Here you’ll find the answers to the challenges in 2.4 Unix essentials
How many times ORF|Uncharacterized appears on the 2nd column?
$ cat output_A_nidulans_filtered_features.txt | sed '1,8d' | cut -f 2 | grep -c 'ORF|Uncharacterized'
9312
How many times pseudogene appears on the 2nd column?
$ cat output_A_nidulans_filtered_features.txt | sed '1,8d' | cut -f 2 | grep -c 'pseudogene'
58
Does the 1st column list each gene name (those named ‘AN###’) only once?
$ cat A_nidulans_FGSC_A4_current_chromosomal_feature.tab | sed '1,8d' | cut -f 1 | grep 'AN' -c
10779
$ cat A_nidulans_FGSC_A4_current_chromosomal_feature.tab | sed '1,8d' | cut -f -1 | sort | uniq | grep 'AN' -c
10779
Why a single and straight ‘wc -l ’ won’t work?
Did you tail? There are genes that do not start with ‘AN’.
Which word appears 199 times on the 2nd column?
$ cat output_A_nidulans_filtered_features.txt | sed '1,8d' | cut -f 2 | sort | uniq -c
189 ORF|Merged/Split|Uncharacterized
4 ORF|Merged/Split|Verified
9235 ORF|Uncharacterized
1 ORF|Uncharacterized|Merged/Split
49 ORF|Uncharacterized|transposable element gene
1209 ORF|Verified
1 multigene locus
1 ncRNA|Uncharacterized
1 ncRNA|Verified
55 pseudogene
2 pseudogene|Verified
1 pseudogene|transposable element gene
2 rRNA|Uncharacterized
199 tRNA|Uncharacterized
9 tRNA|Verified
27 uORF|Uncharacterized
4 uORF|Verified
It’s tRNA|Uncharacterized.
Download A. flavus genome, and unzip it.
$ curl -O http://www.aspergillusgenome.org/download/sequence/A_flavus_NRRL_3357/current/A_flavus_NRRL_3357_chromosomes.fasta.gz
A_flavus_NRRL_3357_chromosomes.fasta.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 10.9M 100 10.9M 0 0 6618k 0 0:00:01 0:00:01 --:--:-- 6616k
$ gunzip A_flavus_NRRL_3357_chromosomes.fasta.gz
$ ls *flavus*
A_flavus_NRRL_3357_chromosomes.fasta
Then, ultimately I want you to create a for loop that will execute the following on both Asperillus genomes:
$ for file in A_*.fasta; do echo $file; a=`grep -c '>' $file`; echo $a sequences; echo ; grep '>' $file; echo; done
A_flavus_NRRL_3357_chromosomes.fasta
126 sequences
>1041045516887_A_flavus_NRRL_3357 (3491 nucleotides)
>1041045516889_A_flavus_NRRL_3357 (4170 nucleotides)
>1041045516890_A_flavus_NRRL_3357 (20049 nucleotides)
>1041045516891_A_flavus_NRRL_3357 (2076547 nucleotides)
>1041045516892_A_flavus_NRRL_3357 (3256 nucleotides)
>1041045516893_A_flavus_NRRL_3357 (2183 nucleotides)
>1041045516894_A_flavus_NRRL_3357 (2614 nucleotides)
>1041045516895_A_flavus_NRRL_3357 (2135 nucleotides)
>1041045516896_A_flavus_NRRL_3357 (2529 nucleotides)
>1041045516897_A_flavus_NRRL_3357 (2052 nucleotides)
>1041045516898_A_flavus_NRRL_3357 (2187 nucleotides)
>1041045516899_A_flavus_NRRL_3357 (2177 nucleotides)
>1041045516900_A_flavus_NRRL_3357 (2275 nucleotides)
>1041045516901_A_flavus_NRRL_3357 (2401 nucleotides)
>1041045516902_A_flavus_NRRL_3357 (2719 nucleotides)
(...)
A_nidulans_FGSC_A4_current_chromosomes.fasta
9 sequences
>ChrIII_A_nidulans_FGSC_A4 (3470897 nucleotides)
>ChrII_A_nidulans_FGSC_A4 (4070060 nucleotides)
>ChrIV_A_nidulans_FGSC_A4 (2887738 nucleotides)
>ChrI_A_nidulans_FGSC_A4 (3759208 nucleotides)
>ChrVIII_A_nidulans_FGSC_A4 (4934093 nucleotides)
>ChrVII_A_nidulans_FGSC_A4 (4550218 nucleotides)
>ChrVI_A_nidulans_FGSC_A4 (3407944 nucleotides)
>ChrV_A_nidulans_FGSC_A4 (3403833 nucleotides)
>mito_A_nidulans_FGSC_A4 (33227 nucleotides)
BONUS
Redirect output of a for loop:
$ for file in A_*.fasta; do echo $file ; a=`grep -c '>' $file`; echo $a sequences; echo ; grep '>' $file; echo ; done > output_genomes_fasta_headers.txt
$ ls output*.txt
output_A_nidulans_fasta_headers.txt
output_A_nidulans_filtered_features.txt
output_genomes_fasta_headers.txt
$ cat output_genomes_fasta_headers.txt
(...)