diff ensembl_rest.py @ 0:da1b538b87e5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/retrieve_ensembl_bed commit 88cf1e923a8c9e5bc6953ad412d15a7c70f054d1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ensembl_rest.py	Mon Jan 22 13:13:47 2018 -0500
@@ -0,0 +1,129 @@
+#!/usr/bin/env python
+"""
+#
+#------------------------------------------------------------------------------
+#                         University of Minnesota
+#         Copyright 2017, Regents of the University of Minnesota
+#------------------------------------------------------------------------------
+# Author:
+#
+#  James E Johnson
+#
+#------------------------------------------------------------------------------
+"""
+
+from __future__ import print_function
+from __future__ import unicode_literals
+
+import sys
+
+from time import sleep
+
+import requests
+
+
+server = "https://rest.ensembl.org"
+ext = "/info/assembly/homo_sapiens?"
+max_region = 4000000
+debug = False
+
+
+def ensembl_rest(ext, headers):
+    if debug:
+        print("%s" % ext, file=sys.stderr)
+    r = requests.get(server+ext, headers=headers)
+    if r.status_code == 429:
+        print("response headers: %s\n" % r.headers, file=sys.stderr)
+        if 'Retry-After' in r.headers:
+            sleep(r.headers['Retry-After'])
+            r = requests.get(server+ext, headers=headers)
+    if not r.ok:
+        r.raise_for_status()
+    return r
+
+
+def get_species():
+    results = dict()
+    ext = "/info/species"
+    req_header = {"Content-Type": "application/json"}
+    r = ensembl_rest(ext, req_header)
+    for species in r.json()['species']:
+        results[species['name']] = species
+        print("%s\t%s\t%s\t%s\t%s" %
+              (species['name'], species['common_name'],
+               species['display_name'],
+               species['strain'],
+               species['taxon_id']), file=sys.stdout)
+    return results
+
+
+def get_biotypes(species):
+    biotypes = []
+    ext = "/info/biotypes/%s?" % species
+    req_header = {"Content-Type": "application/json"}
+    r = ensembl_rest(ext, req_header)
+    for entry in r.json():
+        if 'biotype' in entry:
+            biotypes.append(entry['biotype'])
+    return biotypes
+
+
+def get_toplevel(species):
+    coord_systems = dict()
+    ext = "/info/assembly/%s?" % species
+    req_header = {"Content-Type": "application/json"}
+    r = ensembl_rest(ext, req_header)
+    toplevel = r.json()
+    for seq in toplevel['top_level_region']:
+        if seq['coord_system'] not in coord_systems:
+            coord_systems[seq['coord_system']] = dict()
+        coord_system = coord_systems[seq['coord_system']]
+        coord_system[seq['name']] = int(seq['length'])
+    return coord_systems
+
+
+def get_transcripts_bed(species, refseq, start, length, strand='',
+                        params=None):
+    bed = []
+    param = params if params else ''
+    req_header = {"Content-Type": "text/x-bed"}
+    regions = list(range(start, length, max_region))
+    if not regions or regions[-1] < length:
+        regions.append(length)
+    for end in regions[1:]:
+        ext = "/overlap/region/%s/%s:%d-%d%s?feature=transcript;%s"\
+            % (species, refseq, start, end, strand, param)
+        start = end + 1
+        r = ensembl_rest(ext, req_header)
+        if r.text:
+            bed += r.text.splitlines()
+    return bed
+
+
+def get_seq(id, seqtype, params=None):
+    param = params if params else ''
+    ext = "/sequence/id/%s?type=%s;%s" % (id, seqtype, param)
+    req_header = {"Content-Type": "text/plain"}
+    r = ensembl_rest(ext, req_header)
+    return r.text
+
+
+def get_cdna(id, params=None):
+    return get_seq(id, 'cdna', params=params)
+
+
+def get_cds(id, params=None):
+    return get_seq(id, 'cds', params=params)
+
+
+def get_genomic(id, params=None):
+    return get_seq(id, 'genomic', params=params)
+
+
+def get_transcript_haplotypes(species, transcript):
+    ext = "/transcript_haplotypes/%s/%s?aligned_sequences=1"\
+        % (species, transcript)
+    req_header = {"Content-Type": "application/json"}
+    r = ensembl_rest(ext, req_header)
+    decoded = r.json()
+    return decoded