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Copy pathsustrate_tables.py
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70 lines (54 loc) · 2.88 KB
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import sys
import csv
introns = set([])
def main(Final_table1, Final_table2):
black_list = set([])
for row in csv.reader(open(Final_table2), delimiter = '\t'):
gene, intron, chr, strand, istart, iend, ilength, dn, dn_type, dn_type_score, bodymap_coverage, gm12878_coverage, hg19_cDNA_coverage, hg19_EST_coverage, mm9_cDNA_coverage, mm9_EST_coverage, genecode_coverage, tissues_coverage, n_tissues, tissues_names, intron_retention_exon, skipped_exons_names, alt_introns, alt_no_skipper_introns, alt_skipper_introns, alt_exon_variant_introns, shift, non_canonical_shift = row
istart = int(istart)
iend = int(iend)
ilength = int(ilength)
dn_type_score = float(dn_type_score)
bodymap_coverage = int(bodymap_coverage)
gm12878_coverage = int(gm12878_coverage)
hg19_cDNA_coverage = int(hg19_cDNA_coverage)
hg19_EST_coverage = int(hg19_EST_coverage)
mm9_cDNA_coverage = int(mm9_cDNA_coverage)
mm9_EST_coverage = int(mm9_EST_coverage)
genecode_coverage = int(genecode_coverage)
n_tissues = int(n_tissues)
intron_retention_exon = intron_retention_exon.split(",")
skipped_exons_names = skipped_exons_names.split(",")
alt_introns = alt_introns.split(",")
alt_no_skipper_introns = alt_no_skipper_introns.split(",")
alt_skipper_introns = alt_skipper_introns.split(",")
alt_exon_variant_introns = alt_exon_variant_introns.split(",")
shift = shift.split(",")
non_canonical_shift = non_canonical_shift.split(",")
black_list.add(intron)
for row in csv.reader(open(Final_table1), delimiter = '\t'):
gene, intron, chr, strand, istart, iend, ilength, dn, dn_type, dn_type_score, bodymap_coverage, gm12878_coverage, hg19_cDNA_coverage, hg19_EST_coverage, mm9_cDNA_coverage, mm9_EST_coverage, genecode_coverage, tissues_coverage, n_tissues, tissues_names, intron_retention_exon, skipped_exons_names, alt_introns, alt_no_skipper_introns, alt_skipper_introns, alt_exon_variant_introns, shift, non_canonical_shift = row
istart = int(istart)
iend = int(iend)
ilength = int(ilength)
dn_type_score = float(dn_type_score)
bodymap_coverage = int(bodymap_coverage)
gm12878_coverage = int(gm12878_coverage)
hg19_cDNA_coverage = int(hg19_cDNA_coverage)
hg19_EST_coverage = int(hg19_EST_coverage)
mm9_cDNA_coverage = int(mm9_cDNA_coverage)
mm9_EST_coverage = int(mm9_EST_coverage)
genecode_coverage = int(genecode_coverage)
n_tissues = int(n_tissues)
intron_retention_exon = intron_retention_exon.split(",")
skipped_exons_names = skipped_exons_names.split(",")
alt_introns = alt_introns.split(",")
alt_no_skipper_introns = alt_no_skipper_introns.split(",")
alt_skipper_introns = alt_skipper_introns.split(",")
alt_exon_variant_introns = alt_exon_variant_introns.split(",")
shift = shift.split(",")
non_canonical_shift = non_canonical_shift.split(",")
if (intron in black_list) == False:
print '\t'.join(row)
if __name__ == '__main__':
main(sys.argv[1], sys.argv[2])