Mercurial > repos > earlhaminst > gafa
comparison GAFA.py @ 7:b9f1bcf5ee59 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/ commit fa875eea77a9471acada2b7b8882a0467994c960
| author | earlhaminst |
|---|---|
| date | Wed, 25 Apr 2018 10:59:55 -0400 |
| parents | 117fc7414307 |
| children |
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| 6:c15476d4271c | 7:b9f1bcf5ee59 |
|---|---|
| 5 import re | 5 import re |
| 6 import shutil | 6 import shutil |
| 7 import sqlite3 | 7 import sqlite3 |
| 8 | 8 |
| 9 version = "0.3.0" | 9 version = "0.3.0" |
| 10 compatible_version = ['0.3.0', '0.4.0'] | |
| 10 | 11 |
| 11 Sequence = collections.namedtuple('Sequence', ['header', 'sequence']) | 12 Sequence = collections.namedtuple('Sequence', ['header', 'sequence']) |
| 12 | 13 |
| 13 | 14 |
| 14 def FASTAReader_gen(fasta_filename): | 15 def FASTAReader_gen(fasta_filename): |
| 52 cur = conn.cursor() | 53 cur = conn.cursor() |
| 53 # Check that the version of the input database is compatible | 54 # Check that the version of the input database is compatible |
| 54 cur.execute('SELECT version FROM meta') | 55 cur.execute('SELECT version FROM meta') |
| 55 result = cur.fetchone() | 56 result = cur.fetchone() |
| 56 input_meta_version = result[0] | 57 input_meta_version = result[0] |
| 57 if input_meta_version != '0.3.0': | 58 if input_meta_version not in compatible_version: |
| 58 raise Exception("Incompatible input meta version '%s'" % input_meta_version) | 59 raise Exception("Incompatible input meta version '%s'" % input_meta_version) |
| 59 cur.execute('UPDATE meta SET version=?', | 60 cur.execute('UPDATE meta SET version=?', |
| 60 (version, )) | 61 (version, )) |
| 61 | 62 |
| 62 cur.execute('''CREATE TABLE gene_family ( | 63 cur.execute('''CREATE TABLE gene_family ( |
| 66 cur.execute('''CREATE TABLE gene_family_member ( | 67 cur.execute('''CREATE TABLE gene_family_member ( |
| 67 gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id), | 68 gene_family_id INTEGER NOT NULL REFERENCES gene_family(gene_family_id), |
| 68 protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id), | 69 protein_id VARCHAR KEY NOT NULL REFERENCES transcript(protein_id), |
| 69 protein_alignment VARCHAR NOT NULL, | 70 protein_alignment VARCHAR NOT NULL, |
| 70 PRIMARY KEY (gene_family_id, protein_id))''') | 71 PRIMARY KEY (gene_family_id, protein_id))''') |
| 72 | |
| 71 conn.commit() | 73 conn.commit() |
| 72 | 74 |
| 73 | 75 |
| 74 def align_to_db(conn, i, fname): | 76 def align_to_db(conn, i, fname): |
| 75 cur = conn.cursor() | 77 cur = conn.cursor() |