Mercurial > repos > triasteran > ribogalaxy_umi_processing
changeset 7:be394fb47250 draft
Uploaded
| author | triasteran |
|---|---|
| date | Tue, 21 Jun 2022 09:50:49 +0000 |
| parents | 1ce4b52212c4 |
| children | 701804f5ad4b |
| files | UMI_riboseq_processing/UMI.py UMI_riboseq_processing/UMI_riboseq.xml |
| diffstat | 2 files changed, 16 insertions(+), 13 deletions(-) [+] |
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--- a/UMI_riboseq_processing/UMI.py Tue Jun 21 09:33:27 2022 +0000 +++ b/UMI_riboseq_processing/UMI.py Tue Jun 21 09:50:49 2022 +0000 @@ -27,18 +27,21 @@ seq = lines[1] sep = lines[2] qual = lines[3] - trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode - UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN - split_header = header.split(" ") - new_header = split_header[0]+"_"+UMI+" "+split_header[1] - if qual[-1:] == "\n": - new_qual = qual[2:-6]+"\n" - else: - new_qual = qual[2:-6] - output.write(new_header) - output.write(trimmed_seq) - output.write(sep) - output.write(new_qual) + # check if header is OK + if (header.startswith('@')): + trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode + UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN + split_header = header.split(" ") + print (split_header) + new_header = split_header[0]+"_"+UMI+" "+split_header[1] + if qual[-1:] == "\n": + new_qual = qual[2:-6]+"\n" + else: + new_qual = qual[2:-6] + output.write(new_header) + output.write(trimmed_seq) + output.write(sep) + output.write(new_qual) output.close()
--- a/UMI_riboseq_processing/UMI_riboseq.xml Tue Jun 21 09:33:27 2022 +0000 +++ b/UMI_riboseq_processing/UMI_riboseq.xml Tue Jun 21 09:50:49 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.6"> +<tool id="UMI_riboseq" name="move UMIs from reads to header" version="0.1.6a"> <requirements> </requirements> <command detect_errors="exit_code">