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How To Differentiate Files With One Record From Files With Multiple Records?

I'm working with biopython, python, and gtk to create a program to load files of bioinformatic interest.

These files have multiple sequence in them

http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk

http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.fasta

but this ones only have one (long) sequence.

http://biopython.org/SRC/biopython/Tests/GenBank/NC_005816.gb

http://biopython.org/SRC/biopython/Tests/GenBank/NC_005816.fna

Is there any way to know this before processing the file? How to differentiate the ones with one sequence from others with multiple sequences? I want to know when to use exactly Bio.SeqIO.read() or Bio.SeqIO.parse()

Thanks for your time, I tried to search for answers, but I didn't find something similar to this.

fasta python genbank biopython
• 3,408 views • link
updated by Ram Ram • written by Cako Fuentes • Cako Fuentes

is there any way to know this before processing the file?

You'd have to process it somehow to determine whether the file contains one or multiple sequences. Given this, consider using Bio.SeqIO.parse(), since it handles both cases.

• 134 views • link
written by Kenosis Kenosis

1 answer

If you don't know how many records there are, assume at least one, and use Bio.SeqIO.parse() with a for loop. If the file happens to have only one record, your code will just do the for loop once. Easy :)

• 129 views • link
written by Peter Peter

Thanks, i'm testing the loading times for different files, just wanna go with the most optimized code.

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written by Cako Fuentes • Cako Fuentes

Well internally Bio.SeqIO.read() calls Bio.SeqIO.parse() anyway, and checks there was exactly one record.

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written by Peter Peter

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