Merge pull request #376 from VoSeq/genbankfasta

Genbankfasta. Ref #373
VoSeq · Jan 7, 2018 · 8190787 · 8190787
2 parents 2bfb0d7 + dafbd11
commit 8190787
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Showing 3 changed files with 49 additions and 5 deletions.
diff --git a/README.rst b/README.rst
@@ -582,3 +582,17 @@ and place them in the ``config.json`` configuration file of VoSeq:
     * Save and exit.
 
 Thus, every picture that you upload into your VoSeq installation will be uploaded into your Flickr account.
+
+Lineages
+========
+
+GenBank fasta files have the optional field Lineages. You can add lineages in the form:
+
+LINEAGES = {
+    # superfamily: lineage from domain Eukaryota to suborder Ditrysia
+    "Papilionoidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
+    "Hesperioidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
+    "Hedyloidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",
+}
+
+by editing the file `voseq/create_dataset/utils.py`.
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -16,6 +16,6 @@ django-haystack==2.5.0
 easy-thumbnails==2.2
 flickrapi==2.0
 
-dataset-creator==0.3.17
-seqrecord-expanded==0.2.8
+dataset-creator==0.3.19
+seqrecord-expanded==0.2.9
 degenerate-dna==0.0.9
diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py
@@ -1,3 +1,5 @@
+import re
+
 from seqrecord_expanded import SeqRecordExpanded
 from seqrecord_expanded.exceptions import MissingParameterError
 from seqrecord_expanded.exceptions import TranslationErrorMixedGappedSeq
@@ -13,6 +15,13 @@
 from public_interface.models import Sequences
 from public_interface.models import Vouchers
 
+LINEAGES = {
+    # superfamily: lineage from domain Eukaryota to suborder Ditrysia
+    "Papilionoidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",  # noqa
+    "Hesperioidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",  # noqa
+    "Hedyloidea": "Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; ",  # noqa
+}
+
 
 class CreateDataset(object):
     """Accepts form input to create a dataset in several formats.
@@ -171,29 +180,49 @@ def build_seq_obj(self, code, gene_code, our_taxon_names, all_seqs):
             seq = self.create_seq_record(this_voucher_seqs)
 
         if code in our_taxon_names:
+            lineage = self.get_lineage(code)
             seq_record = SeqRecordExpanded(
                 seq,
                 voucher_code=code.replace(" ", "_"),
                 taxonomy=our_taxon_names[code],
                 gene_code=gene_code,
                 reading_frame=self.gene_codes_metadata[gene_code]['reading_frame'],
                 table=self.gene_codes_metadata[gene_code]['genetic_code'],
+                lineage=lineage,
             )
             return seq_record
         else:
             return None
 
+    def get_lineage(self, code):
+        voucher = Vouchers.objects.get(code=code)
+        try:
+            lineage = LINEAGES[voucher.superfamily]
+        except KeyError:
+            lineage = ""
+
+        additional_lineage = ";".join([
+            voucher.family, voucher.subfamily, voucher.tribe, voucher.subtribe,
+            voucher.genus, voucher.species, voucher.subspecies,
+        ])
+        lineage += re.sub(";+", "; ", additional_lineage)
+        return lineage.strip()
+
     def extract_sequence_from_all_seqs_in_db(self, all_seqs, code, gene_code):
         try:
             voucher_sequences = all_seqs[code]
         except KeyError:
-            self.warnings += ['Could not find sequences for voucher {0} and gene_code {1}'.format(code, gene_code)]
+            self.warnings += [
+                'Could not find sequences for voucher {0} and gene_code {1}'.format(
+                    code, gene_code)]
             return '?'
 
         try:
             this_voucher_seqs = voucher_sequences[gene_code]
         except KeyError:
-            self.warnings += ['Could not find sequences for voucher {0} and gene_code {1}'.format(code, gene_code)]
+            self.warnings += [
+                'Could not find sequences for voucher {0} and gene_code {1}'.format(
+                    code, gene_code)]
             return '?'
         return this_voucher_seqs
 
@@ -242,7 +271,8 @@ def get_gene_codes_metadata(self):
         """
         :return: dictionary with genecode and base pair number.
         """
-        queryset = Genes.objects.all().values('gene_code', 'length', 'reading_frame', 'genetic_code')
+        queryset = Genes.objects.all().values(
+            'gene_code', 'length', 'reading_frame', 'genetic_code')
         gene_codes_metadata = dict()
         for i in queryset:
             gene_code = i['gene_code']