Try samtools

samtools faidx genome.fa

cut -f1,2 genome.fa.fai > genome.size

~$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg19 -N -e 'select chrom,size from chromInfo' > out.txt

$ cat out.txt
chr1    249250621
chr2    243199373
chr3    198022430
chr4    191154276
chr5    180915260
(....)

or just

 curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" | gunzip -c | cut -f 1,2 > out.txt

these numbers are pre-computed from the fasta genome files. e.g for chr1:

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr1.fa.gz" | gunzip -c | grep -v '^>' | tr -d '\n' | wc -c
249250621

The chrom.sizes file is computed in the following way for all assemblies at UCSC:

faToTwoBit organism.fa organism.2bit
twoBitInfo out.2bit stdout | sort -k2rn > organism.chrom.sizes

If you know the URL to a 2bit file we've already made, twoBitInfo accepts a URL like so:

twoBitInfo -udcDir=. http://genome-test.cse.ucsc.edu/~hiram/hubs/Plants/ricCom1/ricCom1.2bit stdout | sort -k2nr > ricCom1.chrom.sizes

If you want the chrom.sizes file for a particular assembly, you can download from a URL like the following: http://hgdownload.cse.ucsc.edu/goldenPath/$dbbigZips/$db.chrom.sizes

where $db is the assembly name like hg38, mm10, anoCar2, panTro5, etc.

You can find the faToTwoBit and twoBitInfo programs in our list of publicly available utilities in the directory appropriate to your operating system:

http://hgdownload.soe.ucsc.edu/admin/exe/

If you have further questions about the UCSC Genome Browser or our utilites or data, feel free to send an email to one of mailing lists below:

• genome@soe.ucsc.edu for general questions (public list)
• genome-www@soe.ucsc.edu for question concerning private data (private list)
• genome-mirror@soe.ucsc.edu for questions concerning the setup and running of your own UCSC Genome Browser installation

ChrisL from the UCSC Genome Browser

Try faCount form UCSC kent utils. Usage and output would look like this:

$ faCount hg38.fa

#seq    len A   C   G   T   N   cpg
chr1    248956422   67070277    48055043    48111528    67244164    18475410    2375159
chr10   133797422   38875926    27639505    27719976    39027555    534460  1388978
chr11   135086622   39286730    27903257    27981801    39361954    552880  1333114
chr11_KI270721v1_random 100316  18375   31042   31012   19887   0   3394
.
.
.
total   3209286105  898285419   623727342   626335137   900967885   159970322   30979743

For your purpose, first two columns would suffice.

$ pip install pyfaidx
$ faidx -i chromsizes input.fa > output.chromsizes