Regular expression challange

TASK 1

Input

Candidate Choice    Absentee Mail   Early Voting    Election Day    Total Votes
TODD RUSS   7,021   8,194   135,216   150,431
CLARK JOLLEY    7,012   5,835   107,714   120,561

Regression expression used

  1. Removing , in the numbers: Find , and replace with nothing.

  2. Removing multiple spaces and replacing with , followed by one space: Find \s[ ]+ and replace with , followed by one space.

Output

Candidate Choice, Absentee Mail, Early Voting, Election Day, Total Votes
TODD RUSS, 7021, 8194, 135216, 150431
CLARK JOLLEY, 7012, 5835, 107714, 120561

TASK 2

Input

Adamic, Emily M.    ema3896@utulsa.edu
Bierbaum, Emily L.  elb0588@utulsa.edu
Cartmell, Laci J.   ljc454@utulsa.edu
Delaporte, Elise    eld0070@utulsa.edu
Hansen, Rebekah E.  reh9623@utulsa.edu
Herrboldt, Madison A.   mah1626@utulsa.edu
Lewis, Cari D.  cdl5261@utulsa.edu
Mierow, Tanner T.   ttm5619@utulsa.edu
Naranjo, Daniel S.  dsn8679@utulsa.edu
Paslay, Caleb   cap1050@utulsa.edu
Pletcher, Olivia M. omp9336@utulsa.edu
West, Amy C.    acw1471@utulsa.edu

Regression expression used

  1. Find (\w+),\s+(\w+).[^X].\s+(\w+@\w+.\w+) and replace with \2 \1 (\3)

Output

Emily Adamic (ema3896@utulsa.edu)
Emily Bierbaum (elb0588@utulsa.edu)
Laci Cartmell (ljc454@utulsa.edu)
Elise Delaporte (eld0070@utulsa.edu)
Rebekah Hansen (reh9623@utulsa.edu)
Madison Herrboldt (mah1626@utulsa.edu)
Cari Lewis (cdl5261@utulsa.edu)
Tanner Mierow (ttm5619@utulsa.edu)
Daniel Naranjo (dsn8679@utulsa.edu)
Cale Paslay (cap1050@utulsa.edu)
Olivia Pletcher (omp9336@utulsa.edu)
Amy West (acw1471@utulsa.edu)

TASK 3

Input

Banded sculpin, Cottus carolinae, 5
Redspot chub, Nocomis asper, 5
Northern hog sucker, Hypentelium nigricans, 6
Creek chub, Semotilus atromaculatus, 8
Stippled darter, Etheostoma punctulatum, 9
Smallmouth bass, Micropterus dolomieu, 10
Logperch, Percina caprodes, 13
Slender madtom, Noturus exilis, 14

Regression expression used

  1. Finding genus species name ,\s+(\w+.\w+) and replace with nothing.

Output

Banded sculpin, 5
Redspot chub, 5
Northern hog sucker, 6
Creek chub, 8
Stippled darter, 9
Smallmouth bass, 10
Logperch, 13
Slender madtom, 14

TASK 4

Regression expression used

  1. Finding genus species name ,\s+(\w)\w+.(\w+) and replacing it with , \1_\2

Output

Banded sculpin, C_carolinae, 5
Redspot chub, N_asper, 5
Northern hog sucker, H_nigricans, 6
Creek chub, S_atromaculatus, 8
Stippled darter, E_punctulatum, 9
Smallmouth bass, M_dolomieu, 10
Logperch, P_caprodes, 13
Slender madtom, N_exilis, 14

TASK 5

Regression expression used

  1. Finding genus species name and capturing first letter of genus and first three letters of species name ,\s+(\w)\w+.(\w{3})\w+ and replacing with , \1_\2.

Output

Banded sculpin, C_car., 5
Redspot chub, N_asp., 5
Northern hog sucker, H_nig., 6
Creek chub, S_atr., 8
Stippled darter, E_pun., 9
Smallmouth bass, M_dol., 10
Logperch, P_cap., 13
Slender madtom, N_exi., 14

Working with Human protein FASTA files

For making a file with all fasta headers: grep '^>' GCF_000001405.40_GRCh38.p14_protein.faa > header_protein_homo.txt

Output

Anands-MacBook-Pro:Dr_toomey_class anandkarki$ head header_protein_homo.txt 
>NP_000005.3 alpha-2-macroglobulin isoform a precursor [Homo sapiens]
>NP_000006.2 arylamine N-acetyltransferase 2 [Homo sapiens]
>NP_000007.1 medium-chain specific acyl-CoA dehydrogenase, mitochondrial isoform a precursor [Homo sapiens]
>NP_000008.1 short-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor [Homo sapiens]
>NP_000009.1 very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor [Homo sapiens]
>NP_000010.1 acetyl-CoA acetyltransferase, mitochondrial isoform b precursor [Homo sapiens]
>NP_000011.2 serine/threonine-protein kinase receptor R3 precursor [Homo sapiens]
>NP_000012.1 presenilin-1 isoform I-467 [Homo sapiens]
>NP_000013.2 adenosine deaminase isoform 1 [Homo sapiens]
>NP_000014.1 alpha-sarcoglycan isoform 1 precursor [Homo sapiens]

Creating a new file with ribosomal protein sequences

Command line

sed -e 's/>/ \n>/g' GCF_000001405.40_GRCh38.p14_protein.faa |sed -n '/ribosom/,/^ /p' > human_ribosomal.txt

head human_ribosomal.txt

Output

>NP_000652.2 60S ribosomal protein L9 [Homo sapiens]
MKTILSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELATVRTICSHVQNM
IKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAAL
IQQATTVKNKDIRKFLDGIYVSEKGTVQQADE
 
>NP_000958.1 60S ribosomal protein L3 isoform a [Homo sapiens]
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVE
TPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVI
RVIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGF