fixed test-data names and included further documentation

estebanpw · Sep 29, 2020 · ea5b3f2 · ea5b3f2
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diff --git a/README.md b/README.md
@@ -123,6 +123,26 @@ You can test CHROMEISTER with the two mycoplasma sequences provided in the 'test
 
 Note: in this example we used size 500 since the two sequences are quite small.
 
+## Example runs
+
+### Chromosome example 
+
+Comparing two chromosomes (Homo sapiens Chr X vs Mus musculus Chr X) in a minute:
+
+run_and_plot_chromeister.sh HOMSA.Chr.X.fasta MUSMU.Chr.X.fasta 32 1000 4
+
+![HOMSA vs MUSMU](https://github.com/estebanpw/chromeister/blob/master/images/HOMSA.Chr.X.fasta-MUSMU.Chr.X.fasta.mat.filt.png)
+
+
+### Multi-fasta
+
+Comparing the full genome of the Gallus gallus against the Meleagris gallopavo with all their chromosomes including auto-generated grid:
+
+run_and_plot_chromeister.sh GALGA.Chr.complete.fasta MELGA.Chr.complete.fasta 32 1000 4 grid
+
+![MULTI-FASTA](https://github.com/estebanpw/chromeister/blob/master/images/GALGA.Chr.complete.fasta-MELGA.Chr.complete.fasta.mat.filt.png)
+
+
 ## Help
 
 1. Hanging output and program does not finish

diff --git a/images/GALGA.Chr.complete.fasta-MELGA.Chr.complete.fasta.mat.filt.png b/images/GALGA.Chr.complete.fasta-MELGA.Chr.complete.fasta.mat.filt.png
diff --git a/images/HOMSA.Chr.X.fasta-MUSMU.Chr.X.fasta.mat.filt.png b/images/HOMSA.Chr.X.fasta-MUSMU.Chr.X.fasta.mat.filt.png
diff --git a/...data/hits-XY-mycoplasma-232-7422.mat.hits → ...-232.fasta-mycoplasma-7422.fasta.mat.hits b/...data/hits-XY-mycoplasma-232-7422.mat.hits → ...-232.fasta-mycoplasma-7422.fasta.mat.hits
diff --git a/test-data/mycoplasma-232-7422.mat.filt.png b/test-data/mycoplasma-232-7422.mat.filt.png
diff --git a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.log b/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.log
@@ -0,0 +1,15 @@
+[INFO] Generating a 500x500 matrix
+[INFO] Loading database
+1%...2%...3%...4%...5%...6%...7%...8%...9%...10%...11%...12%...13%...14%...15%...16%...17%...18%...19%...20%...21%...22%...23%...24%...25%...26%...27%...28%...29%...30%...31%...32%...33%...34%...35%...36%...37%...38%...39%...40%...41%...42%...43%...44%...45%...46%...47%...48%...49%...50%...51%...52%...53%...54%...55%...56%...57%...58%...59%...60%...61%...62%...63%...64%...65%...66%...67%...68%...69%...70%...71%...72%...73%...74%...75%...76%...77%...78%...79%...80%...81%...82%...83%...84%...85%...86%...87%...88%...89%...90%...91%...92%...93%...94%...95%...96%...97%...98%...99%...100%...[INFO] Database loaded and of length 898495.
+[INFO] Ratios: Q [1.785516e+03] D [1.796990e+03]. Lenghts: Q [892758] D [898495]
+[INFO] Pixel size: Q [5.600622e-04] D [5.564861e-04].
+[INFO] Computing absolute hit numbers.
+1%...2%...3%...4%...5%...6%...7%...8%...9%...10%...11%...12%...13%...14%...15%...16%...17%...18%...19%...20%...21%...22%...23%...24%...25%...26%...27%...28%...29%...30%...31%...32%...33%...34%...35%...36%...37%...38%...39%...40%...41%...42%...43%...44%...45%...46%...47%...48%...49%...50%...51%...52%...53%...54%...55%...56%...57%...58%...59%...60%...61%...62%...63%...64%...65%...66%...67%...68%...69%...70%...71%...72%...73%...74%...75%...76%...77%...78%...79%...80%...81%...82%...83%...84%...85%...86%...87%...88%...89%...90%...91%...92%...93%...94%...95%...96%...97%...98%...99%...100%...Scanning hits table.
+1%...1%...2%...3%...4%...5%...6%...7%...8%...9%...10%...11%...12%...13%...14%...15%...16%...17%...18%...19%...20%...21%...22%...23%...24%...25%...26%...27%...28%...29%...30%...31%...32%...33%...34%...35%...36%...37%...38%...39%...40%...41%...42%...43%...44%...45%...46%...47%...48%...49%...50%...51%...52%...53%...54%...55%...56%...57%...58%...59%...60%...61%...62%...63%...64%...65%...66%...67%...68%...69%...70%...71%...72%...73%...74%...75%...76%...77%...78%...79%...80%...81%...82%...83%...84%...85%...86%...87%...88%...89%...90%...91%...92%...93%...94%...95%...96%...97%...98%...99%...100%...
+[INFO] Query length 892758.
+[INFO] Writing matrix.
+[INFO] Found 20083 unique hits for z = 4.
+
+real	0m0.816s
+user	0m0.432s
+sys	0m0.384s

diff --git a/test-data/mycoplasma-232-7422.mat → ...lasma-232.fasta-mycoplasma-7422.fasta.mat b/test-data/mycoplasma-232-7422.mat → ...lasma-232.fasta-mycoplasma-7422.fasta.mat
diff --git a/test-data/mycoplasma-232-7422.mat.csv → ...a-232.fasta-mycoplasma-7422.fasta.mat.csv b/test-data/mycoplasma-232-7422.mat.csv → ...a-232.fasta-mycoplasma-7422.fasta.mat.csv
diff --git a/test-data/mycoplasma-232-7422.mat.events.txt → ...asta-mycoplasma-7422.fasta.mat.events.txt b/test-data/mycoplasma-232-7422.mat.events.txt → ...asta-mycoplasma-7422.fasta.mat.events.txt
diff --git a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png b/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.mat.filt.png
diff --git a/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt b/test-data/mycoplasma-232.fasta-mycoplasma-7422.fasta.scr.txt
@@ -0,0 +1,3 @@
+[1] 0.048
+null device 
+          1