I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with
wget, not from a web browser). But I found an "equivalent" file in ftp://ftp.ncbi.nlm.nih.gov/sra/refseq/NC_001416.1
This file is an SRA file that should be processed with the SRA-toolkit. In particular, fastq-dump seems to be the tools of choice.
fastq-dump --fasta NC_001416.1
and I got a
NC_001416.1.fasta file. But the file contains the sequence I'm looking for in chunks of 5000 bases. The IDs in the output file are:
>NC_001416.1.1 length=5000 >NC_001416.1.2 length=5000 >NC_001416.1.3 length=5000 >NC_001416.1.4 length=5000 >NC_001416.1.5 length=5000 >NC_001416.1.6 length=5000 >NC_001416.1.7 length=5000 >NC_001416.1.8 length=5000 >NC_001416.1.9 length=5000 >NC_001416.1.10 length=3502
I need that sequence under a single ID:
I cannot find the proper parameters to supply to
fastq-dump to achieve the desired result.
Does anyone know how could I get the FastA file I'm expecting? How to process properly the SRA file or where I could download the FastA file directly.