diff options
| -rw-r--r-- | Makefile | 4 | ||||
| -rw-r--r-- | README.md | 24 | ||||
| -rwxr-xr-x | SelectiveWholeGenomeAmplification (renamed from SelectiveGenomeAmplification) | 0 | ||||
| -rwxr-xr-x | SelectiveWholeGenomeAmplificationUI (renamed from SelectiveGenomeAmplificationUI) | 4 |
4 files changed, 16 insertions, 16 deletions
@@ -26,8 +26,8 @@ install: all install -c bin/strstreamone $(DEST) install -c bin/sequence_end_points $(DEST) # bash scripts - install -c SelectiveGenomeAmplification $(DEST) - install -c SelectiveGenomeAmplificationUI $(DEST) + install -c SelectiveWholeGenomeAmplification $(DEST) + install -c SelectiveWholeGenomeAmplificationUI $(DEST) # python scripts install -c src/select_mers.py $(DEST) install -c src/score_mers.py $(DEST) @@ -1,4 +1,4 @@ -SelectiveGenomeAmplification +SelectiveWholeGenomeAmplification ============================ SWGA is a tool for choosing primers for the selective amplification of a @@ -42,21 +42,21 @@ To use this you'll need: ## Setup - git clone git@github.com:mutantturkey/SelectiveGenomeAmplification.git - cd SelectiveGenomeAmplification + git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification".git + cd SelectiveWholeGenomeAmplification" make sudo make install ## Example Usage -Standard use of (SGA) SelectiveGenomeAmplification is easy. it takes two arguments, +Standard use of (SGA) SelectiveWholeGenomeAmplification" is easy. it takes two arguments, the foreground and background - SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; + SelectiveWholeGenomeAmplification" PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers ### SGA User Interface -SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. +SGA also comes with a easy to use user prompt called SelectiveWholeGenomeAmplification"UI. It allows for a less experienced user to use SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifcationUI and you'll see a series of prompts asking the user about tunables like below @@ -69,7 +69,7 @@ SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifc Input the path to your foreground file:target.fa Input the path to your background file:humangenome.fa Would you like to output your inserted variables to a string you can later paste? (Y/N/Default=y): n - Run SelectiveGenomeAmplification? (Y/N/Default=y): y + Run SelectiveWholeGenomeAmplification"? (Y/N/Default=y): y ### Setting Tunable Parameters @@ -78,19 +78,19 @@ below. For user customizable variables, they need to be passed in as environmental variables like so: max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \ - SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta + SelectiveWholeGenomeAmplification".sh PfalciparumGenome.fasta half.fasta ### Running individual steps -By default SelectiveGenomeAmplification runs all four steps, but you can +By default SelectiveWholeGenomeAmplification" runs all four steps, but you can specify the program to run other steps, like in these examples. - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta score + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta score - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta select score + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta select score - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta 3 4 + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta 3 4 valid steps are these: diff --git a/SelectiveGenomeAmplification b/SelectiveWholeGenomeAmplification index e778cbd..e778cbd 100755 --- a/SelectiveGenomeAmplification +++ b/SelectiveWholeGenomeAmplification diff --git a/SelectiveGenomeAmplificationUI b/SelectiveWholeGenomeAmplificationUI index 98021a9..decf5a1 100755 --- a/SelectiveGenomeAmplificationUI +++ b/SelectiveWholeGenomeAmplificationUI @@ -96,7 +96,7 @@ def run(variables_as_a_string): import subprocess try: - subprocess.check_call(variables_as_a_string + " " + "SelectiveGenomeAmplification " + foreground + " " + background, shell=True) + subprocess.check_call(variables_as_a_string + " " + "SelectiveWholeGenomeAmplification " + foreground + " " + background, shell=True) except: pass @@ -122,5 +122,5 @@ else: if(bool_ask("Would you like to output your inserted variables to a string you can later paste?", "y")): print variables_to_string(variables) - if(bool_ask("Run SelectiveGenomeAmplification?", "y")): + if(bool_ask("Run SelectiveWholeGenomeAmplification?", "y")): run(variables_to_string(variables)) |