequences\
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
347 found')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
348 parser.add_argument('-l', '--logfile', help='log file (default=stderr)')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
349 parser.add_argument('--loglevel', choices=LOG_LEVELS, default='INFO',
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
350 help='logging level (default: INFO)')
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
351 args = parser.parse_args()
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
352 return args
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
353
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
354
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
355 def __main__():
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
356 """ main function """
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
357 args = command_parse()
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
358 log_level = getattr(logging, args.loglevel)
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
359 kwargs = {'format': LOG_FORMAT,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
360 'datefmt': LOG_DATEFMT,
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
361 'level': log_level}
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
362 if args.logfile:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
363 kwargs['filename'] = args.logfile
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
364 logging.basicConfig(**kwargs)
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
365 logger = logging.getLogger('data_from_NCBI')
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
366
3
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
367 E = Eutils(args, logger)
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
368 if args.count_ids:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
369 try:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
370 E.dry_run()
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
371 except Exception:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
372 sys.exit(1)
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
373 else:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
374 try:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
375 E.retrieve()
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
376 except Exception:
8be88084f89c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit ab45487db8cc69750f92a40d763d51ffac940e25
artbio
parents: 2
diff changeset
377 sys.exit(1)
1
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
378
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
379
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
380 if __name__ == "__main__":
7e41bbb94159 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit 6008aafac37eec1916d6b72c05d9cfcb002b8095
artbio
parents:
diff changeset
381 __main__()