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.
I ran
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:
>NC_001416.1 length=48502
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.
.fasta
. using your own capitalization generates confusion. $\endgroup$.fasta
,.fa
or.fas
. In natural language, I use what it feels better for me. I'm sorry if it confuses you. To me, this capitalization is clearer. If we have to go purists, the proper way to refer the format isFASTA
, all capitals (check en.wikipedia.org/wiki/FASTA_format or zhanglab.ccmb.med.umich.edu/FASTA). But that notation hurt my eyes. It's like it's shouting to me. $\endgroup$