Python spacedOut 예제들

예제 #1

# Reference options

if args.spec == "all":
    spec = specs_ordered
else:
    spec = args.spec.replace(", ", ",").split(",")
    for s in spec:
        if s not in spec_ids:
            sys.exit("SF2", "Cannot find specified species: " + s)
# Parse the input species.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent BAM commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(
        mcore.spacedOut("# Current step:", pad) + "BAM merging", jobfile)
    mcore.PWS(mcore.spacedOut("# Input directory:", pad) + indir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Species job directory:", pad) + jobs_dir, jobfile)
    if not os.path.isdir(jobs_dir):
        mcore.PWS("# Creating jobs directory.", jobfile)
        os.system("mkdir " + jobs_dir)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)
    mcore.PWS(mcore.spacedOut("# Logfile directory:", pad) + logdir, jobfile)
    if not os.path.isdir(logdir):
        mcore.PWS("# Creating logfile directory.", jobfile)

예제 #2

    spec = specs_ordered
else:
    spec = args.spec.replace(", ", ",").split(",")
    for s in spec:
        if s not in spec_ids:
            sys.exit(" * ERROR SF2: Cannot find specified species: " + s)
# Parse the input species.

##########################
# Reporting run-time info for records.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent post-dedup reformat commands",
                  jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(mcore.spacedOut("# Current step:", pad) + step, jobfile)
    mcore.PWS(mcore.spacedOut("# Previous step:", pad) + prev_step, jobfile)
    mcore.PWS("# ----------", jobfile)
    mcore.PWS("# I/O INFO", jobfile)
    mcore.PWS(
        mcore.spacedOut("# Input directory:", pad) + prev_step_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Output directory:", pad) + dedup_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Intermediate reformat directory:", pad) +
        reformat_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# reformat.sh path:", pad) + args.path, jobfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, jobfile)
    mcore.PWS(mcore.spacedOut("# Seq runs:", pad) + args.runtype, jobfile)
    if not args.name:

예제 #3

파일: 06_map_cmd_generator.py 프로젝트: goodest-goodlab/murinae-seq

base_logdir = os.path.abspath("logs/")
logdir = os.path.join(base_logdir, step + "-logs")
# Step I/O info.

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
print(runtype, runstrs)
# Parse the input run types.

spec = mfiles.parseSpecs(args.spec, specs_ordered)
# Parse the input species.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent BWA commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(mcore.spacedOut("# Current step:", pad) + step, jobfile)
    mcore.PWS(mcore.spacedOut("# Previous step:", pad) + prev_step, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Input directory:", pad) + prev_step_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Assembly directory:", pad) + ref_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Output directory:", pad) + step_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# BWA path:", pad) + args.path, jobfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)
    mcore.PWS(mcore.spacedOut("# Logfile directory:", pad) + logdir, jobfile)
    if not os.path.isdir(logdir):

예제 #4

파일: 05_index_generator.py 프로젝트: goodest-goodlab/murinae-seq

logdir = os.path.join(base_logdir, step + "-logs")
# Step I/O info.

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
print(runtype, runstrs)
# Parse the input run types.

spec = mfiles.parseSpecs(args.spec, specs_ordered)
# Parse the input species.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent BWA commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    #mcore.PWS(mcore.spacedOut("# Reads directory:", pad) + read_dir, jobfile);
    mcore.PWS(
        mcore.spacedOut("# Assembly input directory:", pad) + assembly_indir,
        jobfile)
    mcore.PWS(
        mcore.spacedOut("# Assembly output directory:", pad) + assembly_outdir,
        jobfile)
    #mcore.PWS(mcore.spacedOut("# Output directory:", pad) + bam_dir, jobfile);
    #mcore.PWS(mcore.spacedOut("# Pseudo-it path:", pad) + args.path, jobfile);
    mcore.PWS(mcore.spacedOut("# Species:", pad) + str(args.spec), jobfile)
    mcore.PWS(
        mcore.spacedOut("# Run types:", pad) + str(args.runtype), jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)
    mcore.PWS(mcore.spacedOut("# Logfile directory:", pad) + logdir, jobfile)

예제 #5

파일: count_reads.py 프로젝트: goodest-goodlab/murinae-seq

# Job files

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
# Parse the input run types.

specs = mfiles.parseSpecs(args.spec, specs_ordered)
specs = [s for s in specs if "(no WGA)" not in s and "pos_ctrl" not in s]
specs = [s for s in specs if any(r in spec_ids[s] for r in runtype)]
# Parse the input species.

##########################
# Reporting run-time info for records.
with open(output_file, "w") as outfile, mp.Pool(processes=args.procs) as pool:
    mcore.runTime("# Rodent read counting", outfile)
    mcore.PWS(
        mcore.spacedOut("# Input directory:", pad) + args.indir, outfile)
    mcore.PWS(mcore.spacedOut("# Output file:", pad) + output_file, outfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, outfile)
    mcore.PWS(mcore.spacedOut("# Seq runs:", pad) + args.runtype, outfile)
    mcore.PWS(mcore.spacedOut("# Job file:", pad) + output_file, outfile)
    mcore.PWS("# ----------", outfile)
    mcore.PWS("# BEGIN OUTPUT", outfile)

    ##########################
    headers = ["Total bases", "Total reads"]
    mcore.PWS("Species" + "," + ",".join(headers))

    outlines = {}
    chunk_num, spec_num = 1, 1
    cur_specs = []

예제 #6

for line in open(target_file):
    line = line.strip().split("\t")
    total_target_len += (float(line[2]) - float(line[1]))

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
# Parse the input run types.

specs = mfiles.parseSpecs(args.spec, specs_ordered)
specs = [s for s in specs if "(no WGA)" not in s and "pos_ctrl" not in s]
specs = [s for s in specs if any(r in spec_ids[s] for r in runtype)]
# Parse the input species.

with open(outfilename, "w") as outfile, mp.Pool(processes=args.procs) as pool:
    mcore.runTime("# Rodent assembly and mapping stats", outfile)
    mcore.PWS(
        mcore.spacedOut("# Total species:", pad) + str(len(specs)), outfile)
    mcore.PWS(
        mcore.spacedOut("# Total target length:", pad) + str(total_target_len),
        outfile)
    mcore.PWS(mcore.spacedOut("# Mapping directory:", pad) + map_dir, outfile)
    mcore.PWS(
        mcore.spacedOut("# Assembly directory:", pad) + assembly_dir, outfile)
    mcore.PWS(mcore.spacedOut("# Output file:", pad) + outfilename, outfile)
    mcore.PWS("# ----------", outfile)

    cols = [
        'num-scaffs', 'avg-scaff-len', 'asm-len', 'asm-n50', 'asm-l50',
        'asm-reads-mapped', 'asm-perc-reads-mapped', 'asm-paired-mapped',
        'asm-perc-paired-mapped', 'asm-pair-mapped-diff-chr',
        'asm-single-mapped', 'asm-perc-single-mapped', 'asm-duplicate-reads',
        'asm-avg-depth', 'asm-avg-start-depth', 'asm-avg-mid-depth',

예제 #7

파일: 07_pileup_cmd_generatory.py 프로젝트: goodest-goodlab/murinae-seq

logdir = os.path.join(base_logdir, step + "-logs")
# Step I/O info.

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
#print(runtype, runstrs);
# Parse the input run types.

specs = mfiles.parseSpecs(args.spec, specs_ordered)
specs = [s for s in specs if "(no WGA)" not in s and "pos_ctrl" not in s]
specs = [s for s in specs if any(r in spec_ids[s] for r in runtype)]
# Parse the input species.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent pileup commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(mcore.spacedOut("# BAM directory:", pad) + bam_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Assembly directory:", pad) + assembly_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Output directory:", pad) + pileup_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Pseudo-it path:", pad) + args.path, jobfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + str(args.spec), jobfile)
    mcore.PWS(
        mcore.spacedOut("# Run types:", pad) + str(args.runtype), jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)
    mcore.PWS(mcore.spacedOut("# Logfile directory:", pad) + logdir, jobfile)
    if not os.path.isdir(logdir):

예제 #8

파일: 06.5_samtools_depth_cmd_generator.py 프로젝트: goodest-goodlab/murinae-seq

if args.spec != "all":
    args.spec = args.spec.replace(", ", ",").split(",")
    if any(s not in assembled_specs for s in args.spec):
        sys.exit(" * ERROR 3: Invalid species entered with -s.")
if args.runtype != "all":
    args.runtype = [
        int(r) for r in args.runtype.replace(", ", ",").split(",")
    ]
    if any(r not in [1, 2, 3, 4, 5] for r in args.runtype):
        sys.exit(" * ERROR 4: Invalid run type entered with -r.")

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent BWA commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(mcore.spacedOut("# BAM directory:", pad) + bam_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Output directory:", pad) + bam_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Samtools path:", pad) + args.path, jobfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + str(args.spec), jobfile)
    if args.ref:
        mcore.PWS(
            mcore.spacedOut("# Reference genome:", pad) + args.ref, jobfile)
    else:
        mcore.PWS(
            mcore.spacedOut("# Reference genome:", pad) + "Exome assemblies",
            jobfile)
    mcore.PWS(
        mcore.spacedOut("# Run types:", pad) + str(args.runtype), jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",

예제 #9

logdir = os.path.join(base_logdir, step + "-logs")
# Step I/O info.

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
# Parse the input run types.

spec = mfiles.parseSpecs(args.spec, specs_ordered)
# Parse the input species.

##########################
# Reporting run-time info for records.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent Spades commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(mcore.spacedOut("# Current step:", pad) + step, jobfile)
    mcore.PWS(mcore.spacedOut("# Previous step:", pad) + prev_step, jobfile)
    mcore.PWS("# ----------", jobfile)
    mcore.PWS("# I/O INFO", jobfile)
    mcore.PWS(
        mcore.spacedOut("# Input directory:", pad) + prev_step_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Output directory:", pad) + step_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Spades path:", pad) + args.path, jobfile)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, jobfile)
    mcore.PWS(mcore.spacedOut("# Seq runs:", pad) + args.runtype, jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)
    mcore.PWS(mcore.spacedOut("# Logfile directory:", pad) + logdir, jobfile)

예제 #10

파일: 10_varcall_cmd_generator.py 프로젝트: goodest-goodlab/murinae-seq

# Reference options

runtype, runstrs = mfiles.parseRuntypes(args.runtype, seq_run_ids)
#print(runtype, runstrs);
# Parse the input run types.

specs = mfiles.parseSpecs(args.spec, specs_ordered)
specs = [s for s in specs if "(no WGA)" not in s and "pos_ctrl" not in s]
specs = [s for s in specs if any(r in spec_ids[s] for r in runtype)]
# Parse the input species.

with open(output_file, "w") as jobfile:
    mcore.runTime("#!/bin/bash\n# Rodent variant commands", jobfile)
    mcore.PWS("# STEP INFO", jobfile)
    mcore.PWS(
        mcore.spacedOut("# Current step:", pad) + "Variant calling", jobfile)
    mcore.PWS(
        mcore.spacedOut("# Assembly directory:", pad) + referee_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Map directory:", pad) + remap_dir, jobfile)
    mcore.PWS(mcore.spacedOut("# Output directory:", pad) + step_dir, jobfile)
    mcore.PWS(
        mcore.spacedOut("# Species job directory:", pad) + jobs_dir, jobfile)
    if not os.path.isdir(jobs_dir):
        mcore.PWS("# Creating jobs directory.", jobfile)
        os.system("mkdir " + jobs_dir)
    mcore.PWS(mcore.spacedOut("# Species:", pad) + args.spec, jobfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            jobfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, jobfile)

예제 #11

파일: 03_exonerate_gen_2.py 프로젝트: goodest-goodlab/murinae-seq

cwd = os.getcwd()
# Job vars

output_file = os.path.join(cwd, "jobs", name + ".sh")
submit_file = os.path.join(cwd, "submit", name + ".sh")
logdir = os.path.join(args.output, "logs")
# Job files

##########################
# Reporting run-time info for records.

with open(output_file, "w") as outfile:
    mcore.runTime("#!/bin/bash\n# Exonerate command generator", outfile)
    mcore.PWS("# IO OPTIONS", outfile)
    mcore.PWS(
        mcore.spacedOut("# Input directory:", pad) + args.input, outfile)
    if args.outname:
        mcore.PWS(
            mcore.spacedOut("# --outname:", pad) +
            "Using end of output directory path as job name.", outfile)
    if not args.name:
        mcore.PWS(
            "# -n not specified --> Generating random string for job name",
            outfile)
    mcore.PWS(mcore.spacedOut("# Job name:", pad) + name, outfile)
    mcore.PWS(
        mcore.spacedOut("# Output directory:", pad) + args.output, outfile)
    if args.overwrite:
        mcore.PWS(
            mcore.spacedOut("# --overwrite set:", pad) +
            "Overwriting previous files in output directory.", outfile)