Mercurial > repos > davidmurphy > codonlogo
comparison build_test.sh @ 15:981eb8c3a756 default tip
Uploaded
| author | davidmurphy |
|---|---|
| date | Sat, 31 Mar 2012 16:07:07 -0400 |
| parents | c55bdc2fb9fa |
| children |
comparison
equal
deleted
inserted
replaced
| 14:778f03497adb | 15:981eb8c3a756 |
|---|---|
| 1 | 1 |
| 2 mkdir -p tmp | 2 mkdir -p tmp |
| 3 | 3 |
| 4 echo "# Test weblogo by building logos with many different options." | 4 echo "# Test codonlogo by building logos with many different options." |
| 5 | 5 |
| 6 echo -ne '.' | 6 echo -ne '.' |
| 7 ./weblogo < cap.fa > tmp/logo0.eps ||exit | 7 ./codonlogo < cap.fa > tmp/logo0.eps ||exit |
| 8 | 8 |
| 9 echo -ne '.' | 9 echo -ne '.' |
| 10 ./weblogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit | 10 ./codonlogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit |
| 11 | 11 |
| 12 echo -ne '.' | 12 echo -ne '.' |
| 13 ./weblogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit | 13 ./codonlogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit |
| 14 | 14 |
| 15 echo -ne '.' | 15 echo -ne '.' |
| 16 ./weblogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit | 16 ./codonlogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit |
| 17 | 17 |
| 18 echo -ne '.' | 18 echo -ne '.' |
| 19 ./weblogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit | 19 ./codonlogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit |
| 20 | 20 |
| 21 echo -ne '.' | 21 echo -ne '.' |
| 22 ./weblogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit | 22 ./codonlogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit |
| 23 | 23 |
| 24 echo -ne '.' | 24 echo -ne '.' |
| 25 ./weblogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit | 25 ./codonlogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit |
| 26 | 26 |
| 27 echo -ne '.' | 27 echo -ne '.' |
| 28 ./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit | 28 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit |
| 29 | 29 |
| 30 echo -ne '.' | 30 echo -ne '.' |
| 31 ./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit | 31 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit |
| 32 | 32 |
| 33 echo -ne '.' | 33 echo -ne '.' |
| 34 ./weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit | 34 ./codonlogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit |
| 35 | 35 |
| 36 echo -ne '.' | 36 echo -ne '.' |
| 37 ./weblogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout logo8.eps ||exit | 37 ./codonlogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout logo8.eps ||exit |
| 38 | 38 |
| 39 # Test Y Axis | 39 # Test Y Axis |
| 40 | 40 |
| 41 echo -ne '.' | 41 echo -ne '.' |
| 42 ./weblogo --debug yes --fineprint "Custom yaxis label " --ylabel 'yaxis label' < cap.fa > tmp/logo9a.eps ||exit | 42 ./codonlogo --debug yes --fineprint "Custom yaxis label " --ylabel 'yaxis label' < cap.fa > tmp/logo9a.eps ||exit |
| 43 | 43 |
| 44 echo -ne '.' | 44 echo -ne '.' |
| 45 ./weblogo --debug yes --fineprint "Custom units" --units 'nats' < cap.fa > tmp/logo9b.eps ||exit | 45 ./codonlogo --debug yes --fineprint "Custom units" --units 'nats' < cap.fa > tmp/logo9b.eps ||exit |
| 46 | 46 |
| 47 echo -ne '.' | 47 echo -ne '.' |
| 48 ./weblogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel 'yaxis label' --units nats < cap.fa > tmp/logo9c.eps ||exit | 48 ./codonlogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel 'yaxis label' --units nats < cap.fa > tmp/logo9c.eps ||exit |
| 49 | 49 |
| 50 echo -ne '.' | 50 echo -ne '.' |
| 51 ./weblogo --debug yes --fineprint "Empty ylabel" --ylabel '' < cap.fa > tmp/logo9d.eps | 51 ./codonlogo --debug yes --fineprint "Empty ylabel" --ylabel '' < cap.fa > tmp/logo9d.eps |
| 52 | 52 |
| 53 echo -ne '.' | 53 echo -ne '.' |
| 54 ./weblogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit | 54 ./codonlogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit |
| 55 | 55 |
| 56 # Test X Axis | 56 # Test X Axis |
| 57 | 57 |
| 58 echo -ne '.' | 58 echo -ne '.' |
| 59 ./weblogo --debug yes --format pdf --fineprint "Custom xaxis label " --xlabel 'xaxis label' < cap.fa > tmp/logo10a.pdf ||exit | 59 ./codonlogo --debug yes --format pdf --fineprint "Custom xaxis label " --xlabel 'xaxis label' < cap.fa > tmp/logo10a.pdf ||exit |
| 60 | 60 |
| 61 echo -ne '.' | 61 echo -ne '.' |
| 62 ./weblogo --debug yes --format pdf --fineprint "Empty xlabel" --xlabel '' < cap.fa > tmp/logo10b.pdf ||exit | 62 ./codonlogo --debug yes --format pdf --fineprint "Empty xlabel" --xlabel '' < cap.fa > tmp/logo10b.pdf ||exit |
| 63 | 63 |
| 64 echo -ne '.' | 64 echo -ne '.' |
| 65 ./weblogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit | 65 ./codonlogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit |
| 66 | 66 |
| 67 echo -ne '.' | 67 echo -ne '.' |
| 68 ./weblogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit | 68 ./codonlogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit |
| 69 | 69 |
| 70 # Test Formats | 70 # Test Formats |
| 71 | 71 |
| 72 echo -ne '.' | 72 echo -ne '.' |
| 73 ./weblogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit | 73 ./codonlogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit |
| 74 | 74 |
| 75 echo -ne '.' | 75 echo -ne '.' |
| 76 ./weblogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit | 76 ./codonlogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit |
| 77 | 77 |
| 78 echo -ne '.' | 78 echo -ne '.' |
| 79 ./weblogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit | 79 ./codonlogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit |
| 80 | 80 |
| 81 echo -ne '.' | 81 echo -ne '.' |
| 82 ./weblogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit | 82 ./codonlogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit |
| 83 | 83 |
| 84 echo -ne '.' | 84 echo -ne '.' |
| 85 ./weblogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit | 85 ./codonlogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit |
| 86 | 86 |
| 87 echo -ne '.' | 87 echo -ne '.' |
| 88 ./weblogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit | 88 ./codonlogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit |
| 89 | 89 |
| 90 # Test Sizes | 90 # Test Sizes |
| 91 | 91 |
| 92 echo -ne '.' | 92 echo -ne '.' |
| 93 ./weblogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit | 93 ./codonlogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit |
| 94 | 94 |
| 95 echo -ne '.' | 95 echo -ne '.' |
| 96 ./weblogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit | 96 ./codonlogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit |
| 97 | 97 |
| 98 echo -ne '.' | 98 echo -ne '.' |
| 99 ./weblogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit | 99 ./codonlogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit |
| 100 | 100 |
| 101 echo -ne '.' | 101 echo -ne '.' |
| 102 ./weblogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit | 102 ./codonlogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit |
| 103 | 103 |
| 104 | 104 |
| 105 | 105 |
| 106 echo -ne '.' | 106 echo -ne '.' |
| 107 ./weblogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString | 107 ./codonlogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString |
| 108 > | 108 > |
| 109 GTTGTTGTTGTT | 109 GTTGTTGTTGTT |
| 110 > | 110 > |
| 111 GTCGTCGTCGTC | 111 GTCGTCGTCGTC |
| 112 > | 112 > |
| 118 | 118 |
| 119 | 119 |
| 120 | 120 |
| 121 # Test unit options | 121 # Test unit options |
| 122 echo -ne '.' | 122 echo -ne '.' |
| 123 ./weblogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit | 123 ./codonlogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit |
| 124 | |
| 125 echo -ne '.' | |
| 126 ./weblogo --format pdf --fineprint "bits" --unit bits > tmp/logo14b.pdf < cap.fa ||exit | |
| 127 | |
| 128 echo -ne '.' | |
| 129 ./weblogo --format pdf --fineprint "nats" --unit nats > tmp/logo14c.pdf < cap.fa ||exit | |
| 130 | |
| 131 echo -ne '.' | |
| 132 ./weblogo --format pdf --fineprint "kJ/mol" --unit kJ/mol \ | |
| 133 > tmp/logo14d.pdf < cap.fa ||exit | |
| 134 | |
| 135 echo -ne '.' | |
| 136 ./weblogo --format pdf --fineprint "kT" --unit kT \ | |
| 137 > tmp/logo14e.pdf < cap.fa ||exit | |
| 138 | |
| 139 echo -ne '.' | |
| 140 ./weblogo --format pdf --fineprint "kcal/mol" --unit kcal/mol \ | |
| 141 > tmp/logo14f.pdf < cap.fa || exit | |
| 142 | 124 |
| 143 | 125 |
| 144 | 126 |
| 145 | 127 |
| 146 | 128 |
| 147 | 129 |
| 148 | 130 |
| 131 |