I am trying to filter out sequences using SeqIO but I am getting this error.
Traceback (most recent call last):
File "paralog_warning_filter.py", line 61, in <module>
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SeqIO.write(desired_proteins, "filtered.fasta","fasta")
AttributeError: 'str' object has no attribute 'id'
I checked other similar questions but still couldn't understand what is wrong with my script.
Here is the relevant part of the script I am trying:
fh=open('lineageV_paralog_warning_genes.fasta')
for s_record in SeqIO.parse(fh,'fasta'):
name = s_record.id
seq = s_record.seq
for i in paralogs_in_all:
if name.endswith(i):
desired_proteins=seq
output_file=SeqIO.write(desired_proteins, "filtered.fasta","fasta")
output_file
fh.close()
I have a separate paralagos_in_all list and that is the ID source. When print name it returns a proper string id names which are in this format >coronopifolia_tair_real-AT2G35040.1@10.
Can you help me understand my problem? Thanks in advance.
You're passing the wrong object to SeqIO.write: it expects a SeqRecord, and instead it gets a Seq object. documentation
Output file gets overwrited at every IF .. TRUE condition. I could suggest to add ID-seq as key:value of a dictionary: when looping through records ends, you could write to file every sequence you've stored before. Something like:
fh=open('lineageV_paralog_warning_genes.fasta')
paralog = {}
for s_record in SeqIO.parse(fh,'fasta'):
name = s_record.id
seq = s_record.seq
for i in paralogs_in_all:
if name.endswith(i):
paralog[name] = str(seq)
fh.close()
with open('filtered.fasta', 'w') as oput_file:
for key in paralog.keys():
oput_file.write(key +'\n' + paralog[key])
Thank you for the detailed correction. As above suggestions, both SeqRecord with a for loop for overwriting and your dictionary approached solved my issue. This was the first time I used SeqIO, now I got it!
Just for sake of mentioning I changed the last line and its a bit more tidy now:)
oput_file.write('>' + key +'\n' + paralog[key] +'\n')
Lastly, and just out of curiosity, the order of the sequences are reversed in the dictionary. Can you explain the reason of this?
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I guess you need to write
s_recordinstead of parsed sequence i.e.desired_proteins. Something like this?Bio.SeqIO.write()is expectingSeqRecord. Instead ofdesired_proteins, you can doSeqIO.write(s_record, ...).Note:
filtered.fastawill only have the lasts_recordinlineageV_paralog_warning_genes.fastathat is found inparalogs_in_allbecausefiltered.fastawill be overwritten during the loop.Thank you I understand it now. You were right about overwriting as well. After fixing that script worked smoothly!
desired_proteins=seqyou are assigning only sequence here.