def make_org_db(org_name_file, data_path, exp_path):
"""
function to collect details of each organism
@args org_name_file: text file containing organisms name
@type org_name_file: str
ovis_aries SRR645881 ensembl 78
capra_hircus SRR645885 ensembl 78
@args data_path: data file storage path
@type data_path: str
@args exp_path: experiment related file path
@type exp_path: str
"""
org_fasta_file = dict( A_carolinensis = '%s/A_carolinensis/STARgenome/Anolis_carolinensis.AnoCar2.0.69.stable_genome.fa' % data_path,
M_mulatta = "%s/M_mulatta/STARgenome/ensembl_release-69.fa" % data_path,
O_cuniculus = "%s/O_cuniculus/STARgenome/ensembl_release-69.fa" % data_path,
M_gallopavo = "%s/M_gallopavo/STARgenome/ensembl_release-69.fa" % data_path,
B_anthracis = '%s/B_anthracis/ensembl_release-21/Bacillus_anthracis_str_a0193.GCA_000181915.1.21.dna.toplevel.fa' % data_path,
C_familiaris = '%s/C_familiaris/ensembl_release-69/Canis_familiaris.CanFam3.1.69.dna.toplevel.fa' % data_path,
D_melanogaster = '%s/D_melanogaster/ensembl_release-69/Drosophila_melanogaster.BDGP5.69.dna.toplevel.fa' % data_path,
E_caballus = '%s/E_caballus/ensembl_release-69/Equus_caballus.EquCab2.69_stable.fa.bz2' % data_path,
M_domestica = '%s/M_domestica/ensembl_release-69/Monodelphis_domestica.BROADO5.69.dna.toplevel.fa' % data_path,
O_sativa = '%s/O_sativa/phytozome_v9.0/Osativa_204.fa' % data_path,
A_gambiae = '%s/A_gambiae/ensembl_release-20/Anopheles_gambiae.AgamP3.20.dna.fa' % data_path,
B_rapa = '%s/B_rapa/phytozome_v9.0/Brapa_197_stable.fa' % data_path,
C_japonica = '%s/C_japonica/STARgenome/Caenorhabditis_japonica.C_japonica-7.0.1.22.dna_sm.stable.fa' % data_path,
G_gallus = '%s/G_gallus/ensembl_release-69/Gallus_gallus.WASHUC2.69_stable.fa.bz2' % data_path,
M_musculus = '%s/M_musculus/ensembl_release-69/Mus_musculus.GRCm38.69_stable.fa.bz2' % data_path,
V_vinifera = '%s/V_vinifera/STARgenome/Vvinifera_145.fa' % data_path,
A_mellifera = '%s/A_mellifera/ensembl_release-20/apiMel3_ucsc_chrom.fasta' % data_path,
B_taurus = '%s/B_taurus/STARgenome/ensembl_release-69.fa' % data_path,
C_rubella = '%s/C_rubella/phytozome_v9.0/Crubella_183.fa.gz' % data_path,
D_rerio = '%s/D_rerio/ensembl_release-69/Danio_rerio.Zv9.69.dna.toplevel.fa.bz2' % data_path,
G_max = '%s/G_max/phytozome_v9.0/Gmax_189_filter.fa' % data_path,
M_truncatula = '%s/M_truncatula/STARgenome/Mtruncatula_198.fa' % data_path,
P_pacificus = '%s/P_pacificus/STARgenome/Pristionchus_pacificus.P_pacificus-5.0.22.dna_sm.stable.fa' % data_path,
S_scrofa = '%s/S_scrofa/ensembl_release-69/Sus_scrofa.Sscrofa10.2.69.dna_filter.fasta' % data_path,
X_tropicalis = '%s/X_tropicalis/ensembl_release-69/Xenopus_tropicalis.JGI_4.2.69.dna_stable.fasta.bz2' % data_path,
C_sativus = '%s/C_sativus/phytozome_v9.0/Csativus_122_filtered.fa' % data_path,
D_simulans = '%s/D_simulans/ensembl_release-22/Drosophila_simulans.WUGSC1.22.dna_sm.dna.fa' % data_path,
H_sapiens = '%s/H_sapiens/hg19_bowtie/hg19.fa' % data_path,
O_anatinus = '%s/O_anatinus/ensembl_release-69/Ornithorhynchus_anatinus.OANA5.69-filtered_dna.fa' % data_path,
P_troglodytes = '%s/P_troglodytes/STARgenome/Pan_troglodytes.CHIMP2.1.4.69_stable.fa' % data_path,
S_tuberosum = '%s/S_tuberosum/phytozome_v9.0/Stuberosum_206.fa' % data_path,
Z_mays = '%s/Z_mays/phytozome_v9.0/Zmays_181.fa' % data_path,
A_thaliana = '%s/A_thaliana/arabidopsis_tair10/sequences/TAIR9_chr_all.fas' % data_path,
C_elegans = '%s/C_elegans/ensembl_release-69/Caenorhabditis_elegans.WBcel215.69.dna.toplevel.fa' % data_path,
D_discoideum = '%s/D_discoideum/STARgenome/Dictyostelium_discoideum.dictybase.01.21.dna.toplevel.fa' % data_path,
D_yakuba = '%s/D_yakuba/STARgenome/Drosophila_yakuba.dyak_r1.3_FB2008_07.22.dna_sm_stable.fasta' % data_path,
O_latipes = '%s/O_latipes/STARgenome/ensembl_release-74.fa' % data_path,
R_norvegicus = '%s/R_norvegicus/ensembl_release-69/Rattus_norvegicus.RGSC3.4.69.dna.toplevel.fa.bz2' % data_path,
C_briggsae = '%s/C_briggsae/STARgenome/Caenorhabditis_briggsae.CB4.22.dna_sm_stable.fasta' % data_path,
C_brenneri = '%s/C_brenneri/STARgenome/Caenorhabditis_brenneri.C_brenneri-6.0.1b.22.dna_sm_stable.fa' % data_path,
C_remanei = '%s/C_remanei/STARgenome/Caenorhabditis_remanei.C_remanei-15.0.1.22.dna_sm_stable.fa' % data_path,
D_pseudoobscura = '%s/D_pseudoobscura/STARgenome/Drosophila_pseudoobscura.HGSC2.22.dna_sm_stable.fasta' % data_path,
T_pseudonana = '%s/T_pseudonana/Thaps3/Thaps3_chromosomes_assembly_chromosomes_repeatmasked.fasta' % data_path,
T_nigroviridis = '%s/T_nigroviridis/ensembl_release-69/Tetraodon_nigroviridis.TETRAODON8.69.dna.toplevel.fa' % data_path
)
org_gtf_file = dict( A_carolinensis = '%s/A_carolinensis/STARgenome/Anolis_carolinensis.AnoCar2.0.69.stable.gtf' % data_path,
M_mulatta = "%s/M_mulatta/STARgenome/ensembl_release-69.gtf" % data_path,
O_cuniculus = "%s/O_cuniculus/STARgenome/ensembl_release-69.gtf" % data_path,
M_gallopavo = "%s/M_gallopavo/STARgenome/ensembl_release-69.gtf" % data_path,
B_anthracis = '%s/B_anthracis/ensembl_release-21/Bacillus_anthracis' % data_path,
C_familiaris = '%s/C_familiaris/ensembl_release-69/Canis_familiaris.CanFam3.1.69.gtf' % data_path,
D_melanogaster = '%s/D_melanogaster/ensembl_release-69/Drosophila_melanogaster.BDGP5.69.gtf' % data_path,
E_caballus = '%s/E_caballus/ensembl_release-69/Equus_caballus.EquCab2.69.gtf' % data_path,
M_domestica = '%s/M_domestica/ensembl_release-69/Monodelphis_domestica.BROADO5.69.gtf' % data_path,
O_sativa = '%s/O_sativa/phytozome_v9.0/Osativa_204_gene.gff3' % data_path,
A_gambiae = '%s/A_gambiae/ensembl_release-20/Anopheles_gambiae.AgamP3.20.gtf' % data_path,
B_rapa = '%s/B_rapa/phytozome_v9.0/Brapa_197_gene.gff3' % data_path,
C_japonica = '%s/C_japonica/ensembl_release-22/Caenorhabditis_japonica.C_japonica-7.0.1.22.gff3' % data_path,
G_gallus = '%s/G_gallus/ensembl_release-69/Gallus_gallus.WASHUC2.69.gtf' % data_path,
M_musculus = '%s/M_musculus/ensembl_release-69/Mus_musculus.GRCm38.69.gtf' % data_path,
V_vinifera = '%s/V_vinifera/STARgenome/Vvinifera_145_gene.gff3' % data_path,
A_mellifera = '%s/A_mellifera/ensembl_release-20/apiMel3_ucsc_ensembl_genes.gtf' % data_path,
B_taurus = '%s/ensembl_release-69/Bos_taurus.UMD3.1.69.gtf' % data_path,
C_rubella = '%s/C_rubella/phytozome_v9.0/Crubella_183.gff3' % data_path,
D_rerio = '%s/D_rerio/ensembl_release-69/Danio_rerio.Zv9.69.gtf' % data_path,
G_max = '%s/G_max/phytozome_v9.0/Gmax_189_gene.gff3' % data_path,
M_truncatula = '%s/M_truncatula/' % data_path,
P_pacificus = '%s/P_pacificus/ensembl_release-22/Pristionchus_pacificus.P_pacificus-5.0.22.gtf' % data_path,
S_scrofa = '%s/S_scrofa/ensembl_release-69/Sus_scrofa.Sscrofa10.2.69.gtf' % data_path,
X_tropicalis = '%s/X_tropicalis/STARgenome/JGIv4-1.gtf' % data_path,
C_sativus = '%s/C_sativus/phytozome_v9.0/Csativus_122_gene.gff3' % data_path,
D_simulans = '%s/D_simulans/ensembl_release-22/Drosophila_simulans.WUGSC1.22.gff3' % data_path,
H_sapiens = '%s/H_sapiens/ensembl_release-69/Homo_sapiens.GRCh37.69.gtf' % data_path,
O_anatinus = '%s/O_anatinus/ensembl_release-69/' % data_path,
P_troglodytes = '%s/P_troglodytes/ensembl_release-69/Pan_troglodytes.CHIMP2.1.4.69.gtf' % data_path,
S_tuberosum = '%s/S_tuberosum/phytozome_v9.0/Stuberosum_206_gene.gff3' % data_path,
Z_mays = '%s/Z_mays/phytozome_v9.0/Zmays_181_gene.gff3' % data_path,
A_thaliana = '%s/A_thaliana/arabidopsis_tair10/annotations/TAIR10_GFF3_genes.gff' % data_path,
C_elegans = '%s/C_elegans/ensembl_release-69/Caenorhabditis_elegans.WBcel215.69.gtf' % data_path,
D_discoideum = '%s/D_discoideum/' % data_path,
D_yakuba = '%s/D_yakuba/ensembl_release-22/Drosophila_yakuba.dyak_r1.3_FB2008_07.22.gff3' % data_path,
O_latipes = '%s/O_latipes/STARgenome/Oryzias_latipes.MEDAKA1.74.gtf' % data_path,
R_norvegicus = '%s/R_norvegicus/ensembl_release-69/Rattus_norvegicus.RGSC3.4.69.gtf' % data_path,
C_briggsae = '%s/C_briggsae/ensembl_release-22/Caenorhabditis_briggsae.CB4.22.gff3' % data_path,
C_brenneri = '%s/C_brenneri/ensembl_release-22/Caenorhabditis_brenneri.C_brenneri-6.0.1b.22.gff3' % data_path,
C_remanei = '%s/C_remanei/ensembl_release-22/Caenorhabditis_remanei.C_remanei-15.0.1.22.gff3' % data_path,
D_pseudoobscura = '%s/D_pseudoobscura/ensembl_release-22/Drosophila_pseudoobscura.HGSC2.22.gff3' % data_path,
T_pseudonana = '%s/T_pseudonana/Thaps3/Thaps3_chromosomes_geneModels_FilteredModels2.gff' % data_path,
T_nigroviridis = '%s/T_nigroviridis/ensembl_release-69/Tetraodon_nigroviridis.TETRAODON8.69.gtf' % data_path
)
org_db = defaultdict()
## get the organisms name and details on the experiment
with open(org_name_file, "rU") as fh:
for name in fh:
name = name.strip('\n\r').split('\t')
#print name
## name shortening
token = name[0].split("_")
genus, species = token[0], token[-1]
short_name = "%s_%s" % (genus[0].upper(), species.lower())
## adding details
org_db[short_name] = dict(name = name[0])
org_db[short_name]['short_name'] = short_name
## sequencing reads files
sra_files = []
if os.path.isdir("%s/%s/source_data" % (exp_path, short_name)):
for sra_file in os.listdir("%s/%s/source_data" % (exp_path, short_name)):
file_prefix, ext = os.path.splitext(sra_file)
if ext == ".sra":
continue
sra_files.append(sra_file)
else:
# new organism, creating sub directories
for sub_dir in ['source_data', 'read_mapping', 'signal_labels', 'trans_pred']:
try:
os.makedirs("%s/%s/%s" % (exp_path, short_name, sub_dir))
except OSError:
print "Skipping creation of %s/%s/%s because it exists already." % (exp_path, short_name, sub_dir)
org_db[short_name]['fastq_path'] = "%s/%s/source_data" % (exp_path, short_name)
org_db[short_name]['fastq'] = sra_files
org_db[short_name]['star_wd'] = "%s/%s/read_mapping" % (exp_path, short_name)
org_db[short_name]['trsk_wd'] = "%s/%s/trans_pred" % (exp_path, short_name)
org_db[short_name]['labels_wd'] = "%s/%s/signal_labels" % (exp_path, short_name)
org_db[short_name]['bam'] = "%s/%s/read_mapping/unique_map.bam" % (exp_path, short_name)
org_db[short_name]['pred_gff'] = "%s/%s/trans_pred/ss_filter_predgenes.gff" % (exp_path, short_name)
## check for the genome sequence file
if short_name in org_fasta_file:
org_db[short_name]['fasta'] = org_fasta_file[short_name]
else:
if not os.path.isdir("%s" % data_path):
os.makedirs("%s" % data_path)
else:
print "Skipping creation of %s because it exists already." % data_path
org_db[short_name]['fasta'] = "%s" % data_path
## check for the genome index file
if short_name in star_index_file:
org_db[short_name]['index'] = star_index_file[short_name]
else:
if not os.path.isdir("%s" % data_path):
os.makedirs("%s" % data_path)
else:
print "Skipping creation of %s because it exists already." % data_path
org_db[short_name]['index'] = "%s/%s/STARgenome/" % (data_path, short_name)
## TODO remove the dependency of gio from TSKM
if short_name in org_gio_file:
org_db[short_name]['gio'] = org_gio_file[short_name]
else:
org_db[short_name]['gio'] = "%s" % data_path
## check the genome annotation
if short_name in org_gtf_file:
org_db[short_name]['gtf'] = org_gtf_file[short_name]
## get the gtf feature lengths
if os.path.isfile(org_gtf_file[short_name]):
from fetch_remote_data import prepare_data as pd
feat_len_db = pd.make_anno_db(org_gtf_file[short_name])
org_db[short_name]['max_intron'] = feat_len_db['max_intron']
org_db[short_name]['max_exon'] = feat_len_db['max_exon']
else:
org_db[short_name]['gtf'] = data_path
org_db[short_name]['max_intron'] = None
org_db[short_name]['max_exon'] = None
## SRA/ENA run id
try:
org_db[short_name]['sra_run_id'] = name[1]
except:
org_db[short_name]['sra_run_id'] = None
print "SRA run_id missing"
## genome annotation release number
try:
version = name[2].split(' ')
org_db[short_name]['release_db'] = version[0]
org_db[short_name]['release_num'] = version[-1]
#sub_genome_folder = '%s/%s/%s_release_%s' % (data_path, short_name, version[0], version[-1])
## updating the fasta/gtf/index file location
#try:
# os.makedirs(sub_genome_folder)
# org_db[short_name]['fasta'] = sub_genome_folder
# org_db[short_name]['gtf'] = sub_genome_folder
# star_index_folder = '%s/STARgenome' % sub_genome_folder
# try:
# os.makedirs(star_index_folder)
# org_db[short_name]['index'] = star_index_folder
# except OSError:
# print "skipping creation of %s star index dir" % star_index_folder
#except OSError:
# print "skipping creation of %s genome version dir" % sub_genome_folder
except:
org_db[short_name]['release_db'] = None
org_db[short_name]['release_num'] = None
print "Genome annotation release database and number are missing"
fh.close()
return org_db
def experiment_db(config_file, opt_action):
"""
function to collect details of each organism
FIXME descriptions
@args config_file: yaml file contain the information for the experiment
@type config_file: str
"""
## parsing the config file
config_map = yaml.safe_load(open(config_file, "rU"))
data_path = config_map['genome_data_path']['dir']
exp_path = config_map['experiment_data_path']['dir']
org_fasta_file = dict(
A_carolinensis = '%s/A_carolinensis/ensembl_release_79/ensembl_release_79.fas' % data_path,
M_mulatta = "%s/M_mulatta/ensembl_release_79/ensembl_release_79.fas" % data_path,
O_cuniculus = "%s/O_cuniculus/ensembl_release_79/ensembl_release_79.fas" % data_path,
M_gallopavo = "%s/M_gallopavo/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
B_anthracis = '%s/B_anthracis/' % data_path,
C_familiaris = '%s/C_familiaris/ensembl_release_79/ensembl_release_79.fas' % data_path,
D_melanogaster = '%s/D_melanogaster/ensembl_release_79/ensembl_release_79.fas' % data_path,
E_caballus = '%s/E_caballus/ensembl_release_79/ensembl_release_79.fas' % data_path,
M_domestica = '%s/M_domestica/ensembl_release_79/ensembl_release_79.fas' % data_path,
O_sativa = '%s/O_sativa/phytozome_v9.0/Osativa_204.fa' % data_path,
A_gambiae = '%s/A_gambiae/ensembl_release_28/ensembl_release_28.fas' % data_path,
B_rapa = '%s/B_rapa/phytozome_v9.0/Brapa_197_stable.fa' % data_path,
G_gallus = '%s/G_gallus/ensembl_release_79/ensembl_release_79.fas' % data_path,
M_musculus = '%s/M_musculus/ensembl_release_79/ensembl_release_79.fas' % data_path,
V_vinifera = '%s/V_vinifera/phytozome_v9.0/phytozome_v9.0.fas.bz2' % data_path,
A_mellifera = '%s/A_mellifera/ensembl_release_28/ensembl_release_28.fas' % data_path,
B_taurus = '%s/B_taurus/ensembl_release_79/ensembl_release_79.fas' % data_path,
C_rubella = '%s/C_rubella/phytozome_v9.0/Crubella_183.fa.gz' % data_path,
D_rerio = '%s/D_rerio/ensembl_release_79/ensembl_release_79.fas' % data_path,
G_max = '%s/G_max/phytozome_v9.0/Gmax_189_filter.fa' % data_path,
M_truncatula = '%s/M_truncatula/STARgenome/Mtruncatula_198.fa' % data_path,
P_pacificus = '%s/P_pacificus/' % data_path,
S_scrofa = '%s/S_scrofa/ensembl_release_79/ensembl_release_79.fas' % data_path,
X_tropicalis = '%s/X_tropicalis/JGIv4-1/JGIv4-1.fa' % data_path,
C_sativus = '%s/C_sativus/phytozome_v9.0/Csativus_122_filtered.fa' % data_path,
D_simulans = '%s/D_simulans/ensembl_release_28/ensembl_release_28.fas' % data_path,
H_sapiens = '%s/H_sapiens/ensembl_release_79/STARgenome/hg19_chrOnly.fa' % data_path,
N_vitripennis = '%s/N_vitripennis/ensembl_release_22/N_vitripennis_dna_sm.fa' % data_path,
P_troglodytes = '%s/P_troglodytes/ensembl_release_79/ensembl_release_79.fas' % data_path,
S_tuberosum = '%s/S_tuberosum/phytozome_v9.0/Stuberosum_206.fa' % data_path,
Z_mays = '%s/Z_mays/phytozome_v9.0/Zmays_181.fa' % data_path,
A_thaliana = '%s/A_thaliana/arabidopsis_tair10/sequences/TAIR9_chr_all.fas' % data_path,
O_aries = '%s/O_aries/ensembl_release_79/ensembl_release_79.fas' % data_path,
C_jacchus = '%s/C_jacchus/ensembl_release_79/ensembl_release_79.fas' % data_path,
C_elegans = '%s/C_elegans/ensembl_release-69/Caenorhabditis_elegans.WBcel215.69.dna.toplevel.fa' % data_path,
O_latipes = '%s/O_latipes/ensembl_release_79/ensembl_release_79.fas' % data_path,
R_norvegicus = '%s/R_norvegicus/ensembl_release_79/ensembl_release_79.fas' % data_path,
G_gorilla = '%s/G_gorilla/ensembl_release_79/ensembl_release_79.fas' % data_path,
P_paniscus = '%s/P_paniscus/eva_mpg_de/eva_mpg_de.fas' % data_path,
C_porcellus = '%s/C_porcellus/ensembl_release_79/ensembl_release_79.fas' % data_path,
O_anatinus = '%s/O_anatinus/ensembl_release_79/ensembl_release_79.fas' % data_path,
A_platyrhynchos = '%s/A_platyrhynchos/ensembl_release_79/ensembl_release_79.fas' % data_path,
O_niloticus = '%s/O_niloticus/ensembl_release_79/ensembl_release_79.fas' % data_path,
L_chalumnae = '%s/L_chalumnae/ensembl_release_79/ensembl_release_79.fas' % data_path,
H_glaber = '%s/H_glaber/naked_mole_rat_db/naked_mole_rat_db.fas' % data_path,
M_eugenii = '%s/M_eugenii/ensembl_release_79/ensembl_release_79.fas' % data_path,
C_briggsae = '%s/C_briggsae/ensembl_release_28/ensembl_release_28.fas' % data_path,
C_japonica = '%s/C_japonica/ensembl_release_28/ensembl_release_28.fas' % data_path,
C_remanei = '%s/C_remanei/ensembl_release_28/ensembl_release_28.fas' % data_path,
P_marinus = '%s/P_marinus/ensembl_release_79/ensembl_release_79.fas' % data_path,
C_brenneri = '%s/C_brenneri/ensembl_release_28/ensembl_release_28.fas' % data_path,
C_intestinalis = '%s/C_intestinalis/ensembl_release_79/ensembl_release_79.fas' % data_path,
S_cerevisiae = '%s/S_cerevisiae/ensembl_release_79/ensembl_release_79.fas' % data_path,
S_pombe = '%s/S_pombe/ensembl_release_28/ensembl_release_28.fas' % data_path,
A_aegypti = '%s/A_aegypti/ensembl_release_28/ensembl_release_28.fas' % data_path,
C_hircus = '%s/C_hircus/ncbi_genome/ncbi_genome.fas' % data_path,
F_catus = '%s/F_catus/ensembl_release_79/ensembl_release_79.fas' % data_path,
T_nigroviridis = '%s/T_nigroviridis/ensembl_release_79/ensembl_release_79.fas' % data_path
)
#C_elegans = '%s/C_elegans/ensembl_release_79/ensembl_release_79.fas' % data_path,
org_gtf_file = dict(
A_carolinensis = '%s/A_carolinensis/ensembl_release_79/ensembl_release_79.gtf' % data_path,
M_mulatta = "%s/M_mulatta/ensembl_release_79/ensembl_release_79.gtf" % data_path,
O_cuniculus = "%s/O_cuniculus/ensembl_release_79/ensembl_release_79.gtf" % data_path,
M_gallopavo = "%s/M_gallopavo/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
B_anthracis = '%s/B_anthracis/ensembl_release-21/Bacillus_anthracis' % data_path,
C_familiaris = '%s/C_familiaris/ensembl_release_79/ensembl_release_79.gtf' % data_path,
D_melanogaster = '%s/D_melanogaster/ensembl_release_79/ensembl_release_79.gtf' % data_path,
E_caballus = '%s/E_caballus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
M_domestica = '%s/M_domestica/ensembl_release_79/ensembl_release_79.gtf' % data_path,
O_sativa = '%s/O_sativa/phytozome_v9.0/Osativa_204_gene.gff3' % data_path,
A_gambiae = '%s/A_gambiae/ensembl_release_28/ensembl_release_28.gtf' % data_path,
B_rapa = '%s/B_rapa/phytozome_v9.0/Brapa_197_gene.gff3' % data_path,
G_gallus = '%s/G_gallus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
M_musculus = '%s/M_musculus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
V_vinifera = '%s/V_vinifera/phytozome_v9.0/phytozome_v9.0.gff.bz2' % data_path,
A_mellifera = '%s/A_mellifera/ensembl_release_28/ensembl_release_28.gtf' % data_path,
B_taurus = '%s/B_taurus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_jacchus = '%s/C_jacchus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_rubella = '%s/C_rubella/phytozome_v9.0/Crubella_183.gff3' % data_path,
D_rerio = '%s/D_rerio/ensembl_release_79/ensembl_release_79.gtf' % data_path,
G_max = '%s/G_max/phytozome_v9.0/Gmax_189_gene.gff3' % data_path,
N_vitripennis = '%s/N_vitripennis/ensembl_release_22/N_vitripennis.gtf' % data_path,
O_aries = '%s/O_aries/ensembl_release_79/ensembl_release_79.gtf' % data_path,
M_truncatula = '%s/M_truncatula/' % data_path,
P_pacificus = '%s/P_pacificus/ensembl_release-22/.gtf' % data_path,
S_scrofa = '%s/S_scrofa/ensembl_release_79/ensembl_release_79.gtf' % data_path,
X_tropicalis = '%s/X_tropicalis/JGIv4-1/JGIv4-1.gff' % data_path,
C_sativus = '%s/C_sativus/phytozome_v9.0/Csativus_122_gene.gff3' % data_path,
D_simulans = '%s/D_simulans/ensembl_release_28/ensembl_release_28.gtf' % data_path,
H_sapiens = '%s/H_sapiens/ensembl_release_79/ensembl_release_79.gtf' % data_path,
P_troglodytes = '%s/P_troglodytes/ensembl_release_79/ensembl_release_79.gtf' % data_path,
S_tuberosum = '%s/S_tuberosum/phytozome_v9.0/Stuberosum_206_gene.gff3' % data_path,
Z_mays = '%s/Z_mays/phytozome_v9.0/Zmays_181_gene.gff3' % data_path,
A_thaliana = '%s/A_thaliana/arabidopsis_tair10/annotations/TAIR10_GFF3_genes.gff' % data_path,
C_elegans = '%s/C_elegans/ensembl_release_79/ensembl_release_79.gtf' % data_path,
D_discoideum = '%s/D_discoideum/' % data_path,
D_yakuba = '%s/D_yakuba/ensembl_release-22/.gff3' % data_path,
O_latipes = '%s/O_latipes/ensembl_release_79/ensembl_release_79.gtf' % data_path,
R_norvegicus = '%s/R_norvegicus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
D_pseudoobscura = '%s/D_pseudoobscura/ensembl_release-22/.gff3' % data_path,
T_pseudonana = '%s/T_pseudonana/Thaps3/.gff' % data_path,
G_gorilla = '%s/G_gorilla/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_porcellus = '%s/C_porcellus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
O_anatinus = '%s/O_anatinus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
A_platyrhynchos = '%s/A_platyrhynchos/ensembl_release_79/ensembl_release_79.gtf' % data_path,
O_niloticus = '%s/O_niloticus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
L_chalumnae = '%s/L_chalumnae/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_briggsae = '%s/C_briggsae/ensembl_release_28/ensembl_release_28.gtf' % data_path,
M_eugenii = '%s/M_eugenii/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_remanei = '%s/C_remanei/ensembl_release_28/ensembl_release_28.gtf' % data_path,
C_brenneri = '%s/C_brenneri/ensembl_release_28/ensembl_release_28.gtf' % data_path,
C_intestinalis = '%s/C_intestinalis/ensembl_release_79/ensembl_release_79.gtf' % data_path,
S_pombe = '%s/S_pombe/ensembl_release_28/ensembl_release_28.gtf' % data_path,
P_marinus = '%s/P_marinus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
S_cerevisiae = '%s/S_cerevisiae/ensembl_release_79/ensembl_release_79.gtf' % data_path,
C_japonica = '%s/C_japonica/ensembl_release_28/ensembl_release_28.gtf' % data_path,
F_catus = '%s/F_catus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
A_aegypti = '%s/A_aegypti/ensembl_release_28/ensembl_release_28.gtf' % data_path,
C_hircus = '%s/C_hircus/ncbi_genome/ncbi_genome.gff' % data_path,
T_nigroviridis = '%s/T_nigroviridis/ensembl_release_79/ensembl_release_79.gtf' % data_path
)
## TODO algorithms details
#A_aegypti = '%s/A_aegypti/ensembl_release_28/ensembl_release_28.gtf' % data_path,
#F_catus = '%s/F_catus/ensembl_release_79/ensembl_release_79.gtf' % data_path,
#C_hircus = '%s/C_hircus/ncbi_genome/ncbi_genome.gff' % data_path,
#H_glaber = '%s/H_glaber/naked_mole_rat_db/naked_mole_rat_db.gtf' % data_path,
## experiment details
org_db = defaultdict()
for ent in config_map['experiment']:
species_name = ent['organism_name']
sra_run_id = ent['sra_run_id']
genome_build_version = ent['genome_build_version']
db_server = ent['release_db']
## mapping to short names arabidopsis_thaliana --> A_thaliana
genus, species = species_name.strip().split("_")
short_name = "%s_%s" % (genus[0].upper(), species)
org_db[short_name] = dict(short_name = short_name)
org_db[short_name]['long_name'] = species_name
org_db[short_name]['sra_run_id'] = sra_run_id
org_db[short_name]['genome_release_db'] = genome_build_version
## the broad path to the experiment
org_db[short_name]['genome_dir'] = data_path
org_db[short_name]['experiment_dir'] = exp_path
build_release = genome_build_version.split("_")
org_db[short_name]['release_db'] = db_server ## ensembl_metazoa, phytozome
org_db[short_name]['release_nb'] = build_release[-1] ## build number
sra_files = [] ## sequencing reads files
if os.path.isdir("%s/%s/source_data" % (exp_path, short_name)):
for sra_file in os.listdir("%s/%s/source_data" % (exp_path, short_name)):
file_prefx, ext = os.path.splitext(sra_file)
if ext == ".sra": ## skipping the original .sra binary file
continue
if re.search(sra_run_id, sra_file):
sra_files.append(sra_file)
else:
print "warning: missing sequencing read trace file %s/%s/source_data" % (exp_path, short_name)
org_db[short_name]['fastq_path'] = "%s/%s/source_data" % (exp_path, short_name)
org_db[short_name]['fastq'] = sra_files
## read mapping, read assembly and label generation working folders
for sub_dir in ['read_mapping', 'signal_labels', 'trans_pred', 'source_data']:
work_path = "%s/%s/%s" % (exp_path, short_name, sub_dir)
if not os.path.isdir(work_path):
try:
os.makedirs(work_path)
except OSError:
exit("error: cannot create the directory %s." % work_path)
org_db[short_name]['read_map_dir'] = "%s/%s/read_mapping" % (exp_path, short_name)
org_db[short_name]['read_assembly_dir'] = "%s/%s/trans_pred" % (exp_path, short_name)
org_db[short_name]['labels_dir'] = "%s/%s/signal_labels" % (exp_path, short_name)
## calculate the sequence read length
readlength = 0
if opt_action in ["2", "3"]: ## perform this action only for selected options
if sra_files:
fqfile = os.path.join(org_db[short_name]['fastq_path'], sra_files[0])
print 'using sequencing read file %s to determine readLength' % fqfile
fh = helper.open_file(fqfile)
for rec in SeqIO.parse(fh, "fastq"):
readlength = len(rec.seq)
break
fh.close()
org_db[short_name]['read_length'] = readlength
## check for the genome sequence file
if short_name in org_fasta_file:
if os.path.isfile(org_fasta_file[short_name]):
org_db[short_name]['fasta'] = org_fasta_file[short_name]
else:
org_db[short_name]['fasta'] = None
else:
print "warning: missing genome sequence file for %s under %s/%s/%s" % (short_name, data_path, short_name, genome_build_version)
org_db[short_name]['fasta'] = None
if not os.path.isdir("%s/%s/%s/STARgenome" % (data_path, short_name, genome_build_version)):
try:
os.makedirs("%s/%s/%s/STARgenome" % (data_path, short_name, genome_build_version))
except OSError:
exit("error: cannot create the directory %s/%s/%s" % (data_path, short_name, genome_build_version))
org_db[short_name]['genome_index_dir'] = "%s/%s/%s/STARgenome/" % (data_path, short_name, genome_build_version)
## check the genome annotation
if short_name in org_gtf_file:
if os.path.isfile(org_gtf_file[short_name]):
org_db[short_name]['gtf'] = org_gtf_file[short_name]
if opt_action in ["2", "3", "4", "c"]: ## perform this action only for selected options
## get the gtf feature lengths
from fetch_remote_data import prepare_data as pd
feat_len_db = pd.make_anno_db(org_gtf_file[short_name])
org_db[short_name]['max_intron_len'] = feat_len_db['max_intron']
org_db[short_name]['max_exon_len'] = feat_len_db['max_exon']
else:
exit("error: the provided gtf file %s is not available to read. Please check!" % org_gtf_file[short_name])
else:
print("warning: missing annotation file for %s under %s/%s/%s" % (short_name, data_path, short_name, genome_build_version))
org_db[short_name]['gtf'] = None
org_db[short_name]['max_intron_len'] = None
org_db[short_name]['max_exon_len'] = None
print("fetched details for %s" % short_name)
return org_db
def experiment_db(config_file, opt_action):
"""
function to collect details of each organism
FIXME descriptions
@args config_file: yaml file contain the information for the experiment
@type config_file: str
"""
## parsing the config file
config_map = yaml.safe_load(open(config_file, "rU"))
data_path = config_map["genome_data_path"]["dir"]
exp_path = config_map["experiment_data_path"]["dir"]
org_fasta_file = dict(
A_carolinensis="%s/A_carolinensis/ensembl_release_79/ensembl_release_79.fas" % data_path,
M_mulatta="%s/M_mulatta/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
O_cuniculus="%s/O_cuniculus/ensembl_release_79/ensembl_release_79.fas" % data_path,
M_gallopavo="%s/M_gallopavo/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
B_anthracis="%s/B_anthracis/ensembl_release-21/Bacillus_anthracis_str_a0193.GCA_000181915.1.21.dna.toplevel.fa"
% data_path,
C_familiaris="%s/C_familiaris/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
D_melanogaster="%s/D_melanogaster/ensembl_release_79/ensembl_release_79.fas" % data_path,
E_caballus="%s/E_caballus/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
M_domestica="%s/M_domestica/ensembl_release-69/Monodelphis_domestica.BROADO5.69.dna.toplevel.fa" % data_path,
O_sativa="%s/O_sativa/phytozome_v9.0/Osativa_204.fa" % data_path,
A_gambiae="%s/A_gambiae/anoGam1_ucsc/anoGam1_rm.fasta" % data_path,
B_rapa="%s/B_rapa/phytozome_v9.0/Brapa_197_stable.fa" % data_path,
C_japonica="%s/C_japonica/STARgenome/Caenorhabditis_japonica.C_japonica-7.0.1.22.dna_sm.stable.fa" % data_path,
G_gallus="%s/G_gallus/ensembl_release_79/ensembl_release_79.fas" % data_path,
M_musculus="%s/M_musculus/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
V_vinifera="%s/V_vinifera/phytozome_v9.0/phytozome_v9.0.fas.bz2" % data_path,
A_mellifera="%s/A_mellifera/apiMel3_ucsc/apiMel3_sm.fasta" % data_path,
B_taurus="%s/B_taurus/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
C_rubella="%s/C_rubella/phytozome_v9.0/Crubella_183.fa.gz" % data_path,
D_rerio="%s/D_rerio/ensembl_release_79/ensembl_release_79.fas" % data_path,
G_max="%s/G_max/phytozome_v9.0/Gmax_189_filter.fa" % data_path,
M_truncatula="%s/M_truncatula/STARgenome/Mtruncatula_198.fa" % data_path,
P_pacificus="%s/P_pacificus/STARgenome/Pristionchus_pacificus.P_pacificus-5.0.22.dna_sm.stable.fa" % data_path,
S_scrofa="%s/S_scrofa/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
X_tropicalis="%s/X_tropicalis/JGIv4-1/JGIv4-1.fa" % data_path,
C_sativus="%s/C_sativus/phytozome_v9.0/Csativus_122_filtered.fa" % data_path,
D_simulans="%s/D_simulans/ensembl_release_22/ensembl_release_22.fas.bz2" % data_path,
H_sapiens="%s/H_sapiens/hg19_bowtie2/hg19.fa" % data_path,
O_anatinus="%s/O_anatinus/ensembl_release-69/Ornithorhynchus_anatinus.OANA5.69-filtered_dna.fa" % data_path,
N_vitripennis="%s/N_vitripennis/ensembl_release_22/N_vitripennis_dna_sm.fa" % data_path,
P_troglodytes="%s/P_troglodytes/ensembl_release_79/ensembl_release_79.fas.bz2" % data_path,
S_tuberosum="%s/S_tuberosum/phytozome_v9.0/Stuberosum_206.fa" % data_path,
Z_mays="%s/Z_mays/phytozome_v9.0/Zmays_181.fa" % data_path,
A_thaliana="%s/A_thaliana/arabidopsis_tair10/sequences/TAIR9_chr_all.fas" % data_path,
O_aries="%s/O_aries/ensembl_release_79/ensembl_release_79.fas" % data_path,
C_jacchus="%s/C_jacchus/ensembl_release_79/ensembl_release_79.fas" % data_path,
C_elegans="%s/C_elegans/ensembl_release_79/ensembl_release_79.fas" % data_path,
O_latipes="%s/O_latipes/ensembl_release_79/ensembl_release_79.fas" % data_path,
R_norvegicus="%s/R_norvegicus/ensembl_release_79/ensembl_release_79.fas" % data_path,
C_briggsae="%s/C_briggsae/ensembl_release_22/ensembl_release_22.fas.bz2" % data_path,
T_nigroviridis="%s/T_nigroviridis/ensembl_release_79/ensembl_release_79.fas" % data_path,
)
org_gtf_file = dict(
A_carolinensis="%s/A_carolinensis/ensembl_release_79/ensembl_release_79.gtf" % data_path,
M_mulatta="%s/M_mulatta/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
O_cuniculus="%s/O_cuniculus/ensembl_release_79/ensembl_release_79.gtf" % data_path,
M_gallopavo="%s/M_gallopavo/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
B_anthracis="%s/B_anthracis/ensembl_release-21/Bacillus_anthracis" % data_path,
C_familiaris="%s/C_familiaris/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
D_melanogaster="%s/D_melanogaster/ensembl_release_79/ensembl_release_79.gtf" % data_path,
E_caballus="%s/E_caballus/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
M_domestica="%s/M_domestica/ensembl_release-69/Monodelphis_domestica.BROADO5.69.gtf" % data_path,
O_sativa="%s/O_sativa/phytozome_v9.0/Osativa_204_gene.gff3" % data_path,
A_gambiae="%s/A_gambiae/anoGam1_ucsc/anoGam1_ucsc.gtf" % data_path,
B_rapa="%s/B_rapa/phytozome_v9.0/Brapa_197_gene.gff3" % data_path,
C_japonica="%s/C_japonica/ensembl_release-22/Caenorhabditis_japonica.C_japonica-7.0.1.22.gff3" % data_path,
G_gallus="%s/G_gallus/ensembl_release_79/ensembl_release_79.gtf" % data_path,
M_musculus="%s/M_musculus/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
V_vinifera="%s/V_vinifera/phytozome_v9.0/phytozome_v9.0.gff.bz2" % data_path,
A_mellifera="%s/A_mellifera/apiMel3_ucsc/apiMel2_ucsc.gtf" % data_path,
B_taurus="%s/B_taurus/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
C_jacchus="%s/C_jacchus/ensembl_release_79/ensembl_release_79.gtf" % data_path,
C_rubella="%s/C_rubella/phytozome_v9.0/Crubella_183.gff3" % data_path,
D_rerio="%s/D_rerio/ensembl_release_79/ensembl_release_79.gtf" % data_path,
G_max="%s/G_max/phytozome_v9.0/Gmax_189_gene.gff3" % data_path,
N_vitripennis="%s/N_vitripennis/ensembl_release_22/N_vitripennis.gtf" % data_path,
O_aries="%s/O_aries/ensembl_release_79/ensembl_release_79.gtf" % data_path,
M_truncatula="%s/M_truncatula/" % data_path,
P_pacificus="%s/P_pacificus/ensembl_release-22/Pristionchus_pacificus.P_pacificus-5.0.22.gtf" % data_path,
S_scrofa="%s/S_scrofa/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
X_tropicalis="%s/X_tropicalis/JGIv4-1/JGIv4-1.gff" % data_path,
C_sativus="%s/C_sativus/phytozome_v9.0/Csativus_122_gene.gff3" % data_path,
D_simulans="%s/D_simulans/ensembl_release_22/ensembl_release_22.gff.bz2" % data_path,
H_sapiens="%s/H_sapiens/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
O_anatinus="%s/O_anatinus/ensembl_release-69/" % data_path,
P_troglodytes="%s/P_troglodytes/ensembl_release_79/ensembl_release_79.gtf.bz2" % data_path,
S_tuberosum="%s/S_tuberosum/phytozome_v9.0/Stuberosum_206_gene.gff3" % data_path,
Z_mays="%s/Z_mays/phytozome_v9.0/Zmays_181_gene.gff3" % data_path,
A_thaliana="%s/A_thaliana/arabidopsis_tair10/annotations/TAIR10_GFF3_genes.gff" % data_path,
C_elegans="%s/C_elegans/ensembl_release_79/ensembl_release_79.gtf" % data_path,
D_discoideum="%s/D_discoideum/" % data_path,
D_yakuba="%s/D_yakuba/ensembl_release-22/Drosophila_yakuba.dyak_r1.3_FB2008_07.22.gff3" % data_path,
O_latipes="%s/O_latipes/ensembl_release_79/ensembl_release_79.gtf" % data_path,
R_norvegicus="%s/R_norvegicus/ensembl_release_79/ensembl_release_79.gtf" % data_path,
C_briggsae="%s/C_briggsae/ensembl_release_22/ensembl_release_22.gff.bz2" % data_path,
C_brenneri="%s/C_brenneri/ensembl_release-22/Caenorhabditis_brenneri.C_brenneri-6.0.1b.22.gff3" % data_path,
C_remanei="%s/C_remanei/ensembl_release-22/Caenorhabditis_remanei.C_remanei-15.0.1.22.gff3" % data_path,
D_pseudoobscura="%s/D_pseudoobscura/ensembl_release-22/Drosophila_pseudoobscura.HGSC2.22.gff3" % data_path,
T_pseudonana="%s/T_pseudonana/Thaps3/Thaps3_chromosomes_geneModels_FilteredModels2.gff" % data_path,
T_nigroviridis="%s/T_nigroviridis/ensembl_release_79/ensembl_release_79.gtf" % data_path,
)
## TODO algorithms details
## experiment details
org_db = defaultdict()
for ent in config_map["experiment"]:
species_name = ent["organism_name"]
sra_run_id = ent["sra_run_id"]
genome_build_version = ent["genome_build_version"]
db_server = ent["release_db"]
## mapping to short names arabidopsis_thaliana --> A_thaliana
genus, species = species_name.strip().split("_")
short_name = "%s_%s" % (genus[0].upper(), species)
org_db[short_name] = dict(short_name=short_name)
org_db[short_name]["long_name"] = species_name
org_db[short_name]["sra_run_id"] = sra_run_id
org_db[short_name]["genome_release_db"] = genome_build_version
## the broad path to the experiment
org_db[short_name]["genome_dir"] = data_path
org_db[short_name]["experiment_dir"] = exp_path
build_release = genome_build_version.split("_")
org_db[short_name]["release_db"] = db_server ## ensembl_metazoa, phytozome
org_db[short_name]["release_nb"] = build_release[-1] ## build number
sra_files = [] ## sequencing reads files
if os.path.isdir("%s/%s/source_data" % (exp_path, short_name)):
for sra_file in os.listdir("%s/%s/source_data" % (exp_path, short_name)):
file_prefx, ext = os.path.splitext(sra_file)
if ext == ".sra": ## skipping the original .sra binary file
continue
if re.search(sra_run_id, sra_file):
sra_files.append(sra_file)
else:
print "warning: missing sequencing read trace file %s/%s/source_data" % (exp_path, short_name)
org_db[short_name]["fastq_path"] = "%s/%s/source_data" % (exp_path, short_name)
org_db[short_name]["fastq"] = sra_files
## read mapping, read assembly and label generation working folders
for sub_dir in ["read_mapping", "signal_labels", "trans_pred"]:
work_path = "%s/%s/%s" % (exp_path, short_name, sub_dir)
if not os.path.isdir(work_path):
try:
os.makedirs(work_path)
except OSError:
print "error: cannot create the directory %s." % work_path
sys.exit(0)
org_db[short_name]["read_map_dir"] = "%s/%s/read_mapping" % (exp_path, short_name)
org_db[short_name]["read_assembly_dir"] = "%s/%s/trans_pred" % (exp_path, short_name)
org_db[short_name]["labels_dir"] = "%s/%s/signal_labels" % (exp_path, short_name)
## calculate the sequence read length
readlength = 0
if opt_action in ["2", "3"]: ## perform this action only for selected options
if sra_files:
fqfile = os.path.join(org_db[short_name]["fastq_path"], sra_files[0])
print "using sequencing read file %s to determine readLength" % fqfile
fh = helper.open_file(fqfile)
for rec in SeqIO.parse(fh, "fastq"):
readlength = len(rec.seq)
break
fh.close()
org_db[short_name]["read_length"] = readlength
## check for the genome sequence file
if short_name in org_fasta_file:
if os.path.isfile(org_fasta_file[short_name]):
org_db[short_name]["fasta"] = org_fasta_file[short_name]
else:
org_db[short_name]["fasta"] = None
else:
print "warning: missing genome sequence file for %s under %s/%s/%s" % (
short_name,
data_path,
short_name,
genome_build_version,
)
org_db[short_name]["fasta"] = None
if not os.path.isdir("%s/%s/%s/STARgenome" % (data_path, short_name, genome_build_version)):
try:
os.makedirs("%s/%s/%s/STARgenome" % (data_path, short_name, genome_build_version))
except OSError:
print "error: cannot create the directory %s/%s/%s" % (data_path, short_name, genome_build_version)
sys.exit(0)
org_db[short_name]["genome_index_dir"] = "%s/%s/%s/STARgenome/" % (data_path, short_name, genome_build_version)
## check the genome annotation
if short_name in org_gtf_file:
if os.path.isfile(org_gtf_file[short_name]):
org_db[short_name]["gtf"] = org_gtf_file[short_name]
if opt_action in ["2", "3", "4", "c"]: ## perform this action only for selected options
## get the gtf feature lengths
from fetch_remote_data import prepare_data as pd
feat_len_db = pd.make_anno_db(org_gtf_file[short_name])
org_db[short_name]["max_intron_len"] = feat_len_db["max_intron"]
org_db[short_name]["max_exon_len"] = feat_len_db["max_exon"]
else:
print "error: the provided gtf file %s is not available to read. Please check!" % org_gtf_file[
short_name
]
sys.exit(-1)
else:
print "warning: missing annotation file for %s under %s/%s/%s" % (
short_name,
data_path,
short_name,
genome_build_version,
)
org_db[short_name]["gtf"] = None
org_db[short_name]["max_intron_len"] = None
org_db[short_name]["max_exon_len"] = None
print "fetched details for %s" % short_name
return org_db
