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ArtPoon / gotoh2

Lightweight and customizable Python/C extension for pairwise alignment of genetic sequences using the Gotoh algorithm
GNU Affero General Public License v3.0
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Convert_fasta doesn't strip \r line terminators #21

Closed ewong347 closed 4 years ago

ewong347 commented 4 years ago

Probably would be a quick fix (gotoh2_utils.py line 90) from 

sequence += line.strip('\n').upper()

to 

sequence += line.strip('\n').strip('\r').upper()
>>> handle = open(cwd+'/data/weeklydumps/baseline/GISAID-0417_0508.fasta')
>>> fasta=convert_fasta(handle)
>>> handle.close()
>>> fasta[0]
['hCoV-19/Australia/NT12/2020|EPI_ISL_426900|2020-03-25\r', ''NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA\rAA........