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s1.process_sams.smk
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s1.process_sams.smk
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import pandas as pd
METADATA = pd.read_table(config["METADATA"])
REF_INDEX = pd.read_table(config["REF"] + ".fai", header = None)
workdir: config['workdir']
rule all:
input:
expand("bam/{sample}_labeled.sam", sample = METADATA['SM'] )
rule get_splice_juncs:
params:
sge_opts = "-cwd -V -l h_data=16G,h_rt=1:00:00 \
-N get_splice_juncs \
-o log/get_splice_juncs.out \
-e log/get_splice_juncs.err",
TrCleanDir = config["TranscriptCleanDir"]
input:
gtf = config["GTF"],
ref = config["REF"],
output:
jxn = config["annot_version"] + ".SJ.tab"
shell:
"""
mkdir -p log
python {params.TrCleanDir}/TranscriptClean-2.0.3/accessory_scripts/get_SJs_from_gtf.py \
--f {input.gtf} \
--g {input.ref} \
--o {output.jxn}
"""
rule sort_index_bam:
params:
sge_opts = "-cwd -V -l h_data=8G,h_rt=1:00:00 \
-N sort_index_bam \
-o log/sort_index_bam.{sample}.err \
-e log/sort_index_bam.{sample}.out"
input:
bam = "raw_bam/{sample}.bam",
output:
bam = "bam/{sample}.sorted.bam",
bai = "bam/{sample}.sorted.bam.bai"
shell:
"""
mkdir -p bam
samtools sort -o {output.bam} {input.bam}
samtools index {output.bam}
"""
rule transcript_clean:
params:
sge_opts = "-cwd -V -l h_data=14G,h_rt=7:00:00,highp -pe shared 2 \
-N transcript_clean \
-o log/transcript_clean.{sample}.out \
-e log/transcript_clean.{sample}.err",
prefix = "bam/{sample}",
tmpdir = "tmp/{sample}",
threads = 4,
TrCleanDir = config["TranscriptCleanDir"]
input:
bam = "bam/{sample}.sorted.bam",
ref = config["REF"],
fai = config["REF"] + ".fai",
jxn = config["annot_version"] + ".SJ.tab"
output:
sam = "bam/{sample}.sorted.sam",
tc_cleaned_sam = 'bam/{sample}_clean.sam',
tc_cleaned_fa = 'bam/{sample}_clean.fa',
tc_cleaned_te_log = 'bam/{sample}_clean.TE.log',
tc_cleaned_log = 'bam/{sample}_clean.log'
shell:
"""
samtools view -h {input.bam} $(cut -f1 {input.fai}) | samtools calmd - {input.ref} > {output.sam}
mkdir -p {params.tmpdir}
python {params.TrCleanDir}/TranscriptClean-2.0.4/TranscriptClean.py \
--correctMismatches False \
--correctIndels False \
--threads {params.threads} \
--sam {output.sam} \
--genome {input.ref} \
--spliceJns {input.jxn} \
--outprefix {params.prefix} \
--tmpDir {params.tmpdir}
"""
rule talon_label_reads:
params:
sge_opts = "-cwd -V -l h_data=8G,h_rt=1:00:00 \
-N talon_label_reads \
-o log/talon_label_reads.{sample}.out \
-e log/talon_label_reads.{sample}.err ",
prefix = "bam/{sample}",
tmp = "tmp/{sample}"
input:
sam = "bam/{sample}_clean.sam",
ref = config["REF"]
output:
sam = 'bam/{sample}_labeled.sam',
tsv = 'bam/{sample}_read_labels.tsv'
shell:
"""
mkdir -p {params.tmp}
talon_label_reads \
--f {input.sam} \
--g {input.ref} \
--o {params.prefix} \
--tmpDir {params.tmp}
"""