From bda829e2c4001a46ce6551d1315f4d7844e04473 Mon Sep 17 00:00:00 2001 From: Ben Taylor Date: Mon, 21 Dec 2015 13:24:39 +0000 Subject: [PATCH 1/3] Fix section title --- Notebooks/Unix/basic/basic.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Notebooks/Unix/basic/basic.ipynb b/Notebooks/Unix/basic/basic.ipynb index 589099e..467e4bd 100644 --- a/Notebooks/Unix/basic/basic.ipynb +++ b/Notebooks/Unix/basic/basic.ipynb @@ -241,7 +241,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "#### Tab completion\n", + "## Tab completion\n", "\n", "Typing out file names is really boring and you're likely to make typos which will at best make your command fail with a strange error and at worst overwrite some of your carefully crafted analysis. _Tab completion_ is a trick which normally reduces this risk significantly.\n", "\n", From 4ef59f50e5c1c7e8422ce84303a7d77997a6ea67 Mon Sep 17 00:00:00 2001 From: Ben Taylor Date: Mon, 21 Dec 2015 13:55:12 +0000 Subject: [PATCH 2/3] Fix lists in cheat sheet --- Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb b/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb index ade0f92..811483f 100644 --- a/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb +++ b/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb @@ -169,17 +169,21 @@ "## Which tool should I use?\n", "\n", "You should probably use awk if:\n", + "\n", "* your data has columns\n", "* you need to do simple maths\n", "\n", "You should probable use grep if:\n", + "\n", "* you're looking for files which contain some specific text (e.g. `grep -r foo bar/`: look in all the files in `bar/` for any with the word 'foo')\n", "\n", "You should use find if:\n", + "\n", "* you know something about a file (like it's name or creation date) but not where it is\n", "* you want a list of all the files in a subdirectory and its subdirectories etc.\n", "\n", "You should write a script if:\n", + "\n", "* your code doesn't fit on one line\n", "* it's doing something you might want to do again in 3 months\n", "* you want someone else to be able to do it without asking loads of questions\n", @@ -187,6 +191,7 @@ "* you're doing something lots of times\n", "\n", "You should probably use less or head:\n", + "\n", "* always, you should always use less or head to check intermediary steps in your analysis\n" ] } From f495f14bc91d714e584f0611c1207a2fad9ec1ef Mon Sep 17 00:00:00 2001 From: Ben Taylor Date: Mon, 21 Dec 2015 15:44:08 +0000 Subject: [PATCH 3/3] Split lines in Unix cheat sheet --- .../Unix/cheat_sheet/unix_cheat_sheet.ipynb | 29 ++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb b/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb index 811483f..454890a 100644 --- a/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb +++ b/Notebooks/Unix/cheat_sheet/unix_cheat_sheet.ipynb @@ -13,7 +13,8 @@ "ls # What else is in this directory\n", "ls .. # What is in the directory above me\n", "ls foo/bar/ # What is inside the bar directory which is inside the foo/ directory\n", - "ls -lah foo/ # Give the the details (-l) of all files and folders (-a) using human readable file sizes (-h)\n", + "ls -lah foo/ # Give the the details (-l) of all files and folders (-a) using human\n", + " # readable file sizes (-h)\n", "cd ../.. # Move up two directories\n", "cd ../foo/bar # Move up one directory and down into the foo/bar/ subdirectories\n", "cp -r foo/ baz/ # Copy the foo/ directory into the baz/ directory\n", @@ -26,7 +27,8 @@ "\n", "```\n", "less bar.bed # scroll through bar.bed\n", - "grep chrom bar.bed | less -S # Only look at lines in bar.bed which have 'chrom' and don't wrap lines (`-S`)\n", + "grep chrom bar.bed | less -S # Only look at lines in bar.bed which have 'chrom' and\n", + " # don't wrap lines (-S)\n", "head -20 bar.bed # show me the first 20 lines of bar.bed\n", "tail -20 bar.bed # show me the last 20 lines\n", "cat bar.bed # show me all of the lines (bad for big files)\n", @@ -43,7 +45,8 @@ "grep -r foo baz/ # show me all examples of foo in baz/ and every subdirectory within it\n", "grep '^foo' bar.bed # show me all of the lines begining with foo\n", "grep 'foo$' bar.bed # show me all of the lines ending in foo\n", - "grep -i '^[acgt]$' bar.bed # show me all of the lines which only have the characters a,c,g and t (ignoring their case)\n", + "grep -i '^[acgt]$' bar.bed # show me all of the lines which only have the characters\n", + " # a,c,g and t (ignoring their case)\n", "grep -v foo bar.bed # don't show me any files with foo in them\n", "```\n", "\n", @@ -56,7 +59,9 @@ "awk -F\"\\t\" '{print $NF}' bar.bed # ignore spaces and print the last column\n", "awk -F\"\\t\" '{print $(NF-1)}' bar.bed # print the penultimate column\n", "awk '{sum+=$2} END {print sum}' bar.bed # print the sum of the second column\n", - "awk '/^foo/ {sum+=$2; count+=1} END {print sum/count}' bar.bed # print the average of the second value of lines starting with foo\n", + "awk '/^foo/ {sum+=$2; count+=1} END {print sum/count}' bar.bed # print the average of the\n", + " # second value of lines starting\n", + " # with foo\n", "```\n", "\n", "## Piping, redirection and more advanced queries\n", @@ -74,7 +79,7 @@ "# awk => NR: is the row number\n", "# NR%10: is the modulo (remander) of dividing my 10\n", "# awk is therefore giving you every 10th line\n", - "# head => only show the first 20 \n", + "# head => only show the first 20\n", "\n", "awk '{l=($3-$2+1)}; (l<300 && $2>200000 && $3<250000)' exercises.bed\n", "# Gives:\n", @@ -122,7 +127,8 @@ " exit 2\n", "fi\n", "\n", - "# Get the lines which aren't headers, take the first column and return the unique values\n", + "# Get the lines which aren't headers,\n", + "# take the first column and return the unique values\n", "number_of_contigs_in_one=$(awk '$1 !~ /^#/ {print $1}' $file_one | sort -u | wc -l)\n", "number_of_contigs_in_two=$(awk '/^[^#]/ {print $1}' $file_two | sort -u | wc -l)\n", "\n", @@ -151,7 +157,7 @@ "* `man the_name_of_a_command` often gives you help\n", "* Google is normally better at giving examples (prioritise stackoverflow.com results, they're normally good)\n", "\n", - "#### Build commands slowly\n", + "## Build commands slowly\n", "\n", "If you wanted me to calculate the sum of all of the scores for genes on contig-1 in a bed file, I'd probably run each of the following commands before moving onto the next:\n", "\n", @@ -161,9 +167,12 @@ "awk '{print $1}' bar.bed | sort -u | less # check the contigs don't look wierd\n", "awk '{print $4}' bar.bed | sort -u | less # check the genes don't look wierd\n", "awk '$4 ~ /gene-/' bar.bed | head -20 # check that I can spot genes\n", - "awk '($1 == \"contig-1\" && $4 ~ /gene-/)' bar.bed | head -20 # check I can find genes on contig-1\n", - "head -20 bar.bed | awk '($1 == \"contig-1\" && $4 ~ /gene-/) {sum+=$5}; END {print sum}' # check my maths\n", - "awk '($1 == \"contig-1\" && $4 ~ /gene-/) {sum+=$5}; END {print sum}' bar.bed # get the answer you actually want\n", + "awk '($1 == \"contig-1\" && $4 ~ /gene-/)' bar.bed | head -20 # check I can find\n", + " # genes on contig-1\n", + "# check my algorithm works on a subset of the data\n", + "head -20 bar.bed | awk '($1 == \"contig-1\" && $4 ~ /gene-/) {sum+=$5}; END {print sum}'\n", + "# apply the algorithm to all of the data\n", + "awk '($1 == \"contig-1\" && $4 ~ /gene-/) {sum+=$5}; END {print sum}' bar.bed\n", "```\n", "\n", "## Which tool should I use?\n",