advanced_linux_history.txt

  374  cd RNASeq/
  375  ls
  376  cd Results/
  377  ls
  378  cd Cufflinks/
  379  ls
  380  cd sample
  381  cd sample37
  382  ls
  383  cd ..
  384  ls
  385  cd sample40
  386  ls
  387  cd ..
  388  ls
  389  cd ..
  390  ls
  391  cd TopHat/
  392  ls
  393  cd sample37
  394  ls
  395  cd
  396  tmux -h
  397  man tmux
  398  source activate py27
  399  jupyter lab --no-browser
  400  ls
  401  cd Accreditation/
  402  ls
  403  cd RNASeq/
  404  ls
  405  exi
  406  exit
  407  source activate iccipe-env
  408  source activate icipe-env
  409  jupyter lab --no-browser
  410  ls
  411  cd EANBiT/
  412  ls
  413  cd Python/
  414  ls
  415  cd Python
  416  cd Python4Bioinfo/
  417  ls
  418  git status
  419  git checkout training
  420  git status
  421  git merge master
  422  git status
  423  git log
  424  git revert HEAD
  425  ls
  426  cd Intro-to-Python/
  427  ls
  428  cd ..
  429  ls
  430  git pull
  431  ls
  432  git merge --abort
  433  git status
  434  cd Intro-to-Python/
  435  ls
  436  git checkout master
  437  git merge training
  438  git status
  439  git commit
  440  git add ../README.md 
  441  git commit
  442  git status
  443  ls
  444  cd ..
  445  ls
  446  git status
  447  git push
  448  ls
  449  git chekout training
  450  git checkout training
  451  ls
  452  cd Intro-to-Python/
  453  ls
  454  cd ..
  455  ls
  456  cd Intro-to-Python/
  457  ls
  458  cp 03.ipynb ../../
  459  ls
  460  cd ..
  461  ls
  462  cd ..
  463  ls
  464  cd Python
  465  cd Python4Bioinfo/
  466  ls
  467  cp -r Intro-to-Python/ ../../
  468  ls
  469  cd ..
  470  ls
  471  cd ..
  472  ls
  473  cd  Intro-to-Python/
  474  ls
  475  git status
  476  cd ..
  477  cd Python/
  478  cd Python4Bioinfo/
  479  ls
  480  git status
  481  git checkout master
  482  ls
  483  cd Careen/BED/
  484  ls
  485  modules av
  486  modules -av
  487  modules avail
  488  module avail
  489  module av
  490  ls
  491  cd ..
  492  ls
  493  cp -r BED/ /tmp/
  494  ls
  495  cd /tmp/
  496  ls
  497  cd BED/
  498  ls
  499  cd
  500  cd Accreditation/
  501  ls
  502  cd RNASeq/
  503  ls
  504  cd Results/
  505  ls
  506  mkdir Cufflinks
  507  ols
  508  ls
  509  cd ../Data/
  510  ls
  511  cd p
  512  cd Practice/
  513  ls
  514  ls |grep 'sample'
  515  ls |grep 'sample'|cut -f1 -d'_'
  516  ls |grep 'sample'|cut -f1 -d'_'|uniq
  517  ls |grep 'sample'|cut -f1 -d'_'|uniq >../../Code/samples
  518  ls
  519  cd
  520  cd Accreditation/RNASeq/Code/
  521  ls
  522  chmod +x run_tophat.sh 
  523  cat run_tophat.sh 
  524  ls
  525  c
  526  ./run_
  527  ./run_tophat.sh 
  528  ls
  529  which python
  530  cd
  531  cd EANBiT/
  532  ls
  533  cd Python/
  534  ls
  535  cd Python4Bioinfo/
  536  cd ..
  537  ls
  538  mv Python.pdf ../
  539  ls
  540  cd Python4Bioinfo/
  541  ls
  542  git status
  543  ls
  544  cd ../
  545  ls
  546  cd ..
  547  ls
  548  cd Intro-to-Python/
  549  ls
  550  cp 04.ipynb ../Python/Python4Bioinfo/Intro-to-Python/
  551  ls
  552  cd ../Python/Python4Bioinfo/
  553  git status
  554  git add Intro-to-Python/03.ipynb Intro-to-Python/execution.png 
  555  git commit -m'Adding Data structures notes'
  556  git push
  557  git status
  558  git add Intro-to-Python/04.ipynb 
  559  git commit -m'Dictionaries Notebook'
  560  git push
  561  ls
  562  cp ../../Intro-to-Python/05.ipynb ./Intro-to-Python/
  563  ls
  564  git status
  565  git add Intro-to-Python/04.ipynb 
  566  git add Intro-to-Python/05.ipynb 
  567  git commit -m'Adding notes for conditionals'
  568  git push
  569  ls
  570  ls ../../Intro-to-Python/
  571  cp ../../Intro-to-Python/06.ipynb Intro-to-Python/
  572  ls Intro-to-Python/
  573  ls
  574  git status
  575  git add Intro-to-Python/06.ipynb 
  576  git commit -m"Adding the functions notebook"
  577  git push
  578  git status
  579  git add Intro-to-Python/06.ipynb 
  580  git commit -m"Updating the functions notebook"
  581  git push
  582  ls
  583  git status
  584  git add Files/
  585  git add Intro-to-Python/0*
  586  git status
  587  git add Intro-to-Python/*.py
  588  git status
  589  git add Intro-to-Python/08.ipynb 
  590  ls
  591  git commit -m"File, Scripts and modules'
  592  "
  593  git push
  594  ls
  595  git status
  596  ls
  597  git status
  598  git add Intro-to-Python/0*
  599  git status
  600  git add README.md 
  601  git commit -m"Adding Pands and Bioinformatics Notebooks"
  602  git push 
  603  git status
  604  git add Intro-to-Python/00.ipynb 
  605  git add README.md 
  606  git commit -m'minor edits'
  607  git push
  608  ed
  609  man ed
  610  man sed
  611  exit
  612  cd Accreditation/RNASeq/Code/
  613  ls
  614  source activate py27
  615  ls
  616  ./run_tophat.sh 
  617  exit
  618  ls
  619  source activate py27
  620  conda install -c bioconda cufflinks
  621  exit
  622  tmux
  623  tmux new -s accredit
  624  exit
  625  ls
  626  mkdir MARS
  627  ls
  628  source activate icipe-env
  629  jupyter lab --no-browser
  630  exiit
  631  exit
  632  source activate icipe-env
  633  jupyter lab --no-browser
  634  ls
  635  cd EANBiT/
  636  ls
  637  cd R/
  638  ls
  639  cd Data/
  640  ls
  641  cd ..
  642  ls
  643  cd ..
  644  ls
  645  cd Linux/
  646  ls
  647  cd Notebooks/
  648  ls
  649  mv file1.txt ../
  650  ls
  651  cd ..
  652  ls
  653  mv file1.txt Practice/
  654  ls
  655  cd Practice/
  656  ls
  657  awk '{print $1}' file1.txt 
  658  cut -f1 file1.txt 
  659  cut -f1 -d" " file1.txt 
  660  awk '{print $1}' file1.txt 
  661  awk '{print $2}' file1.txt 
  662  awk NR!=1'{print $2}' file1.txt 
  663  awk 'NR!=1{print $2}' file1.txt 
  664  awk 'NR!=1{print $1}' file1.txt 
  665  nano file2
  666  cat file2
  667  awk '{print $2}' file2.txt 
  668  awk '{print $2}' file2
  669  awk '{print $1}' file2
  670  awk -F',' '{print $1}' file2
  671  awk -F',' '{print $3}' file2
  672  awk -F',' '{print $2}' file2
  673  cd ..
  674  ftp ftp.oreilly.com
  675  sudo yum-install ftp
  676  sudo yum install ftp
  677  ftp ftp.oreilly.com
  678  ls
  679  gunzip progs.tar.Z 
  680  ls
  681  untar progs.tar 
  682  tar -xz  progs.tar 
  683  tar -xvf  progs.tar 
  684  ls
  685  cd awkprogs/
  686  ls
  687  cat awkro 
  688  ls
  689  cd ..
  690  ls
  691  rm progs.tar 
  692  ls
  693  cd p
  694  cd Practice/
  695  ls
  696  awk -F, '{print $2}' file2
  697  awk -F" " '{print $2}' file2
  698  awk -F"," '{print $2}' file2
  699  awk -FS"," '{print $2}' file2
  700  awk FS"," '{print $2}' file2
  701  awk FS="," '{print $2}' file2
  702  awk FS=",", '{print $2}' file2
  703  awk '{print $2}' FS="," file2
  704  ls
  705  nano file3
  706  ls
  707  echo $x
  708  x=3
  709  echo $x
  710  awk -v val=$x '{print $0+val}' file3
  711  cat file3
  712  clear
  713  ls
  714  awk -v val=$x '{print $0+val}' file3
  715  man awk
  716  awk -v val=$x '{print $0+val}' file3
  717  nano
  718  cat list 
  719  sed ’s/ MA/, Massachusetts/’ list
  720  sed 's/ MA/, Massachusetts/' list
  721  ls
  722  cat list 
  723  nano sedscr
  724  sed -f sedscr file
  725  sed -f sedscr list 
  726  ls
  727  stringZ=abcABC123ABCabc
  728  expr 3 + 5
  729  3 + 5
  730  expr 3 + 5
  731  y=2
  732  total = `expr $y + 2`
  733  total=`expr $y + 2`
  734  $total
  735  total
  736  y
  737  expr y
  738  expr $y
  739  expr $total
  740  ls
  741  man sed
  742  sed 's/ MA/, Massachusetts/' list
  743  sed 's/ MA/, Massachusetts/g' list
  744  sed 's/ MA/, Massachusetts/' list
  745  man sed
  746  cd
  747  cd EANBiT/
  748  ls
  749  cd Linux/
  750  ls
  751  git status
  752  git add Practice/
  753  git status
  754  git add Notebooks/*
  755  git status
  756  git add README.md 
  757  git ccommit -m'advanced Linux'
  758  git commit -m'advanced Linux'
  759  git push
  760  cd
  761  cd EANBIT/
  762  cd Linux/
  763  cd Data/
  764  ls
  765  head nrf1_seq.fa 
  766  grep '>"
  767  nrf1_seq.fa |head
  768  '
  769  grep '>' nrf1_seq.fa |head
  770  grep '>' nrf1_seq.fa |cut -f2,3 -d" "|head
  771  grep '>' nrf1_seq.fa |cut -f2,3 -d" "
  772  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" "
  773  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed 's\PREDICTED:  \\'|head
  774  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed 's\PREDICTED:  \\g'|head
  775  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's\PREDICTED:  \\g'|head
  776  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED:  //'|head
  777  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED://'|head
  778  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|head
  779  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" "
  780  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" "
  781  ## Advanced Linux
  782  The planned topics include:
  783  1. Reminder on the structure of a command line: command name, parameters (short and long format) and arguments
  784  2. Variables and variable expansion with the $ sign. The effect of single- or double-quoting
  785  3. String manipulation in Bash, with constructs like "${var:2:5}" or "${var%.tar} (see https://www.tldp.org/LDP/abs/html/string-manipulation.html)
  786  4. Arithmetic calculations in Bash, with "expr" or constructs like "$(( var + 1 ))"
  787  5. Shell scripts
  788  5. Tests and control structures. Things like `if \[ $a -ne 0 ]`, loops (for and while)
  789  6. Refresher on grep. Simple examples
  790  7. Bash utilities like diff, cut, join
  791  8. Simple file processing with sed.
  792  9. awk.
  793  ### Regular expressions
  794  See [this](https://www.rexegg.com/regex-quickstart.html) detailed regular expression cheat sheat. 
  795  ## sed
  796          `sed [-e] 'instruction' file`
  797  The command line options are:
  798          -e Editing instruction follows.
  799          -f Filename of the script follows.
  800          -n Suppress automatic output of input lines.
  801  You can pass multiple sed commands by preceding each with `-e` or a semicolon (`;`)
  802      
  803      ` sed -e 's/old/new/' -e ’s/old1/new2/' file`
  804      
  805  You can also pass commands to `sed` in a file using `-f`.
  806      
  807      `sed -f sedcscript -e `
  808      
  809  For further resources on sed, see: [Provide a good link]
  810  ## awk
  811  Named after the three developers. 
  812  `awk 'instructions’ files`
  813  For example, in this example where sed works like `cut`,
  814  `awk '{ print $1 }' file`, The instruction is to print the first field in the file. By default, the fields are delimited by space. Where another character delimits the fields, `-F` is used to specify the delimiter. 
  815   `awk -F, '{ print $1 }' file` (a comma in this example)
  816  You can also print each field in its line by separating the print statements with a semicolon. 
  817   `awk -F, '{ print $1; print $2; print $3 }' file`
  818      
  819  git push
  820  cd p
  821  echo grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" "
  822  echo grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" " >text
  823  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" " >text
  824  ## Advanced Linux
  825  The planned topics include:
  826  1. Reminder on the structure of a command line: command name, parameters (short and long format) and arguments
  827  2. Variables and variable expansion with the $ sign. The effect of single- or double-quoting
  828  3. String manipulation in Bash, with constructs like "${var:2:5}" or "${var%.tar} (see https://www.tldp.org/LDP/abs/html/string-manipulation.html)
  829  4. Arithmetic calculations in Bash, with "expr" or constructs like "$(( var + 1 ))"
  830  5. Shell scripts
  831  5. Tests and control structures. Things like `if \[ $a -ne 0 ]`, loops (for and while)
  832  6. Refresher on grep. Simple examples
  833  7. Bash utilities like diff, cut, join
  834  8. Simple file processing with sed.
  835  9. awk.
  836  ### Regular expressions
  837  See [this](https://www.rexegg.com/regex-quickstart.html) detailed regular expression cheat sheat. 
  838  ## sed
  839          `sed [-e] 'instruction' file`
  840  The command line options are:
  841          -e Editing instruction follows.
  842          -f Filename of the script follows.
  843          -n Suppress automatic output of input lines.
  844  You can pass multiple sed commands by preceding each with `-e` or a semicolon (`;`)
  845      
  846      ` sed -e 's/old/new/' -e ’s/old1/new2/' file`
  847      
  848  You can also pass commands to `sed` in a file using `-f`.
  849      
  850      `sed -f sedcscript -e `
  851      
  852  For further resources on sed, see: [Provide a good link]
  853  ## awk
  854  Named after the three developers. 
  855  `awk 'instructions’ files`
  856  For example, in this example where sed works like `cut`,
  857  `awk '{ print $1 }' file`, The instruction is to print the first field in the file. By default, the fields are delimited by space. Where another character delimits the fields, `-F` is used to specify the delimiter. 
  858   `awk -F, '{ print $1 }' file` (a comma in this example)
  859  You can also print each field in its line by separating the print statements with a semicolon. 
  860   `awk -F, '{ print $1; print $2; print $3 }' file`
  861      
  862  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" "
  863  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" " |sort -u
  864  grep '>' nrf1_seq.fa |cut -f2,3,4 -d" " |sed -e 's/PREDICTED: //'|cut -f1,2 -d" " |sort -u |wc -l
  865  grep '>' nrf1_seq.fa |cut -f2,3 -d" " |sort -u |wc -l
  866  man cut
  867  grep 'mRNA' nrf1_seq.fa 
  868  grep -c 'mRNA' nrf1_seq.fa 
  869  man grep
  870  grep -c -o 'mRNA' nrf1_seq.fa 
  871  grep -c -i 'mRNA' nrf1_seq.fa 
  872  ls
  873  grep -c -i 'mRNA' nrf1_seq.fa 
  874  grep '>' nrf1_seq.fa 
  875  heead
  876  head
  877  head nrf1_seq.fa 
  878  man grep
  879  cd EANBIT/
  880  ls
  881  cd Linux/
  882  ls
  883  cd Data/
  884  ls
  885  grep -m18 nrf1_seq.fa 
  886  grep -m18 '>' nrf1_seq.fa 
  887  grep -m18 '>' nrf1_seq.fa |wc -l
  888  man grep
  889  grep -m18 -n '>' nrf1_seq.fa |wc -l
  890  grep -m18 -n '>' nrf1_seq.fa
  891  grep -m19 -n '>' nrf1_seq.fa
  892  grep -m19 -n '>' nrf1_seq.fa|tail -n2
  893  grep -m19 -n '>' nrf1_seq.fa|tail 2
  894  grep -m19 -n '>' nrf1_seq.fa|tail -n 2
  895  grep -m19 -n '>' nrf1_seq.fa|tail -n 2|cut -f1 -d":"
  896  head -n 3445 nrf1_seq.fa |tail -n -794
  897  head -n 3445 nrf1_seq.fa |tail -n -793
  898  head -n 3444 nrf1_seq.fa |tail -n -794
  899  head -n 3444 nrf1_seq.fa |tail -n -794 |wc -c
  900  grep -m19 -n '>' nrf1_seq.fa|tail -n 2|cut -f1 -d":"
  901  grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"
  902  last=grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"
  903  last=expr `grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"`
  904  `grep -m19 -n '>' nrf1_seq.fa|tail -n 1|cut -f1 -d":"`
  905  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"` |wc -c
  906  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"`
  907  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 2 |cut -f1 -d":"`
  908  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n - `grep -m19 -n '>' nrf1_seq.fa|head -n 2 |cut -f1 -d":"`
  909  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n - `grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"`
  910  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"` |wc -c
  911  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f
  912  grep -m19 -n '>' nrf1_seq.fa|head -n 1 |cut -f1 -d":"
  913  grep -m19 -n '>' nrf1_seq.fa|head -n 1
  914  head nrf1_seq.fa 
  915  grep -m19 -n '>' nrf1_seq.fa|head -n 1
  916  grep -m19 -n '>' nrf1_seq.fa
  917  grep -m19 -n '>' nrf1_seq.fa|tail -n 2
  918  grep -m19 -n '>' nrf1_seq.fa|tail -n 2|head -1
  919  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |wc -c
  920  history >history
  921  cat history 
  922  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |wc -c
  923  man wc
  924  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |wc -m
  925  man wc
  926  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |wc -l
  927  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |grep '>'
  928  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |head -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"`
  929  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |head -n -`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |grep '>'
  930  man head
  931  man tail
  932  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |grep '>'
  933  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |grep '>' |head
  934  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head
  935  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |tail
  936  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1
  937  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +1
  938  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +1|grep '>'
  939  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +1|head
  940  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +2
  941  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +2|head
  942  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +1|head
  943  head -n `grep -m19 -n '>' nrf1_seq.fa|tail -n 1 | cut -f1 -d":"`  nrf1_seq.fa |tail -n +`grep -m19 -n '>' nrf1_seq.fa|tail -n 2| head -n 1 |cut -f1 -d":"` |head -n -1 |tail -n +1|wc -m
  944  history 
  945  cd EANBIT/
  946  l
  947  ls
  948  cd Linux/
  949  ls
  950  cd da
  951  cd Data/
  952  ls
  953  awk ‘BEGIN {RS=">"} /Chr2/ {print ">"$0}’ nrf1_seq.fa 
  954  awk `BEGIN {RS=">"} /Chr2/ {print ">"$0}` nrf1_seq.fa 
  955  awk `BEGIN {RS=">"} /Chr2/ {print ">"$0}` nrf1_seq.fa
  956  awk `BEGIN {RS=">"} /Chr2/{print ">"$0}` nrf1_seq.fa
  957  grep -m18 '>' nrf1_seq.fa 
  958  awk `BEGIN {RS=">"} /AC161538.7/{print ">"$0}` nrf1_seq.fa
  959  awk `BEGIN {RS=">"} /AC161538.7/{print ">" $0}` nrf1_seq.fa
  960  exit
  961  ls
  962  cd EANBIT/
  963  ls
  964  printenv
  965  clear
  966  ls
  967  cd Linux/
  968  ls
  969  cd Data/
  970  ls
  971  clear
  972  ls
  973  pwd
  974  cd
  975  pwd
  976  cd -
  977  cd 
  978  cd -
  979  cd ~
  980  cd -
  981  ls
  982  ls -l
  983  ls -lht
  984  man ls
  985  ls
  986  touch test1
  987  nano test1
  988  cat test1
  989  man cat
  990  mkdir tmp
  991  mkdir temp
  992  ls
  993  cp test1 temp/
  994  ls temp/
  995  ls
  996  rm test1
  997  ls
  998  mkdir test
  999  ls
 1000  rmdir test
 1001  ls
 1002  rmdir temp
 1003  rmdir -r temp
 1004  rm -r temp
 1005  ls
 1006  cp file1 /home/caleb/
 1007  cd
 1008  ls
 1009  rm file1 
 1010  cd -
 1011  ls
 1012  pwd
 1013  cp file1 ../../../
 1014  ls /home/caleb/
 1015  ls
 1016  head nrf1_seq.fa 
 1017* head nrf1_seq.fa |wc
 1018  less nrf1_seq.fa 
 1019  less -h
 1020  less --help
 1021  man
 1022  man less
 1023  ls nrf1_seq.fa 
 1024  less nrf1_seq.fa 
 1025  more nrf1_seq.fa 
 1026  less nrf1_seq.fa 
 1027  ls
 1028  pwd
 1029  ls
 1030  head nrf1_seq.fa 
 1031  less nrf1_seq.fa 
 1032  grep '>' nrf1_seq.fa |wc -l
 1033  ls
 1034  grep '>' nrf1_seq.fa |head
 1035  grep '>' nrf1_seq.fa
 1036  grep '>' nrf1_seq.fa|cut -f1 |head
 1037  grep '>' nrf1_seq.fa|cut -f1 -d" "
 1038  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"
 1039  clear
 1040  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"
 1041  cd .
 1042  ls
 1043  cd ..
 1044  wget https://www.dropbox.com/s/4ul7d3qlfr066hy/nrf1_seq.fa?dl=0
 1045  ls
 1046  mv nrf1_seq.fa\?dl\=0 nrf1_seq.fa dl\=0 
 1047  mv nrf1_seq.fa\?dl\=0 'nrf1_seq.fa dl\=0'
 1048  ls
 1049  ls
 1050  mv nrf1_seq.fa\ dl\\\=0 nrf1_seq.fa 
 1051  ls
 1052  cd Data/
 1053  ls
 1054  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"
 1055  ls
 1056  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"
 1057  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort|uniq
 1058  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort|uniq |wc -l
 1059  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort -u
 1060  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort -u >nrf1_ids.txt
 1061  ls
 1062  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort -u >nrf1_ids.txtclear
 1063  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort -u >nrf1_ids.txtclearclear
 1064  clear
 1065  grep '>' nrf1_seq.fa|cut -f1 -d" "|cut -f2 -d">"|sort -u >nrf1_ids.txt
 1066  grep 'mRNA' nrf1_seq.fa |wc -l
 1067  grep -c 'mRNA' nrf1_seq.fa |wc -l
 1068  grep -c 'mRNA' nrf1_seq.fa
 1069  man grep
 1070  grep -c 'mrna' nrf1_seq.fa
 1071  grep -c -i 'mrna' nrf1_seq.fa
 1072  grep -c '>' nrf1_seq.fa 
 1073  grep '>' nrf1_seq.fa 
 1074  grep '>' nrf1_seq.fa |cut -f2,3 -d" "
 1075  grep '>' nrf1_seq.fa |cut -f2,3 -d" "|sort -u
 1076  grep '>' nrf1_seq.fa |cut -f2,3 -d" "|sort -u -c
 1077  grep '>' nrf1_seq.fa |cut -f2,3 -d" "|sort -u|wc -l
 1078  cleqr
 1079  clear
 1080  grep '^>' nrf1_seq.fa > identifier_lines
 1081  wc -l identifier_lines 
 1082  cleqr
 1083  clear
 1084  grep 'PREDICTED:' identifier_lines 
 1085  grep 'PREDICTED:' identifier_lines  | less
 1086  grep 'PREDICTED:' identifier_lines  | less -S
 1087  grep 'PREDICTED:' identifier_lines  | cut -d ' ' -f 3,4
 1088  grep 'PREDICTED:' identifier_lines  | cut -d ' ' -f 3,4 | wc -l
 1089  grep 'PREDICTED:' identifier_lines  | cut -d ' ' -f 3,4 > genus_species
 1090  less -S genus_species 
 1091  man grep
 1092  grep -v 'PREDICTED:' identifier_lines 
 1093* grep -v 'PREDICTED:' identifier_lines | 
 1094  grep -v 'PREDICTED:' identifier_lines  | cut -d ' ' -f 2,3 >> genus_species
 1095  wc -l genus_species 
 1096  clear
 1097  sort -u genus_species | wc -l
 1098  clear
 1099  grep '^>' nrf1_seq.fa > identifier_lines
 1100  grep 'PREDICTED:' identifier_lines  | cut -d ' ' -f 3,4 > genus_species
 1101  grep -v 'PREDICTED:' identifier_lines  | cut -d ' ' -f 2,3 >> genus_species
 1102  sort -u genus_species | wc -l
 1103  ls *.fa
 1104  less -S nrf1_seq.fa 
 1105  less -S identifier_lines 
 1106  man bash
 1107  less -S identifier_lines 
 1108  grep "PREDICTED:" identifier_lines # greps lines
 1109  grep -o "PREDICTED:" identifier_lines # outputs exactly the matched strings
 1110  grep -o 'Mu..' identifier_lines 
 1111  grep -o 'Mu...' identifier_lines | less -S
 1112  grep -o 'mu...' identifier_lines | less -S
 1113  less -S identifier_lines 
 1114  grep -o '[0135647982] day' identifier_lines | less -S
 1115  # same as using a range:
 1116  grep -o '[0-9] day' identifier_lines | less -S
 1117  grep -o '[0-9]* day' identifier_lines | less -S
 1118  grep -o '[0-9]* days?' identifier_lines | less -S
 1119  egrep -o '[0-9]* days?' identifier_lines | less -S
 1120  grep -o '[0-9]* days\?' identifier_lines | less -S
 1121  man grep
 1122  egrep -o '[0-9]* days?' identifier_lines | less -S
 1123  egrep -o '[0-9]*days?' identifier_lines | less -S
 1124  egrep -o '[0-9]*days?' identifier_lines
 1125  egrep -o 'Homo' identifier_lines
 1126  egrep -o 'Pan' identifier_lines
 1127  egrep 'Pan' identifier_lines
 1128  egrep 'Pan|Homo' identifier_lines
 1129  egrep -o 'Pan|Homo' identifier_lines
 1130  egrep -o 'Pan|Homo [a-z]*' identifier_lines
 1131  egrep -o 'Pan|Homo [a-z ]*' identifier_lines
 1132  grep 'Homo sapiens alpha palindromic binding protein m' identifier_lines 
 1133  egrep -o 'Pan|Homo [a-z]*' identifier_lines
 1134  egrep -o '(Pan|Homo) [a-z]*' identifier_lines
 1135  egrep -o 'Homo sapiens' identifier_lines
 1136  egrep 'Homo sapiens' identifier_lines
 1137  egrep 'Homo sapiens&respiratory' identifier_lines
 1138  egrep 'Homo sapiens\&respiratory' identifier_lines
 1139  egrep '(Homo sapiens)&(respiratory)' identifier_lines
 1140  egrep 'Homo sapiens.*respiratory' identifier_lines
 1141  cleqr
 1142  clear
 1143  egrep 'Homo sapiens.*respiratory' identifier_lines
 1144  egrep 'Homo sapiens.*complete' identifier_lines
 1145  less -S identifier_lines 
 1146  egrep '[0-9]' identifier_lines
 1147  egrep [0-9] identifier_lines
 1148  egrep [A-Z][0-9] identifier_lines
 1149  egrep '[A-Z][0-9]' identifier_lines
 1150  egrep -o '[A-Z_0-9]' identifier_lines 
 1151  egrep -o '[A-Z_0-9]' identifier_lines | less -S
 1152  egrep -o '[A-Z_0-9]*' identifier_lines | less -S
 1153  egrep -o '[A-Z]*[0-9]' identifier_lines | less -S
 1154  egrep -o '[A-Z]*[0-9]*' identifier_lines | less -S
 1155  egrep -o '[A-Z][A-Z]*[0-9]*' identifier_lines | less -S
 1156  egrep -o '[A-Z][A-Z]*[0-9][0-9]*' identifier_lines | less -S
 1157  egrep -o '[A-Z]+[0-9]+' identifier_lines | less -S
 1158  egrep -o '[A-Z]+_?[0-9]+' identifier_lines | less -S
 1159  egrep -o '>[A-Z]+_?[0-9]+' identifier_lines | less -S
 1160  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S
 1161  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S| cut -f 2 -d ">"
 1162  man cut
 1163  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S| cut -c 2-5
 1164  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S| cut -c 1-5
 1165  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S| cut -c 2-5
 1166  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | less -S| cut -c 2-
 1167  echo gdjgterttotwj34343,435,554,645545uyri
 1168  echo gdj343,435,554,645545uyri | tr -d '45'
 1169  echo gdj343,435,554,645545uyri | tr -d ','
 1170  egrep -o '^>[A-Z]+_?[0-9]+' identifier_lines | tr -d '>'
 1171  egrep -o '^>[A-Z]+_?[0-9]+Pan' identifier_lines | tr -d '>'
 1172  egrep -o '^>[A-Z]+_?[0-9]+ Pan' identifier_lines | tr -d '>'
 1173  egrep -o '^>[A-Z]+_?[0-9]+... Pan ' identifier_lines | tr -d '>'
 1174  egrep -o '^>[A-Z]+_?[0-9]+.. Pan ' identifier_lines | tr -d '>'
 1175  egrep -o '^>[A-Z]+_?[0-9]+.* Pan ' identifier_lines | tr -d '>'
 1176  egrep -o '^>[A-Z]+_?[0-9]+.* Pan ' identifier_lines | tr -d '>' | cut -d '.' -f 1
 1177  egrep -o '^>[A-Z]+_?[0-9]+.* Mus ' identifier_lines | tr -d '>' | cut -d '.' -f 1
 1178  grep Mus identifier_lines | less -S
 1179  myvar=5
 1180  mystring="Hello, John"
 1181  $myvar
 1182  5
 1183  echo $myvar
 1184  myvar = 4
 1185  myvar =4
 1186  myvar= 4
 1187  myvar=4
 1188  echo $myvar
 1189  echo $mystring
 1190  echo $mystring2
 1191  echo $mystring2 is a sentence
 1192  echo $mystring is a sentence
 1193  shortname=John
 1194  echo $shortname3
 1195  echo ${shortname}3
 1196  echo ${#shortname}
 1197  echo ${#mystring}
 1198  echo ${mystring:2}
 1199  echo ${mystring:2:4}
 1200  ls
 1201  ls nrf1*
 1202  filename="nrf1_ids.txtclear"
 1203  echo $filename
 1204  echo ${filename#nrf1}
 1205  echo ${filename#nrf1_}
 1206  for filename in nrf1* ; do echo ${filename#nrf1_}; done
 1207  cleqr
 1208  clear
 1209  ls nrf1*
 1210  for filename in nrf1* ; do echo ${filename#nrf1_}; done
 1211  removing a substring from beginning of string: echo ${mystring#pattern}
 1212  ls
 1213  history
 1214  clear
 1215  nano myscript.sh
 1216  ls
 1217  nano myscript.sh
 1218  echo Mpenda, Please come to my party
 1219  nano myscript.sh
 1220  ls
 1221  bash myscript.sh 
 1222  chmod +x myscript.sh 
 1223  ls
 1224  ./myscript.sh 
 1225  nano myscript.sh
 1226  which bash
 1227  nano myscript.sh
 1228  ./myscript.sh 
 1229  nano myscript.sh
 1230  ./myscript.sh 
 1231  nano myscript.sh
 1232  ./myscript.sh 
 1233  ls
 1234  nano myscript.sh
 1235  which bash
 1236  for fasta in *fa*; do echo grep '>' $fasta |wc -l; ;done
 1237  for fasta in *fa*; do echo grep '>' $fasta |wc -l; done
 1238  for fasta in *fa*; do echo `grep '>' $fasta |wc -l`; done
 1239  ls
 1240  mv PlasmoDB-9.0_Pfalciparum_BarcodeIsolates.fasta PlasmoDB-9.0_Pfalciparum_BarcodeIsolates.fa
 1241  ls
 1242  nano count_seq.sh
 1243* 
 1244  nano count_seq.sh
 1245  chmod +x count_seq.sh
 1246  ./count_seq.sh 
 1247  nano count_seq.sh
 1248  ./count_seq.sh 
 1249  nano count_seq.sh
 1250  cat count_seq.sh 
 1251  nano count_seq.sh
 1252  ./count_seq.sh 
 1253  nano count_seq.sh
 1254  ./count_seq.sh 
 1255  nano count_seq.sh
 1256  ./count_seq.sh 
 1257  nano while_loop.sh
 1258  n=1
 1259  echo $n<=5
 1260  echo `$n<=5`
 1261  expr [$n<=5]
 1262  nano while_loop.sh
 1263  chmod +x while_loop.sh 
 1264  ./while_loop.sh 
 1265  nano while_loop.sh
 1266  ./while_loop.sh 
 1267  nano while_loop.sh
 1268  ./while_loop.sh 
 1269  nano while_loop.sh
 1270  ./while_loop.sh 
 1271  nano while_loop.sh
 1272  ./while_loop.sh 
 1273  nano while_loop.sh
 1274  ./while_loop.sh 
 1275  nano while_loop.sh
 1276  pwd
 1277  wget ftp://ftp.phylomedb.org/phylomedb/phylomes/phylome_0170/best_trees.txt.gz
 1278  clear
 1279  ls -l
 1280  gunzip best_trees.txt.gz 
 1281  ls best_trees.txt 
 1282  less -S best_trees.txt 
 1283  wc -l best_trees.txt 
 1284  less -S best_trees.txt 
 1285  sort best_trees.txt | head
 1286  sort best_trees.txt | head | less -S
 1287  man sort
 1288  less -S best_trees.txt 
 1289  man sort
 1290  sort -k3,3g best_trees.txt | less -S
 1291  man sort
 1292  sort -k3,3gr best_trees.txt | less -S
 1293   less -S best_trees.txt 
 1294  sed 's/Dayhoff/DF/' best_trees.txt 
 1295  sed 's/Dayhoff/DF/' best_trees.txt > output
 1296  less output 
 1297  less -S output 
 1298  vim test
 1299  cat test
 1300  cleat
 1301  clear
 1302  sed 's/Dayhoff/DF/' test
 1303  sed 's/Dayhoff/DF/g' test
 1304  awk '{print $2}' best_trees.txt 
 1305  awk '{print $2}' best_trees.txt | sort | uniq -c
 1306  awk '$2=="MtREV" {print $1}' best_trees.txt
 1307  awk '$2=="MtREV" {print $1, $3}' best_trees.txt
 1308  less best_trees.txt 
 1309  less -S best_trees.txt 
 1310  grep -c Phy004ANAQ_99287 best_trees.txt 
 1311  awk '/Phy004ANAQ_99287/ {print $1}' best_trees.txt
 1312  awk '$3 ~ /Phy004ANAQ_99287/ {print $1}' best_trees.txt
 1313  awk '$4 ~ /Phy004ANAQ_99287/ {print $1}' best_trees.txt
 1314  awk '$4 ~ /Phy004ANAQ_992[0-9]7/ {print $1}' best_trees.txt
 1315  awk '$4 ~ /Phy004ANAQ/ {print $1}' best_trees.txt
 1316  awk '$4 ~ /Phy004/ {print $1}' best_trees.txt
 1317  awk '$4 ~ /Phy004ANAQ/ {print $1}' best_trees.txt
 1318  awk '$4 ~ /Phy00[4-9]ANAQ/ {print $1}' best_trees.txt
 1319  awk '$4 ~ /Phy00[4-9]A/ {print $1}' best_trees.txt
 1320  awk '$4 ~ /Phy004A/ {print $1}' best_trees.txt
 1321  less best_trees.txt
 1322  less -S best_trees.txt
 1323  cleqr
 1324  clear
 1325  # check with awk that all lines have exactly four fields
 1326  awk 'NF != 4 { print "Warning! Line " NR "does not have 4 fields"}' best_trees.txt 
 1327  awk 'NF != 4 { print "Warning! Line " NR " does not have 4 fields." }' best_trees.txt 
 1328  awk '{ print NF }' best_trees.txt | sort | uniq -c
 1329  wc -l best_trees.txt 
 1330  # to change the field separator: option -F
 1331  awk -F, '{ print NF }' best_trees.txt | sort | uniq -c
 1332  awk -F, '{ print NF }' best_trees.txt | less -S
 1333  awk '$1 ~ /,/ { print }' best_trees.txt 
 1334  awk '$4 ~ /,/ { print }' best_trees.txt 
 1335  awk -F, '{ print "Tree", $1, "contains", NF, "taxa." }' best_trees.txt | less
 1336  awk -F, '{ print "Tree", $1, "contains", NF, "taxa." }' best_trees.txt | less -S 
 1337  awk -F, '{ print "Tree", substr($1,1,16), "contains", NF, "taxa." }' best_trees.txt | less -S 
 1338  grep Phy001VK96_HAEIN best_trees.txt 
 1339  awk -F, '{ print $NF }' best_trees.txt | less -S
 1340  awk -F, '{ print $NF-1 }' best_trees.txt | less -S
 1341  awk -F, '{ print $(NF-1) }' best_trees.txt | less -S
 1342  awk -F, '{ print "Tree", substr($1,1,16), "contains", NF, "taxa." }' best_trees.txt | less -S 
 1343  awk -F, '{ print "hello" "you" }' best_trees.txt | less -S
 1344  awk -F, '{ print substr($1,1,16) NF }' best_trees.txt | less
 1345  awk -F, '{ print substr($1,1,16) "\t" NF }' best_trees.txt | less
 1346  echo '{ print substr($1,1,16) "\t" NF }' > script1.awk
 1347  cat script1.awk 
 1348  # how do I call this script?
 1349  awk -f script1.awk best_trees.txt | less
 1350  cat script1.awk 
 1351  awk -f script1.awk best_trees.txt | less -S
 1352  awk -f script1.awk -F, best_trees.txt | less
 1353  vim script1.awk 
 1354  awk -f script1.awk  best_trees.txt | less
 1355  less -S nrf1_seq.fa 
 1356  touch script_counting_nucleotides.awk
 1357  vim script_counting_nucleotides.awk 
 1358  awk -f script_counting_nucleotides.awk nrf1_seq.fa | less -S
 1359  vim script_counting_nucleotides.awk 
 1360  awk -f script_counting_nucleotides.awk nrf1_seq.fa | less -S
 1361  grep '>' nrf1_seq.fa | tail
 1362  vim script_counting_nucleotides.awk 
 1363  awk -f script_counting_nucleotides.awk nrf1_seq.fa | less -S
 1364  vim script_counting_nucleotides.awk 
 1365  awk -f script_counting_nucleotides.awk nrf1_seq.fa | less -S
 1366  head -n 1 nrf1_seq.fa 
 1367  awk -f script_counting_nucleotides.awk nrf1_seq.fa | less -S
 1368  awk -f script_counting_nucleotides.awk nrf1_seq.fa | wc -l
 1369  grep -c '^>' nrf1_seq.fa 
 1370  vim script_counting_nucleotides.awk 
 1371  ls
 1372  history
 1373  history > advanced_linux_history.txt