User: ajsakla

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Posts by ajsakla

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Comment: C: Extract pairs of sequences from a fasta file based on a CSV list of headers
... I realize now I should provide exact examples of the data I'm working with. I was able to get your script to work with my data which saved me many hours of parsing thousands of pairs manually. Thank you for your time. ...
written 9 weeks ago by ajsakla0
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Comment: C: Extract pairs of sequences from a fasta file based on a CSV list of headers
... I'm getting a similar error as before. Key error is the id of the first sequence in the first pair: Traceback (most recent call last): File "extract.py", line 18, in file.write('>' + p[0] + '\n' + primer[p[0]]) KeyError: 'ccRepeat-46449' If it helps, here's a sampling of my primer pairs ...
written 9 weeks ago by ajsakla0
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Comment: C: Extract pairs of sequences from a fasta file based on a CSV list of headers
... So now I get this error: Traceback (most recent call last): File "extract.py", line 18, in with open('file' + str(pairs.index(p)) + '.fasta') as out: IOError: [Errno 2] No such file or directory: 'file0.fasta' It looks like it's looking for the file or directory file0.fasta so when I make ...
written 9 weeks ago by ajsakla0
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Comment: C: Extract pairs of sequences from a fasta file based on a CSV list of headers
... I still get the same error: Traceback (most recent call last): File "parse.py", line 11, in for line in f: ValueError: I/O operation on closed file ...
written 9 weeks ago by ajsakla0
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Comment: C: Extract pairs of sequences from a fasta file based on a CSV list of headers
... Thanks. I'm having some trouble getting this to run. 1. I've copied and pasted this script into a text file as extract.sh 2. I've chmod u+x extract.sh 3. I've replaced the 'pairs.txt' and 'file.fasta' with the appropriate file names 4. I've run ./extract.sh within the folder containing the two ...
written 9 weeks ago by ajsakla0
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Extract pairs of sequences from a fasta file based on a CSV list of headers
... I have a fasta file of primer sequences and I have a csv file with the sequence ids of primer sequence pairs that I need to parse out into their own fasta files. What I need to do is extract each pair of sequences from the fasta and put them into their own fasta files. So my files look something li ...
fasta extract written 9 weeks ago by ajsakla0 • updated 9 weeks ago by st.ph.n1.9k

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