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Merge pull request #203 from rhysnewell/dev
merging v0.9.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,25 @@ | ||
| __version__ = "0.9.0" | ||
| __version__ = "0.9.1" | ||
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| # CONSTANTS | ||
| LONG_READ_TYPES = ["ont", "ont_hq", "rs", "sq", "ccs", "hifi"] | ||
| MEDAKA_MODELS = [ | ||
| "r103_fast_g507", "r103_fast_snp_g507", "r103_fast_variant_g507", "r103_hac_g507", "r103_hac_snp_g507", | ||
| "r103_hac_variant_g507", "r103_min_high_g345", "r103_min_high_g360", "r103_prom_high_g360", "r103_prom_snp_g3210", | ||
| "r103_prom_variant_g3210", "r103_sup_g507", "r103_sup_snp_g507", "r103_sup_variant_g507", "r1041_e82_260bps_fast_g632", | ||
| "r1041_e82_260bps_fast_variant_g632", "r1041_e82_260bps_hac_g632", "r1041_e82_260bps_hac_variant_g632", "r1041_e82_260bps_sup_g632", | ||
| "r1041_e82_260bps_sup_variant_g632", "r1041_e82_400bps_fast_g615", "r1041_e82_400bps_fast_g632", | ||
| "r1041_e82_400bps_fast_variant_g615", "r1041_e82_400bps_fast_variant_g632", "r1041_e82_400bps_hac_g615", | ||
| "r1041_e82_400bps_hac_g632", "r1041_e82_400bps_hac_variant_g615", "r1041_e82_400bps_hac_variant_g632", "r1041_e82_400bps_sup_g615", | ||
| "r1041_e82_400bps_sup_variant_g615", "r104_e81_fast_g5015", "r104_e81_fast_variant_g5015", "r104_e81_hac_g5015", | ||
| "r104_e81_hac_variant_g5015", "r104_e81_sup_g5015", "r104_e81_sup_g610", "r104_e81_sup_variant_g610", "r10_min_high_g303", | ||
| "r10_min_high_g340", "r941_e81_fast_g514", "r941_e81_fast_variant_g514", "r941_e81_hac_g514", "r941_e81_hac_variant_g514", | ||
| "r941_e81_sup_g514", "r941_e81_sup_variant_g514", "r941_min_fast_g303", "r941_min_fast_g507", "r941_min_fast_snp_g507", | ||
| "r941_min_fast_variant_g507", "r941_min_hac_g507", "r941_min_hac_snp_g507", "r941_min_hac_variant_g507", "r941_min_high_g303", | ||
| "r941_min_high_g330", "r941_min_high_g340_rle", "r941_min_high_g344", "r941_min_high_g351", "r941_min_high_g360", "r941_min_sup_g507", | ||
| "r941_min_sup_snp_g507", "r941_min_sup_variant_g507", "r941_prom_fast_g303", "r941_prom_fast_g507", "r941_prom_fast_snp_g507", | ||
| "r941_prom_fast_variant_g507", "r941_prom_hac_g507", "r941_prom_hac_snp_g507", "r941_prom_hac_variant_g507", "r941_prom_high_g303", | ||
| "r941_prom_high_g330", "r941_prom_high_g344", "r941_prom_high_g360", "r941_prom_high_g4011", "r941_prom_snp_g303", "r941_prom_snp_g322", | ||
| "r941_prom_snp_g360", "r941_prom_sup_g507", "r941_prom_sup_snp_g507", "r941_prom_sup_variant_g507", "r941_prom_variant_g303", | ||
| "r941_prom_variant_g322", "r941_prom_variant_g360", "r941_sup_plant_g610", "r941_sup_plant_variant_g610" | ||
| ] |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,89 @@ | ||
| import subprocess | ||
| import os | ||
| import sys | ||
| from typing import List | ||
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| def spades_asssembly( | ||
| input_fastq: str, | ||
| input_long_reads: str, | ||
| output_fasta: str, | ||
| output_spades_folder: str, | ||
| max_memory: int, | ||
| threads: int, | ||
| kmer_sizes: List[int], | ||
| tmp_dir: str, | ||
| long_read_type: str, | ||
| log: str): | ||
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| ''' | ||
| Assemble short reads and long reads (if any) using spades | ||
| :param input_fastq: short reads fastq file | ||
| :param input_long_reads: long reads fastq file | ||
| :param output_fasta: output fasta file | ||
| :param output_spades_folder: output spades folder | ||
| :param max_memory: maximum memory to use | ||
| :param threads: number of threads | ||
| :param tmpdir: temporary directory | ||
| :param kmer_sizes: list of kmer sizes | ||
| :param long_read_type: type of long reads | ||
| :param log: log file | ||
| :return: | ||
| ''' | ||
| if tmp_dir: | ||
| tmp_dir_arg = f"--tmp-dir {tmp_dir}" | ||
| else: | ||
| try: | ||
| tmp_dir = os.environ["TMPDIR"] | ||
| tmp_dir_arg = f"--tmp-dir {tmp_dir}" | ||
| except KeyError: | ||
| tmp_dir_arg = "" | ||
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| if os.path.exists("data/spades_assembly/tmp"): | ||
| with open(log, 'a') as logf: | ||
| subprocess.run("rm -rf data/spades_assembly/tmp".split(), stdout=logf, stderr=subprocess.STDOUT) | ||
| # remove existing temporary directory | ||
| minimumsize=500000 | ||
| actualsize = int(subprocess.check_output('stat -c%s data/short_reads.filt.fastq.gz', shell=True)) | ||
| # check if directory exists | ||
| if os.path.exists("data/spades_assembly"): | ||
| # resume previous assembly | ||
| command = f"spades.py --restart-from last --memory {max_memory} -t {threads} " \ | ||
| f"-o data/spades_assembly -k {kmer_sizes} {tmp_dir_arg}" | ||
| # run cmd | ||
| with open(log, 'a') as logf: | ||
| logf.write(f"Queueing command {command}\n") | ||
| subprocess.run(command.split(), stdout=logf, stderr=subprocess.STDOUT) | ||
| subprocess.run("cp data/spades_assembly/scaffolds.fasta data/spades_assembly.fasta".split(), stdout=logf, stderr=subprocess.STDOUT) | ||
| elif actualsize >= minimumsize: | ||
| if long_read_type in ["ont","ont_hq"]: | ||
| command = f"spades.py --checkpoints all --memory {max_memory} --meta --nanopore {input_long_reads} --12 {input_fastq} "\ | ||
| f"-o data/spades_assembly -t {threads} -k {kmer_sizes} {tmp_dir_arg} " | ||
| else: | ||
| command = f"spades.py --checkpoints all --memory {max_memory} --meta --pacbio {input_long_reads} --12 {input_fastq} "\ | ||
| f"-o data/spades_assembly -t {threads} -k {kmer_sizes} {tmp_dir_arg} " | ||
| # run cmd | ||
| with open(log, 'a') as logf: | ||
| logf.write(f"Queueing command {command}\n") | ||
| subprocess.run(command.split(), stdout=logf, stderr=subprocess.STDOUT) | ||
| subprocess.run("cp data/spades_assembly/scaffolds.fasta data/spades_assembly.fasta".split(), stdout=logf, stderr=subprocess.STDOUT) | ||
| else: | ||
| with open(log, 'a') as logf: | ||
| subprocess.run(f"mkdir -p {output.spades_folder} && touch {output.fasta}".split(), stdout=logf, stderr=subprocess.STDOUT) | ||
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| if __name__ == '__main__': | ||
| log = snakemake.log[0] | ||
| with open(log, 'w') as logf: pass | ||
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| spades_asssembly( | ||
| snakemake.input.fastq, | ||
| snakemake.input.long_reads, | ||
| snakemake.output.fasta, | ||
| snakemake.output.spades_folder, | ||
| snakemake.params.max_memory, | ||
| snakemake.threads, | ||
| snakemake.params.kmer_sizes, | ||
| snakemake.params.tmpdir, | ||
| snakemake.params.long_read_type, | ||
| log | ||
| ) |
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