BioE-201-230

Repo for assignments after week 3/4/5

Assignment Week 3

Download the Dataset Through NCBI-Dataset Package

Install the package

conda install -c conda-forge ncbi-datasets-cli

Download the dataset

datasets download genome taxon 2 --released-after 1980-01-01 --released-before 2001-12-31 --include genome

Tab-separated values (TSV) downloaded through website and uploaded through MobaXterm

name	GC Percent	Contig N50	scaffolds count	size
Vibrio cholerae O1 biovar El Tor str. N16961	47.5	2961149	2	4033464
Brucella melitensis bv. 1 str. 16M	57	2117144	2	3294931
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	66.5	2648638	4	3284156
Lactococcus lactis subsp. lactis Il1403	35.5	2365589	1	2365589
Pasteurella multocida subsp. multocida str. Pm70	40.5	2257487	1	2257487
Thermotoga maritima MSB8	46	1860725	1	1860725
Haemophilus influenzae Rd KW20	38	1830138	1	1830138
Helicobacter pylori 26695	39	1667867	1	1667867
Helicobacter pylori J99	39	1643831	1	1643831
Aquifex aeolicus VF5	43.5	1551335	2	1590791
Chlamydia pneumoniae CWL029	40.5	1230230	1	1230230
Chlamydia pneumoniae AR39	40.5	1229853	1	1229853
Treponema pallidum subsp. pallidum str. Nichols	53	1138011	1	1138011
Chlamydia trachomatis D/UW-3/CX	41.5	1042519	1	1042519

Find the smallest (largest) genome

Biggest size ouput:

awk -F'\t' 'NR == 1 || $5 > min {min = $5; line = $0} END {print line}' summary.tsv

Output: Vibrio cholerae O1 biovar El Tor str. N16961 47.5 2961149 2 4033464

Smallest size ouput:

awk -F'\t' 'NR == 1 || $5 < min {min = $5; line = $0} END {print line}' summary.tsv

Output: Chlamydia trachomatis D/UW-3/CX 41.5 1042519 1 1042519

Biggest with size ouput only:

awk -F'\t' 'NR==1{next} {if(max=="" || $5 > max){max=$5}} END{print max}' summary.tsv

Output: 4033464

Smallest with size ouput only:

awk -F'\t' 'NR==1{next} {if(max=="" || $5 < max){max=$5}} END{print max}' summary.tsv

Output: 1042519

Find the number of genomes that contain at least two “c” in the species name

awk -F'\t' 'BEGIN{count=0} {if(gsub(/[Cc]/,"c",$1) >= 2) count++} END{print count}' summary.tsv

Output: 7

How many of the species names contain two or more “c” but do not contain the word “coccus”

awk -F'\t' 'BEGIN{count=0} {if(gsub(/c/,"c",$1) >= 2 && $1 !~ /coccus/) count++} END{print count}' summary.tsv

Output: 3

Use the find command to find all genome files (FASTA) larger than 3MB

awk -F'\t' '$5 > 3000000 {count++} END{print count}' summary.tsv

Output: 3