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changed the input gtf to output introns to the corrected cds gff #370

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changed the input gtf to output introns to the corrected cds gff #370

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2 changes: 1 addition & 1 deletion sqanti_reads.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ def make_UJC_hash(args, df):
print("**** Calculating UJCs...", file = sys.stdout)

## Take the corrected GTF
introns_cmd = f"""gtftools -i {outputPathPrefix}tmp_introns.bed -c "$(cut -f 1 {outputPathPrefix}_corrected.gtf | sort | uniq | paste -sd ',' - | sed 's/chr//g')" {outputPathPrefix}_corrected.gtf"""
introns_cmd = f"""gtftools -i {outputPathPrefix}tmp_introns.bed -c "$(cut -f 1 {outputPathPrefix}_corrected.gtf.cds.gff | sort | uniq | paste -sd ',' - | sed 's/chr//g')" {outputPathPrefix}_corrected.gtf.cds.gff"""
ujc_cmd = f"""awk -F'\t' -v OFS="\t" '{{print $5,"chr"$1,$4,$2+1"_"$3}}' {outputPathPrefix}tmp_introns.bed | bedtools groupby -g 1 -c 2,3,4 -o distinct,distinct,collapse | sed 's/,/_/g' | awk -F'\t' -v OFS="\t" '{{print $1,$2"_"$3"_"$4}}' > {outputPathPrefix}tmp_UJC.txt"""

if subprocess.check_call(introns_cmd, shell=True)!=0:
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