From d4395ecbf556f295803274583a24775cdb4ab5c1 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 9 Apr 2020 16:40:46 +0200
Subject: [PATCH] Delete blastdb.py
---
blastdb.py | 298 -----------------------------------------------------
1 file changed, 298 deletions(-)
delete mode 100755 blastdb.py
diff --git a/blastdb.py b/blastdb.py
deleted file mode 100755
index 2794ccb..0000000
--- a/blastdb.py
+++ /dev/null
@@ -1,298 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import collections
-import json
-import logging as log
-import os
-import sys
-
-from shutil import copyfile
-from subprocess import call
-
-
-class BlastBank:
-
- def __init__(self, raw_org, data_dir_root, rel_path, fasta_file_name, db_dir_root, seq_type, path, is_multi):
- self.raw_org = raw_org
- self.org = prettify(raw_org)
- self.data_dir_root = data_dir_root
- self.rel_path = rel_path
- self.fasta_file_name = fasta_file_name
- self.db_dir_root = db_dir_root
- self.seq_type = seq_type
- self.path = path # http://bipaa.genouest.org/sp/xxx/ Can be the same as raw_org, or something else when having multiple genomes.
- self.is_multi = is_multi
-
- self.fasta = os.path.join(data_dir_root, rel_path, fasta_file_name)
- self.dest_path = os.path.splitext(os.path.join(db_dir_root, self.path, rel_path, fasta_file_name))[0]
- self.title = sanitize(rel_path + '_' + os.path.splitext(self.fasta_file_name)[0])
- if self.is_multi:
- fake_path = rel_path.split('/')
- if len(fake_path) > 2:
- fake_path = [fake_path[1]] + [fake_path[0]] + fake_path[2:]
- fake_path = '/'.join(fake_path)
- self.pretty_name = prettify(fake_path, True)
- else:
- self.pretty_name = self.org + ' ' + prettify(rel_path, False)
-
- with open(self.fasta, 'r') as f:
- self.first_id = f.readline()[1:].rstrip()
-
- if self.seq_type == 'nucl':
- if 'transcript' in self.fasta_file_name.lower() or 'cdna' in self.fasta_file_name.lower():
- self.pretty_name += " transcripts"
- elif 'cds' in self.fasta_file_name.lower():
- self.pretty_name += " CDS"
- else:
- if 'protein' in self.fasta_file_name.lower() or 'pep' in self.fasta_file_name.lower() or 'proteome' in self.fasta_file_name.lower() or self.fasta_file_name.endswith('.faa'):
- self.pretty_name += " proteins"
-
- # Just a stupid/hacky string used for sorting bank list
- self.sort_key = 'a_' if 'genome' in self.title else 'b_'
- self.sort_key += self.pretty_name
-
- def __str__(self):
- return str({
- 'raw_org': self.raw_org,
- 'org': self.org,
- 'data_dir_root': self.data_dir_root,
- 'rel_path': self.rel_path,
- 'fasta_file_name': self.fasta_file_name,
- 'db_dir_root': self.db_dir_root,
- 'seq_type': self.seq_type,
- 'path': self.path,
- 'fasta': self.fasta,
- 'dest_path': self.dest_path,
- 'title': self.title,
- 'pretty_name': self.pretty_name,
- })
-
-
-def main(args):
-
- genome_path = os.path.basename(os.getcwd())
- if not args.multi_org:
- genome_name = genome_path
- data_dir_root = os.path.abspath(os.path.join('src_data'))
- if not os.path.isdir(data_dir_root):
- raise Exception("Could not find data dir: %s" % data_dir_root)
-
- db_dir_root = os.path.abspath(args.dest)
-
- ignore_list = ['func_annot', "apollo_source"]
- if args.ignore:
- ignore_list += args.ignore
-
- # Looking for files
- log.info("Looking for fasta files in %s:" % data_dir_root)
- banks = []
- for root, dirs, files in os.walk(data_dir_root, followlinks=True):
- file_list = [os.path.realpath(os.path.join(root, filename)) for filename in files]
- rel_path = root[len(data_dir_root) + 1:]
-
- skip_current = False
- for ign in ignore_list:
- if ign in rel_path:
- skip_current = True
-
- if not skip_current: # skip useless data
- for f in file_list:
- f = os.path.basename(f)
- if f.endswith('.fasta') or f.endswith('.fa') or f.endswith('.fna') or f.endswith('.faa'):
- if args.multi_org:
- genome_name = rel_path.split('/')[1]
-
- if 'protein' in f or 'pep.' in f or 'proteome' in f or f.endswith('.faa'):
- seq_type = 'prot'
- else:
- seq_type = 'nucl'
- new_bank = BlastBank(genome_name, data_dir_root, rel_path, f, db_dir_root, seq_type, genome_path, args.multi_org)
- log.info("Found '%s' of type: %s" % (new_bank.fasta, new_bank.seq_type))
- banks.append(new_bank)
-
- if not banks:
- log.info("No fasta file found.")
- else:
- for b in banks:
- makeblastdb(b, args.dry_run, args.no_parse_seqids)
-
- nuc_list = collections.OrderedDict()
- prot_list = collections.OrderedDict()
- banks.sort(key=lambda x: x.sort_key)
- for b in banks:
- if b.seq_type == 'nucl':
- if b.pretty_name not in nuc_list:
- nuc_list[b.dest_path] = b.pretty_name
- else:
- nuc_list[b.dest_path] = "%s (%s)" % (b.pretty_name, b.fasta_file_name)
- else:
- if b.pretty_name not in prot_list:
- prot_list[b.dest_path] = b.pretty_name
- else:
- prot_list[b.dest_path] = "%s (%s)" % (b.pretty_name, b.fasta_file_name)
-
- yml_dir = os.path.abspath('blast')
- yml_file_path = os.path.abspath(os.path.join(yml_dir, 'banks.yml'))
- links_file_path = os.path.abspath(os.path.join(yml_dir, 'links.yml'))
- if not args.dry_run:
-
- log.info("List of bank names (to use in links.yml):")
- write_titles(banks)
-
- log.info("Writing bank list in '%s'" % yml_file_path)
- if not os.path.exists(yml_dir):
- os.makedirs(yml_dir, mode=0o755)
- yml_file = open(yml_file_path, 'w')
- write_yml(yml_file, nuc_list, prot_list)
-
- log.info("Writing automatic links to links.yml in '%s'" % links_file_path)
- if os.path.exists(links_file_path):
- log.info("Making backup of previous links.yml to '%s'" % (links_file_path + '.back'))
- copyfile(links_file_path, links_file_path + '.back')
- links_yml_file = open(links_file_path, 'w')
- write_links_yml(links_yml_file, banks, args.apollo)
-
- else:
- log.info("List of bank names (to use in links.yml):")
- write_titles(banks)
- log.info("Would write bank list in '%s'" % yml_file_path)
- write_yml(sys.stdout, nuc_list, prot_list)
- log.info("Would write links.yml in '%s'" % links_file_path)
- write_links_yml(sys.stdout, banks, args.apollo)
-
-
-def write_yml(yml_file, nuc_list, prot_list):
-
- nuc = "~"
- prot = "~"
-
- if nuc_list:
- nuc = "\n ".join(['%s: %s' % (json.dumps(k), json.dumps(v)) for k, v in nuc_list.items()])
- if prot_list:
- prot = "\n ".join(['%s: %s' % (json.dumps(k), json.dumps(v)) for k, v in prot_list.items()])
-
- print("genouest_blast:", file=yml_file)
- print(" db_provider:", file=yml_file)
- print(" list:", file=yml_file)
- print(" nucleic:", file=yml_file)
- print(" %s" % nuc, file=yml_file)
- print(" proteic:", file=yml_file)
- print(" %s" % prot, file=yml_file)
-
-
-def write_links_yml(yml_file, banks, apollo):
-
- for bank in banks:
- print("", file=yml_file)
- print("# %s" % (bank.pretty_name), file=yml_file)
-
- link = ''
- if bank.seq_type == 'prot':
- spl = bank.org.split()
- if len(spl) > 2:
- sp_str = '/'.join(spl[:2])
- sp_str += '-' + '-'.join(spl[2:])
- else:
- sp_str = '/'.join(spl)
- link = 'http://abims-gga.sb-roscoff.fr/sp/%s/feature/%s/polypeptide/{id}' % (bank.path, sp_str)
- elif 'genome' in bank.title:
- dataset_id = bank.org.lower()
- spl = dataset_id.split()
- if len(spl) == 2: # Genus species => gspecies
- dataset_id = spl[0][:1] + spl[1]
- elif len(spl) == 3: # Genus species strain1 => gsstrain1
- dataset_id = spl[0][:1] + spl[1][:1] + spl[2]
- else: # Genus species some garbage => genus_species_some_garbage
- dataset_id = dataset_id.replace(' ', '_')
- if apollo:
- link = '<a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/jbrowse/?data=data%2F' + dataset_id + '&loc={id}{jbrowse_track}">{id}</a> <a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/apollo/annotator/loadLink?loc={id}:1{apollo_track}">Apollo</a>'
- else:
- link = '<a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/jbrowse/?data=data%2F' + dataset_id + '&loc={id}{jbrowse_track}">{id}</a>'
- else:
- spl = bank.org.split()
- if len(spl) > 2:
- sp_str = '/'.join(spl[:2])
- sp_str += '-' + '-'.join(spl[2:])
- else:
- sp_str = '/'.join(spl)
- link = 'http://abims-gga.sb-roscoff.fr/sp/%s/feature/%s/mRNA/{id}' % (bank.path, sp_str)
-
- if link:
- print("%s:" % (bank.title), file=yml_file)
- print(" db: '%s'" % (bank.title), file=yml_file)
- print(" '*': '%s'" % (link), file=yml_file)
- else:
- print("# Skipped", file=yml_file)
-
-
-def write_titles(banks):
-
- for bank in banks:
- print("'%s' -> '%s' [%s]" % (bank.pretty_name, bank.title, bank.first_id))
-
-
-def makeblastdb(bank, dry_run, no_parse_seqids):
- log.info("Formatting bank: %s ---> %s" % (bank.fasta, bank.dest_path))
- dest_dir = os.path.realpath(os.path.join(bank.dest_path, '..'))
- if not os.path.exists(dest_dir):
- log.info("Creating folder: %s" % dest_dir)
- if not dry_run:
- os.makedirs(dest_dir, mode=0o755)
- parse = "-parse_seqids"
- if no_parse_seqids:
- parse = ""
- cmd = "makeblastdb -in '%s' -dbtype '%s' %s -out '%s' -title '%s'" % (bank.fasta, bank.seq_type, parse, bank.dest_path, bank.title)
- log.info("Running: %s" % cmd)
- if not dry_run:
- try:
- retcode = call(cmd, shell=True)
- if retcode != 0:
- raise RuntimeError("Child was terminated by signal " + str(retcode))
- except OSError as e:
- print("Execution failed:" + e, file=sys.stderr)
- sys.exit(1)
-
-
-def prettify(name, capital=True):
- name = name.replace('_', ' ')
- name = name.replace('/', ' ')
- if capital:
- name = name[0].upper() + name[1:]
-
- return name
-
-
-def sanitize(name):
- name = name.lower()
- name = name.replace(' ', '_')
- name = name.replace('/', '_')
-
- return name
-
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser(
- description='Generate blast databanks and update blast forms.'
- )
- parser.add_argument("-v", "--verbose", help="Increase output verbosity.",
- action="store_true")
- parser.add_argument("-d", "--dry-run", help="Dry run: no modification will be done, for testing purpose.",
- action="store_true")
- parser.add_argument("-m", "--multi-org", help="Add this flag if there are multiple organisms in src_data.",
- action="store_true")
- parser.add_argument("-a", "--apollo", help="Add this flag to generate links to apollo.",
- action="store_true")
- parser.add_argument("-p", "--no-parse-seqids", help="Don't use the makeblastdb -parse_seqids option (use this in case you have strange looking sequence ids that make html files unreadable)",
- action="store_true")
- parser.add_argument("--ignore", help='Files or directories to ignore', nargs='*')
- parser.add_argument("dest", help="Destination directory (not including the genome name, should be mounted on compute nodes)")
-
- args = parser.parse_args()
- log.basicConfig(level=log.INFO)
- if args.verbose:
- log.basicConfig(level=log.DEBUG)
-
- main(args)
--
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