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Update assembly_workflow.py
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@WillNickols
WillNickols committed Dec 13, 2023
1 parent 3275837 commit dc71326
Showing 1 changed file with 6 additions and 6 deletions.
12 changes: 6 additions & 6 deletions assembly_workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -571,7 +571,7 @@ def abundance_sample(name, paired):
if paired == "paired":
if input_extension in ["fastq.gz", "fq.gz"]:
if pair_identifier == "kneaddata_default":
command = '''{a} && {b} && {c} && {d} && {e} && {f} && {g} && {h} && {i}'''.format(
command = '''{a} && {b} && {c} && {d}; {e} && {f} && {g} && {h} && {i}'''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
Expand All @@ -583,7 +583,7 @@ def abundance_sample(name, paired):
i = "echo $((paired1+paired2+unpaired1+unpaired2)) &>> [targets[2]]"
)
else:
command = '''{a} && {b} && {c} && {d} && {e} && {f} && {i}'''.format(
command = '''{a} && {b} && {c} && {d}; {e} && {f} && {i}'''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
Expand All @@ -594,7 +594,7 @@ def abundance_sample(name, paired):
)
elif input_extension in ["fastq", "fq"]:
if pair_identifier == "kneaddata_default":
command = '''{a} && {b} && {c} && {d} && {e} && {f} && {g} && {h} && {i}'''.format(
command = '''{a} && {b} && {c} && {d}; {e} && {f} && {g} && {h} && {i}'''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
Expand All @@ -606,7 +606,7 @@ def abundance_sample(name, paired):
i = "echo $((paired1+paired2+unpaired1+unpaired2)) &>> [targets[2]]"
)
else:
command = '''{a} && {b} && {c} && {d} && {e} && {f} && {i}'''.format(
command = '''{a} && {b} && {c} && {d}; {e} && {f} && {i}'''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
Expand All @@ -617,15 +617,15 @@ def abundance_sample(name, paired):
)
elif paired in ["unpaired", "concatenated"]:
if input_extension in ["fastq.gz", "fq.gz"]:
command = '''{a} && {b} && {c} && {d} && {e} '''.format(
command = '''{a} && {b} && {c} && {d}; {e} '''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
d = "samtools view -c -F 260 " + bam_sorted + " -o [targets[2]]; fi",
e = "echo $(zcat " + name + "." + input_extension + "|wc -l)/4|bc &>> [targets[2]]"
)
elif input_extension in ["fastq", "fq"]:
command = '''{a} && {b} && {c} && {d} && {e} '''.format(
command = '''{a} && {b} && {c} && {d}; {e} '''.format(
a = "if [ ! -s " + contigs + " ]; then echo -e \"Sequence Id\tBin Id\tSequence length (bp)\tBam Id\tCoverage\tMapped reads\" > [targets[0]] && echo -e \"Bin Id\tBin size (Mbp)\t" + name.split("/")[-1] + ".sorted: mapped reads\t" + name.split("/")[-1] + ".sorted: % mapped reads\t" + name.split("/")[-1] + ".sorted: % binned populations\t" + name.split("/")[-1] + ".sorted: % community\" > [targets[1]] && echo 0 > [targets[2]]; else samtools index " + bam_sorted + " -@ " + str(cores) + " " + bam_index,
b = "python " + assembly_tasks_folder + "checkm.py coverage " + bin + " [targets[0]] " + bam_sorted + " -x fa -t " + str(cores) + " -r " + args.checkm_coverage_options,
c = "python " + assembly_tasks_folder + "checkm.py profile [targets[0]] --tab_table -f [targets[1]]",
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