Mercurial > repos > dave > abayesqr
changeset 2:d2aa2a22721d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abayesqr commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty
| author | dave |
|---|---|
| date | Wed, 20 Mar 2019 14:28:32 -0400 |
| parents | 3e9704b9d49e |
| children | 67a11eca10f1 |
| files | abayesqr.xml parse_output.py |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/abayesqr.xml Wed Mar 20 13:08:41 2019 -0400 +++ b/abayesqr.xml Wed Mar 20 14:28:32 2019 -0400 @@ -8,7 +8,7 @@ ln -s '$reference' input.fasta && ln -s '$input' input.sam && aBayesQR $abayes_params && - python $__tool_directory__/parse_output.py + python '$__tool_directory__/parse_output.py' ]]> </command> <configfiles>
--- a/parse_output.py Wed Mar 20 13:08:41 2019 -0400 +++ b/parse_output.py Wed Mar 20 14:28:32 2019 -0400 @@ -1,9 +1,11 @@ +import os from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from Bio import SeqIO def parse_abayesqr_output(input_text, output_fasta): - with open(input_text) as input_file: + wd = os.getcwd() + with open(os.path.join(wd, input_text)) as input_file: lines = input_file.readlines() records = [] for i, line in enumerate(lines): @@ -15,7 +17,7 @@ seq = Seq(line.strip()) record = SeqRecord(seq, id=header, description='') records.append(record) - SeqIO.write(records, output_fasta, 'fasta') + SeqIO.write(records, os.path.join(wd, output_fasta), 'fasta') if __name__ == '__main__': parse_abayesqr_output("test_ViralSeq.txt", "haplotypes.fasta")