def readSeqs(spec, tid_list, utr=False):
if spec == "mouse":
exons_file = "../Reference-genomes/mm10/Mus_musculus.GRCm38.exon.all.200flank.fa"
utr5_file = "../Reference-genomes/mm10/Mus_musculus.GRCm38.5utr.fa"
utr3_file = "../Reference-genomes/mm10/Mus_musculus.GRCm38.3utr.fa"
elif spec == "rat":
exons_file = "../Reference-genomes/Rnor6/Rattus_norvegicus.Rnor_6.0.exon.all.200flank.fa"
utr5_file = "../Reference-genomes/Rnor6/Rattus_norvegicus.Rnor_6.0.5utr.fa"
utr3_file = "../Reference-genomes/Rnor6/Rattus_norvegicus.Rnor_6.0.3utr.fa"
# Sequences downloaded from Ensembl Biomart 99
mcore.PWS("# " + mcore.getDateTime() + " Reading " + spec +
" exon sequences: " + exons_file)
exons = mseq.fastaGetDict(exons_file)
# Read the sequences
exons = parseHeaderIds(exons, "exon", tid_list)
# Parse the header IDs so they only contain the exon ID.
mcore.PWS("# Total sequences read: " + str(len(exons)))
mcore.PWS("# ----------------")
# This block reads the exon sequences + 500bp of flanking sequence
utr5, utr3 = "", ""
if utr:
mcore.PWS("# " + mcore.getDateTime() + " Reading " + spec +
" UTR sequences: " + utr5_file + " " + utr3_file)
utr5 = mseq.fastaGetDict(utr5_file)
utr5 = parseHeaderIds(utr5, "utr", tid_list)
utr3 = mseq.fastaGetDict(utr3_file)
utr3 = parseHeaderIds(utr3, "utr", tid_list)
# Read the sequences and parse the header IDs so each exon coincides with the UTR for the transcript
mcore.PWS("# Total 5' UTRs read: " + str(len(utr5)))
mcore.PWS("# Total 3' UTRs read: " + str(len(utr3)))
mcore.PWS("# ----------------")
# This block reads the UTR sequences
return exons, utr5, utr3
transcript_file = "../02-Annotation-data/selected-transcripts.txt"
outdir = "../02-Annotation-data/transcript-seq/"
#outdir = "../02-Annotation-data/ts2/";
logfilename = "get_selected_seqs.log"
# Hardcoded file names
with open(logfilename, "w") as logfile:
mcore.runTime("# Rodent exomes -- get mouse CDS", logfile)
mcore.PWS("# Mouse reference FASTA: " + ref, logfile)
mcore.PWS("# Mouse GTF file: " + gtffile_mouse, logfile)
mcore.PWS("# Transcripts file: " + transcript_file, logfile)
mcore.PWS("# Sequence output dir: " + outdir, logfile)
mcore.PWS("# Log file: " + logfilename, logfile)
mcore.PWS("# ----------------", logfile)
mcore.PWS("# " + mcore.getDateTime() + " Reading mouse transcripts...",
logfile)
mouse_transcripts = {}
transcript_len_sum, first = 0, True
for line in open(transcript_file):
if line[0] == "#" or first:
first = False
continue
line = line.strip().split("\t")
tid, chrome, start, end, length = line[1], line[15], line[16], line[
17], line[18]
transcript_len_sum += int(length)
chrome = "chr" + chrome
mouse_transcripts[tid] = {
'chrome': chrome,
datasets = [
"australian-full-all", "australian-full-coding", "australian-reduced-all",
"australian-reduced-coding", "reproductive-all", "reproductive-coding",
"reproductive-mclennan-all", "reproductive-mclennan-coding",
"reproductive-pahl-all", "reproductive-pahl-coding",
"reproductive-testes-mass-all", "reproductive-testes-mass-coding",
"reproductive-sperm-img-all", "reproductive-sperm-img-coding",
"reproductive-sperm-morpho-all", "reproductive-sperm-morpho-coding",
"full-all", "full-coding"
]
dataset = "reproductive-all"
if dataset not in datasets:
sys.exit(" * ERROR: check dataset.")
mcore.PWS("# " + mcore.getDateTime() + " Separating sequences for dataset: " +
dataset)
####
exclude_samples = []
add_rat = False
add_mouse = False
rm_samples = False
rmdir = "../03-Alignments/samples-to-rm/"
# Job variables
####
orthfile = "../02-Annotation-data/mm10-rnor6-master-transcript-id-table.tab"
# The ortholog file between mouse and rat.
sys.exit(" * ERROR: Species must be provided: macaque or human")
if species == 'mouse':
gtffile = "../Reference-genomes/mm10/Mus_musculus.GRCm38.99.gtf.gz"
regstr = "MUS"
elif species == 'rat':
gtffile = "../Reference-genomes/Rnor6/Rattus_norvegicus.Rnor_6.0.99.gtf.gz"
regstr = "RNO"
outfilename = "intron-sizes-" + species + ".csv"
mcore.runTime("# Rodent exomes -- get intron lengths")
mcore.PWS("# GTF file: " + gtffile)
mcore.PWS("# Output file: " + outfilename)
mcore.PWS("# ----------------")
mcore.PWS("# " + mcore.getDateTime() + " Reading transcripts...")
transcripts = {}
transcript_len_sum, first = 0, True
for line in gzip.open(gtffile):
line = line.decode()
if line[0] == "#":
continue
line = line.strip().split("\t")
feature_type, chrome, start, end, strand, feature_info = line[2], line[
0], int(line[3]), int(line[4]), line[6], line[8]
if feature_type == "transcript" and "protein_coding" in feature_info:
tid = re.findall('ENS' + regstr + 'T[\d]+', feature_info)[0]
length = end - start
transcript_len_sum += int(length)
transcripts[tid] = {
with open(outfilename, "w") as outfile:
mcore.runTime("# Rodent exomes -- select mouse trancsripts", outfile)
mcore.PWS("# Mouse GTF file: " + gtffile_mouse, outfile)
mcore.PWS("# Rat GTF file: " + gtffile_rat, outfile)
mcore.PWS("# Ensembl ortholog file: " + infile, outfile)
if mode == "targets":
mcore.PWS("# Target overlaps file: " + target_overlaps, outfile)
mcore.PWS("# Output file: " + outfilename, outfile)
mcore.PWS("# --------------", outfile)
mcore.PWS("# dS threshold: " + str(ds_thresh), outfile)
mcore.PWS("# --------------", outfile)
if mode == "targets":
mcore.PWS("# " + mcore.getDateTime() + " Reading target overlaps...",
outfile)
mouse_transcript_overlaps = {}
for line in open(target_overlaps):
line = line.strip().split("\t")
if line[4] == ".":
continue
gid, tid, eid = line[7].split(";")
if gid not in mouse_transcript_overlaps:
mouse_transcript_overlaps[gid] = {}
if tid not in mouse_transcript_overlaps[gid]:
mouse_transcript_overlaps[gid][tid] = 0
mouse_transcript_overlaps[gid][tid] += 1
mcore.PWS("# " + mcore.getDateTime() + " Reading mouse feature lengths...",
mcore.PWS(
mcore.spacedOut("# SLURM cpus-per-task:", pad) + str(args.cpus),
outfile)
mcore.PWS(mcore.spacedOut("# SLURM mem:", pad) + str(args.mem), outfile)
mcore.PWS("# ----------", outfile)
mcore.PWS("# BEGIN CMDS", outfile)
##########################
# Generating the commands in the job file.
mouse_aa_dir = "/mnt/beegfs/gt156213e/murinae-seq/02-Annotation-data/seq/mm10-selected-cds-aa-trimmed/"
skip_file = "mm10-exons-w-stops.txt"
seqfiles = os.listdir(mouse_aa_dir)
#targets_file = "../02-Annotation-data/Mus-selected-sequences_metadata_samp-counts_ratids-TESTSET.csv";
targets_file = "../02-Annotation-data/Mus-selected-sequences_metadata_samp-counts_ratids.csv"
mcore.PWS("# " + mcore.getDateTime() + " Reading IDs: " + targets_file)
targets, targ_to_pid, pid_to_targ = {}, {}, defaultdict(list)
first = True
for line in open(targets_file):
if first:
first = False
continue
line = line.strip().split(",")
targ, coding, tid, pid, eid, num_targs = line[0].replace(
"\"", ""), line[1].replace("\"", ""), line[9].replace(
"\"", ""), line[13].replace("\"",
""), line[17].replace("\"",
""), line[22]
if pid == "NA" or num_targs == "NA" or coding == "FALSE":
continue