Mercurial > repos > mheinzl > hd
changeset 5:445442a6aeb0 draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit dda3de3fc961976844f5f44b756fe03e39d3b0db
| author | mheinzl |
|---|---|
| date | Tue, 15 May 2018 10:56:52 -0400 |
| parents | ceb3a9b4bef5 |
| children | e76e404c1719 |
| files | hd.py hd.xml |
| diffstat | 2 files changed, 11 insertions(+), 14 deletions(-) [+] |
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--- a/hd.py Tue May 15 10:47:06 2018 -0400 +++ b/hd.py Tue May 15 10:56:52 2018 -0400 @@ -457,7 +457,7 @@ #min_tagsList = [] #diff11_zeros = [] #min_tagsList_zeros = [] - i = 0 # counter, only used to see how many HDs of tags were already calculated + c = 0 # counter, only used to see how many HDs of tags were already calculated if mate_b is False: # HD calculation for all a's half1_mate1 = array1_half half2_mate1 = array1_half2 @@ -496,21 +496,21 @@ else: # half1, corrects the variable of the HD from both halfs if it is a or b d = d_1 d2 = d_2 - min_valueList[i] = d + d2 - min_tagsList[i] = tag - ham1.append[i] = d - ham2.append[i] = d2 + min_valueList[c] = d + d2 + min_tagsList[c] = tag + ham1.append[c] = d + ham2.append[c] = d2 difference1 = abs(d - d2) - diff11[i] = difference1 + diff11[c] = difference1 rel_difference = round(float(difference1) / (d + d2), 1) - relativeDiffList[i] = rel_difference + relativeDiffList[c] = rel_difference #### tags which have identical parts: if d == 0 or d2 == 0: - min_tagsList_zeros[i] = tag + min_tagsList_zeros[c] = tag difference1_zeros = abs(d - d2) - diff11_zeros[i] = difference1_zeros - i += 1 + diff11_zeros[c] = difference1_zeros + c += 1 #print(i) diff11 = [st for st in diff11 if st != 999] @@ -712,9 +712,6 @@ pdf_files = [title_savedFile_pdf] csv_files = [title_savedFile_csv] - print(type(onlyDuplicates)) - print(onlyDuplicates) - for f, name_file, pdf_f, csv_f in zip(files, names, pdf_files, csv_files): with open(csv_f, "w") as output_file, PdfPages(pdf_f) as pdf: print("dataset: ", name_file)
--- a/hd.xml Tue May 15 10:47:06 2018 -0400 +++ b/hd.xml Tue May 15 10:56:52 2018 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.5"> +<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.6"> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.4">matplotlib</requirement>