User: ajsakla

gravatar for ajsakla
ajsakla0
Reputation:
0
Status:
New User
Last seen:
1 week ago
Joined:
1 week, 3 days ago
Email:
a******@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by ajsakla

<prev • 6 results • page 1 of 1 • next >
0
votes
1
answer
147
views
1
answers
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 days ago by ajsakla0
0
votes
1
answer
147
views
1
answers
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 10 days ago by ajsakla0
0
votes
1
answer
147
views
1
answers
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 10 days ago by ajsakla0
0
votes
1
answer
147
views
1
answers
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 10 days ago by ajsakla0
0
votes
1
answer
147
views
1
answers
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 10 days ago by ajsakla0
1
vote
1
answer
147
views
1
answer
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 10 days ago by ajsakla0 • updated 10 days ago by st.ph.n1.6k

Latest awards to ajsakla

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 568 users visited in the last hour