Mercurial > repos > davidvanzessen > shm_csr
comparison baseline/script_xlsx.py @ 83:729738462297 draft
"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
author | rhpvorderman |
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date | Wed, 15 Sep 2021 12:24:06 +0000 |
parents | c33d93683a09 |
children |
comparison
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82:a103134ee6e0 | 83:729738462297 |
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32 currentId = "" | 32 currentId = "" |
33 with xlrd.open_workbook(args.input, 'r') as wb: | 33 with xlrd.open_workbook(args.input, 'r') as wb: |
34 with open(args.output, 'a') as o: | 34 with open(args.output, 'a') as o: |
35 for sheet in wb.sheets(): | 35 for sheet in wb.sheets(): |
36 if sheet.cell(1,gene_column).value.find("IGHV") < 0: | 36 if sheet.cell(1,gene_column).value.find("IGHV") < 0: |
37 print "Genes not in column " + LETTERS[gene_column] + ", skipping sheet " + sheet.name | 37 print("Genes not in column " + LETTERS[gene_column] + ", skipping sheet " + sheet.name) |
38 continue | 38 continue |
39 o.write(">>>" + sheet.name + "\n") | 39 o.write(">>>" + sheet.name + "\n") |
40 outputdic = dict() | 40 outputdic = dict() |
41 for rowindex in range(1, sheet.nrows): | 41 for rowindex in range(1, sheet.nrows): |
42 ref = sheet.cell(rowindex, gene_column).value.replace(">", "") | 42 ref = sheet.cell(rowindex, gene_column).value.replace(">", "") |
44 outputdic[ref] += [(sheet.cell(rowindex, id_column).value.replace(">", ""), sheet.cell(rowindex, seq_column).value)] | 44 outputdic[ref] += [(sheet.cell(rowindex, id_column).value.replace(">", ""), sheet.cell(rowindex, seq_column).value)] |
45 else: | 45 else: |
46 outputdic[ref] = [(sheet.cell(rowindex, id_column).value.replace(">", ""), sheet.cell(rowindex, seq_column).value)] | 46 outputdic[ref] = [(sheet.cell(rowindex, id_column).value.replace(">", ""), sheet.cell(rowindex, seq_column).value)] |
47 #print outputdic | 47 #print outputdic |
48 | 48 |
49 for k in outputdic.keys(): | 49 for k in list(outputdic.keys()): |
50 if k in refdic: | 50 if k in refdic: |
51 o.write(">>" + k + "\n") | 51 o.write(">>" + k + "\n") |
52 o.write(refdic[k] + "\n") | 52 o.write(refdic[k] + "\n") |
53 for seq in outputdic[k]: | 53 for seq in outputdic[k]: |
54 #print seq | 54 #print seq |
55 o.write(">" + seq[0] + "\n") | 55 o.write(">" + seq[0] + "\n") |
56 o.write(seq[1] + "\n") | 56 o.write(seq[1] + "\n") |
57 else: | 57 else: |
58 print k + " not in reference, skipping " + k | 58 print(k + " not in reference, skipping " + k) |