index file from class FMIndex about seq HOT 4 CLOSED

This example in test/apps/bwa/fastmap.seq might help.

from seq.

Hi. What version of Seq are you using? (I'm using Seq version 0.11.0.)

How did you create the .fai file? As a troubleshooting step, you could download the files used in the Workshop. There is an .fai file included. I just tried again with the curl command shown:
curl -L https://www.dropbox.com/s/8lsngqvn0tzjn1o/data.tar.gz | tar zxf - -C .

When I run section2.seq with seqc run section2.seq data/chr22.fa it outputs the index file chr22.fa.index.

from seq.

You could also possibly try to build the index without using the .fai file. e.g.
for record in FASTA(argv[1], fai=False):

from seq.

Hi Mark, thank you for your reply!

I'm using version 0.11.0. Fasta file could be parsing without .fai.

There is another question, does the magic method pickle() in class FMIndex will create a file for FM-Index? How can I use this method and find the result file?

from seq.