AntonPetrov

"""
Find start/stop coordinates given a Stockholm file with INSDC accessions.

Before:
AE015928_959 GUGUUUUUCAUAGUA
AP006841_261 GUGUUUUUCAUAGUA
CP000139_346 GUGUUUUUCAUAGUA

After:
AE015928.1/959075-959219     GUGUUUUUCAUAGUA

AntonPetrov

"""
A quick and dirty script to generate outlines from R-scape SVG diagrams.

- Based on https://github.com/RNAcentral/auto-traveler
- Requires R-scape (http://eddylab.org/R-scape)

Usage:

1. Run R-scape on your Stockholm file of interest:

AntonPetrov

{
  "hitCount": 3,
  "entries": [
    {
      "id": "URS0000759B6D_9606",
      "source": "rnacentral",
      "fields": {
        "description": [
          "Homo sapiens (human) microRNA hsa-mir-126 precursor"
        ],

AntonPetrov

"""
Copyright [2009-present] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
     http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and

AntonPetrov

1 G 2876
2 G 2875
3 U 2874
4 C 2873
5 A 2872
6 A 2871
7 G 2870
8 A 2869
15 G 535
16 G 534

AntonPetrov

>GenomeXXX
CCAGAACGACAACCGAACACCGCAGCCGAAGACGTCGTGCGGGAGAGTCCTCACCAGCGG
ATGAGGCGCCGAAGGAGCAATACTCCCCGCCAAACTCTCAGGCCCAGTCACCGCACGGCA
CCAGGCTGAACACGGAGAAAAGCAGGGGCGCGCGAGCGCCTCTCGCCCAAGGTGCAAGCC
GCGCGTTCCGGCGTGGTGAAACTCTCAGGCCAATGACTCCGGGGAGACCGCCGACCAGCG
CATGCCCGCGCGGGTCGCAGTCGAGCTGGCCCGGATAAGGTAAGGCCGAAGTGAGCGGCC
CGGCTCTGGACTGCCGACCGGCGCCCCCACCAGGAGGAGTTCCGCACCATGTCGTCGCCC
CGGCAGACACCCCTGCACGAGATCCACGAAGCGCTCGGCGCCACCTTCACCGAGTTCGCC
GGCTGGCGGATGCCGCTGCGCTACACGGGCGACGCGGCCGAGCACAACGCGGTGCGCACC
GCCGCGGGCCTGTTCGACTTGACCCACATGGGTGAAATCCGCATCAGCGGCCCGCAGGCG

AntonPetrov

table rnacentralBed
"BED12+2 RNAcentral Bed"
(
string  chrom;  "Reference sequence chromosome"
uint  chromStart;  "Start position of the first DNA base"
uint  chromEnd;  "End position of the last DNA base"
string  name;  "RNAcentral identifier"
uint  score;  "Always ."
char[1]  strand;  "+ or - for strand"
uint  thickStart;  "Coding region start"

AntonPetrov

# Base image https://hub.docker.com/_/perl/
FROM perl:latest

# install cpanm
RUN curl -L http://cpanmin.us | perl - App::cpanminus

# install dependencies
RUN cpanm Cache::Memcached
RUN cpanm Catalyst::Action::RenderView
RUN cpanm Catalyst::Controller::REST

AntonPetrov

CREATE TABLE backup_rnc_reference_map AS SELECT * FROM rnc_reference_map;

-- choose max reference id out of all references with same pmid
CREATE TEMP TABLE rnc_reference_map_max_id AS
select max(id) as max_id, pmid
from rnc_references
where
pmid is not null
and pmid != ''
group by pmid

AntonPetrov

import requests

EXPERT_DATABASES = [
    'expert_db:"dictybase"',
    'expert_db:"ena"',
    'expert_db:"ensembl"',
    'expert_db:"flybase"',
    'expert_db:"gencode"',
    'expert_db:"greengenes"',
    'expert_db:"gtrnadb"',