Skip to content

Chambers Yamasaki Tutorial_11 #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jchambe5 wants to merge 8 commits into
base: master
Choose a base branch
from
Open

Chambers Yamasaki Tutorial_11 #2

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
df03c0d
Unzip files and place in home directory for easier access
ayamasaki2011 Nov 10, 2017
4c33ef4
added hmmer to directory
jchambe5 Nov 10, 2017
989c2ef
added muscle to directory
jchambe5 Nov 10, 2017
79f0b6a
Create output files for all motifs, create beginning of loop that fin…
ayamasaki2011 Nov 10, 2017
b0deab5
Merge branch 'master' of https://github.com/jchambe5/Intro_Biocom_ND_…
ayamasaki2011 Nov 10, 2017
43623ea
AEY: Finished up code for Problem 2 - output matches the answers give…
ayamasaki2011 Nov 14, 2017
a9307ac
finished problem 1 and it print like Stuart's answer he sent
jchambe5 Nov 16, 2017
354edf2
final output .txt file
jchambe5 Nov 16, 2017
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
The table of contents is too big for display.
Diff view
Diff view
  •  
  •  
  •  
Binary file added Exercise11_files/.DS_Store
View file
Open in desktop
Binary file not shown.
22,215 changes: 22,215 additions & 0 deletions Exercise11_files/Problem1/Arthrobacter.fasta
View file
Open in desktop

Large diffs are not rendered by default.

23,952 changes: 23,952 additions & 0 deletions Exercise11_files/Problem1/Bacillus.fasta
View file
Open in desktop

Large diffs are not rendered by default.

11,021 changes: 11,021 additions & 0 deletions Exercise11_files/Problem1/Clostridium.fasta
View file
Open in desktop

Large diffs are not rendered by default.

31,988 changes: 31,988 additions & 0 deletions Exercise11_files/Problem1/Flavobacterium.fasta
View file
Open in desktop

Large diffs are not rendered by default.

21,882 changes: 21,882 additions & 0 deletions Exercise11_files/Problem1/Limnohabitans.fasta
View file
Open in desktop

Large diffs are not rendered by default.

25 changes: 25 additions & 0 deletions Exercise11_files/Problem1/Problem1.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
#Problem1
#File already unzipped

#muscle steps for each .ref file

../muscle3.8.31_i86win32.exe -in sigma.ref -out sigma.ref.muscle
../muscle3.8.31_i86win32.exe -in sporecoat.ref -out sporecoat.ref.muscle
../muscle3.8.31_i86win32.exe -in transporter.ref -out transporter.ref.muscle

#hmmbuild steps for each .ref file

../hmmer-3.1b2-cygwin64/binaries/hmmbuild.exe sigma.ref.hmm sigma.ref.muscle
../hmmer-3.1b2-cygwin64/binaries/hmmbuild.exe sporecoat.ref.hmm sporecoat.ref.muscle
../hmmer-3.1b2-cygwin64/binaries/hmmbuild.exe transporter.ref.hmm transporter.ref.muscle


for i in *fasta
do
../hmmer-3.1b2-cygwin64/binaries/hmmsearch.exe --tblout $i.sigma.hits sigma.ref.hmm $i
../hmmer-3.1b2-cygwin64/binaries/hmmsearch.exe --tblout $i.sporecoat.hits sporecoat.ref.hmm $i
../hmmer-3.1b2-cygwin64/binaries/hmmsearch.exe --tblout $i.transporter.hits transporter.ref.hmm $i
done

cat *.hits | grep "tr|" | sed -E 's/[tr|A-Z0-9]+\_9//' | awk '{print $1 " " $3 " " $5}' > finalhmmout.txt

@lyy005 lyy005 Dec 11, 2017

Copy link
Copy Markdown
Owner

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good job

32,137 changes: 32,137 additions & 0 deletions Exercise11_files/Problem1/Rhizobium.fasta
View file
Open in desktop

Large diffs are not rendered by default.

27,930 changes: 27,930 additions & 0 deletions Exercise11_files/Problem1/Roseobacter.fasta
View file
Open in desktop

Large diffs are not rendered by default.

12,477 changes: 12,477 additions & 0 deletions Exercise11_files/Problem1/Verrucomicrobia.fasta
View file
Open in desktop

Large diffs are not rendered by default.

104 changes: 104 additions & 0 deletions Exercise11_files/Problem1/finalhmmout.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,104 @@
MICC sigma.ref 4.9e-23
MICC sigma.ref 4.5e-21
MICC sigma.ref 8.2e-16
MICC sigma.ref 3.1e-15
MICC sigma.ref 3.3e-14
MICC sigma.ref 4.5e-13
MICC sigma.ref 7.4e-12
MICC sigma.ref 2.5e-11
MICC sigma.ref 2.6e-11
MICC sigma.ref 9.9e-06
BACI sigma.ref 1.4e-24
BACI sigma.ref 7.6e-23
BACI sigma.ref 5.9e-22
BACI sigma.ref 3.4e-20
BACI sigma.ref 4.8e-19
BACI sigma.ref 1.8e-18
BACI sigma.ref 3.4e-18
BACI sigma.ref 4.5e-18
BACI sigma.ref 6.4e-18
BACI sigma.ref 3.9e-17
BACI sigma.ref 1.2e-16
BACI sigma.ref 1.8e-16
BACI sigma.ref 1.8e-16
BACI sigma.ref 2.4e-16
BACI sigma.ref 4.3e-16
BACI sigma.ref 4.9e-16
BACI sigma.ref 1.2e-15
BACI sigma.ref 1.2e-14
BACI sigma.ref 3.7e-14
BACI sigma.ref 3.7e-13
BACI sigma.ref 9.6e-12
BACI sigma.ref 2.7e-11
BACI sigma.ref 1.6e-09
BACI sigma.ref 5.8e-09
BACI sporecoat.ref 5.9e-35
BACI transporter.ref 1.8e-06
CLOT sigma.ref 1.1e-23
CLOT sigma.ref 1.7e-23
CLOT sigma.ref 6.7e-21
CLOT sigma.ref 6.7e-14
CLOT sigma.ref 1.8e-13
CLOT sigma.ref 9.4e-13
CLOT sigma.ref 1.9e-11
CLOT sigma.ref 2.8e-11
FLAO sigma.ref 8.9e-18
FLAO sigma.ref 9.4e-18
FLAO sigma.ref 1.2e-17
FLAO sigma.ref 1.5e-17
FLAO sigma.ref 2e-16
FLAO sigma.ref 4e-16
FLAO sigma.ref 2.1e-15
FLAO sigma.ref 7.6e-15
FLAO sigma.ref 1.6e-13
FLAO sigma.ref 2.2e-13
FLAO sigma.ref 7.7e-13
FLAO sigma.ref 9e-13
FLAO sigma.ref 1.6e-12
FLAO sigma.ref 9.3e-12
FLAO sigma.ref 1.1e-11
FLAO sigma.ref 2.2e-10
FLAO sigma.ref 3.2e-10
FLAO sigma.ref 7.6e-10
FLAO sigma.ref 1.3e-09
FLAO sigma.ref 3.7e-08
FLAO sigma.ref 5.5e-08
FLAO sigma.ref 2.2e-05
FLAO sigma.ref 5.2e-05
FLAO sigma.ref 0.00041
FLAO transporter.ref 3.5e-09
BURK sigma.ref 5.8e-22
BURK sigma.ref 1.3e-17
BURK sigma.ref 6.4e-17
BURK sigma.ref 4.7e-14
BURK sigma.ref 1.9e-13
BURK sigma.ref 3.7e-13
BURK sigma.ref 3.2e-05
BURK transporter.ref 2e-09
RHIZ sigma.ref 6.4e-22
RHIZ sigma.ref 7.4e-22
RHIZ sigma.ref 7.2e-19
RHIZ sigma.ref 1.4e-17
RHIZ sigma.ref 1.6e-17
RHIZ sigma.ref 5e-17
RHIZ sigma.ref 3.4e-16
RHIZ sigma.ref 7.9e-16
RHIZ sigma.ref 2.6e-15
RHIZ sigma.ref 2e-12
RHIZ sigma.ref 5.4e-12
RHIZ sigma.ref 5.5e-12
RHIZ sigma.ref 1.7e-08
RHIZ sigma.ref 4.5e-06
RHOB sigma.ref 5.4e-22
RHOB sigma.ref 1.2e-18
RHOB sigma.ref 2.2e-18
RHOB sigma.ref 4.7e-18
RHOB sigma.ref 4.8e-18
RHOB sigma.ref 3.7e-16
RHOB sigma.ref 7.7e-14
RHOB transporter.ref 0.05
BACT sigma.ref 2.8e-22
BACT sigma.ref 3.5e-20
BACT sigma.ref 5.6e-18
BACT sigma.ref 2.1e-14
BACT sigma.ref 5.1e-14
Loading