From ba13899c7400cce650fcf58a319b4c696bf5094d Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 29 Dec 2014 09:36:21 -0500 Subject: [PATCH 1/4] remove debug files --- tools/picard.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/tools/picard.py b/tools/picard.py index 6fe517c26..7ec47bdc5 100644 --- a/tools/picard.py +++ b/tools/picard.py @@ -94,6 +94,10 @@ def execute(self, inBams, outBam, PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory) class FilterSamReadsTool(PicardTools) : + ''' TO DO: it might be desirable to replace this tool with a + non-Picard/non-Java approach that uses samtools/pysam, sqlite, + and O(1) memory. + ''' subtoolName = 'FilterSamReads' jvmMemDefault = '4g' def execute(self, inBam, exclude, readList, outBam, @@ -118,12 +122,9 @@ def execute(self, inBam, exclude, readList, outBam, PicardTools.execute(self, 'SamFormatConverter', opts, JVMmemory='50m') else: opts = ['INPUT='+inBam, 'OUTPUT='+outBam, 'READ_LIST_FILE='+readList, - 'FILTER='+(exclude and 'excludeReadList' or 'includeReadList')] + 'FILTER='+(exclude and 'excludeReadList' or 'includeReadList'), + 'WRITE_READS_FILES=false'] PicardTools.execute(self, self.subtoolName, opts + picardOptions, JVMmemory) - for bam in (inBam, outBam): - junk = bam[:-3]+'reads' - if os.path.isfile(junk): - os.unlink(junk) class CreateSequenceDictionaryTool(PicardTools) : subtoolName = 'CreateSequenceDictionary' From 0a267879034697c7aca3b9813a3c9552fe266804 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 29 Dec 2014 09:47:44 -0500 Subject: [PATCH 2/4] some documentation of the way we previously called iSNVs [ci skip] --- .../iSNV/example_files/patients_all.txt | 92 + .../vphaser_iSNVs_combined_NXT1.txt | 1609 ++++++++++++++++ .../vphaser_iSNVs_combined_NXT1_freq.txt | 1012 +++++++++++ ...ser_iSNVs_combined_NXT1_freq_validated.txt | 951 ++++++++++ .../vphaser_iSNVs_combined_NXT2.txt | 1617 +++++++++++++++++ old-scripts/iSNV/iSNV-pipeline.txt | 77 + .../iSNV/scripts/concat_samples_NXT1.py | 37 + .../iSNV/scripts/concat_samples_NXT2.py | 37 + old-scripts/iSNV/scripts/filter_read_bias.pl | 45 + .../iSNV/scripts/nextera_validation.py | 88 + 10 files changed, 5565 insertions(+) create mode 100644 old-scripts/iSNV/example_files/patients_all.txt create mode 100644 old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt create mode 100644 old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt create mode 100644 old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq_validated.txt create mode 100644 old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT2.txt create mode 100644 old-scripts/iSNV/iSNV-pipeline.txt create mode 100755 old-scripts/iSNV/scripts/concat_samples_NXT1.py create mode 100755 old-scripts/iSNV/scripts/concat_samples_NXT2.py create mode 100644 old-scripts/iSNV/scripts/filter_read_bias.pl create mode 100755 old-scripts/iSNV/scripts/nextera_validation.py diff --git a/old-scripts/iSNV/example_files/patients_all.txt b/old-scripts/iSNV/example_files/patients_all.txt new file mode 100644 index 000000000..fa2593a1f --- /dev/null +++ b/old-scripts/iSNV/example_files/patients_all.txt @@ -0,0 +1,92 @@ +patient +EBOV_2014_EM096 +EBOV_2014_EM104 +EBOV_2014_EM106 +EBOV_2014_EM110 +EBOV_2014_EM111 +EBOV_2014_EM112 +EBOV_2014_EM113 +EBOV_2014_EM115 +EBOV_2014_EM119 +EBOV_2014_EM120 +EBOV_2014_EM121 +EBOV_2014_EM124.1 +EBOV_2014_EM124.2 +EBOV_2014_EM124.3 +EBOV_2014_G3670 +EBOV_2014_G3676.1 +EBOV_2014_G3676.2 +EBOV_2014_G3677.1 +EBOV_2014_G3677.2 +EBOV_2014_G3679 +EBOV_2014_G3680 +EBOV_2014_G3682 +EBOV_2014_G3683 +EBOV_2014_G3686 +EBOV_2014_G3687 +EBOV_2014_G3707 +EBOV_2014_G3713.2 +EBOV_2014_G3713.3 +EBOV_2014_G3713.4 +EBOV_2014_G3724 +EBOV_2014_G3729 +EBOV_2014_G3734.1 +EBOV_2014_G3735.1 +EBOV_2014_G3735.2 +EBOV_2014_G3750.1 +EBOV_2014_G3750.2 +EBOV_2014_G3750.3 +EBOV_2014_G3752 +EBOV_2014_G3758 +EBOV_2014_G3764 +EBOV_2014_G3769.1 +EBOV_2014_G3769.2 +EBOV_2014_G3769.3 +EBOV_2014_G3769.4 +EBOV_2014_G3770.1 +EBOV_2014_G3770.2 +EBOV_2014_G3771 +EBOV_2014_G3782 +EBOV_2014_G3786 +EBOV_2014_G3787 +EBOV_2014_G3788 +EBOV_2014_G3789.1 +EBOV_2014_G3795 +EBOV_2014_G3796 +EBOV_2014_G3798 +EBOV_2014_G3799 +EBOV_2014_G3800 +EBOV_2014_G3807 +EBOV_2014_G3808 +EBOV_2014_G3809 +EBOV_2014_G3810.1 +EBOV_2014_G3810.2 +EBOV_2014_G3814 +EBOV_2014_G3816 +EBOV_2014_G3817 +EBOV_2014_G3818 +EBOV_2014_G3819 +EBOV_2014_G3820 +EBOV_2014_G3821 +EBOV_2014_G3822 +EBOV_2014_G3823 +EBOV_2014_G3825.1 +EBOV_2014_G3825.2 +EBOV_2014_G3826 +EBOV_2014_G3827 +EBOV_2014_G3829 +EBOV_2014_G3831 +EBOV_2014_G3834 +EBOV_2014_G3838 +EBOV_2014_G3840 +EBOV_2014_G3841 +EBOV_2014_G3845 +EBOV_2014_G3846 +EBOV_2014_G3848 +EBOV_2014_G3850 +EBOV_2014_G3851 +EBOV_2014_G3856.1 +EBOV_2014_G3856.3 +EBOV_2014_G3857 +EBOV_2014_NM042.1 +EBOV_2014_NM042.3 diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt new file mode 100644 index 000000000..fd5f3a345 --- /dev/null +++ b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt @@ -0,0 +1,1609 @@ +patient pos var ref pval type freq ct_1 ct_2 ct_3 ct_4 extra1 extra2 +EBOV_2014_EM096 2341.0 A G 0.6266 snp 24.83 A:28:9 G:89:23 +EBOV_2014_EM096 18412.0 T C 0.1972 snp 27.81 C:126:131 T:41:58 +EBOV_2014_EM104 5781.0 G A 0.8902 snp 2.347 A:344:280 G:7:8 +EBOV_2014_EM104 8733.0 IA d 0.5694 lp 2.8810000000000002 IA:8:6 d:312:160 +EBOV_2014_EM104 10743.0 T C 0.2492 snp 31.99 A:1:1 C:255:166 T:130:69 +EBOV_2014_EM104 11490.0 IA d 0.331 lp 7.736000000000001 IA:18:9 d:242:80 +EBOV_2014_EM104 12841.0 A G 0.6055 snp 14.18 A:27:28 G:151:182 +EBOV_2014_EM106 1089.0 IT d 0.7096 lp 1.1740000000000002 IT:6:7 ITT:0:1 d:645:448 +EBOV_2014_EM106 2127.0 T C 0.6947 snp 2.384 C:320:376 T:10:7 +EBOV_2014_EM106 4712.0 A G 0.8361 snp 1.7730000000000001 A:9:9 G:523:474 +EBOV_2014_EM106 7203.0 G A 0.4424 snp 2.106 A:254:628 C:0:1 G:7:12 +EBOV_2014_EM106 8377.0 IA d 0.8472 lp 2.8480000000000003 IA:8:10 d:287:327 +EBOV_2014_EM106 8733.0 IA d 0.05875 lp 4.824 IA:33:8 d:536:273 +EBOV_2014_EM106 11490.0 IA d 0.1467 lp 9.826 IA:51:11 d:420:149 +EBOV_2014_EM106 13985.0 IA d 0.7753 lp 2.083 IA:8:7 d:303:402 +EBOV_2014_EM106 17520.0 IT d 0.05955 lp 5.89 IT:36:12 d:471:296 +EBOV_2014_EM110 565.0 G A 0.1657 snp 9.238999999999999 A:8175:6696 C:0:2 G:804:710 +EBOV_2014_EM110 1089.0 IT d 0.6045 lp 1.496 IT:153:117 ITT:1:0 d:10354:7427 +EBOV_2014_EM110 1285.0 A G 0.305 snp 0.1468 A:14:8 G:7884:7075 T:2:0 +EBOV_2014_EM110 2296.0 T C 0.3202 snp 0.1765 A:0:1 C:8762:5944 G:1:1 T:13:13 +EBOV_2014_EM110 4428.0 IT d 0.6134 lp 0.3047 IT:24:17 ITT:1:1 d:7325:6090 +EBOV_2014_EM110 4489.0 G T 9.35e-08 snp 1.151 A:2:0 C:4:0 G:107:28 T:5053:6532 +EBOV_2014_EM110 4976.0 A C 0.01236 snp 36.13 A:3077:3403 C:5661:5794 T:2:0 +EBOV_2014_EM110 5001.0 A G 0.1712 snp 2.5860000000000003 A:250:239 C:2:1 G:9985:8425 T:4:0 +EBOV_2014_EM110 5786.0 C T 0.8117 snp 0.1108 A:1:0 C:9:14 T:12113:8622 +EBOV_2014_EM110 6377.0 IA d 0.9687 lp 0.5175 IA:50:43 d:8303:9576 +EBOV_2014_EM110 6917.0 IA d 0.3979 lp 0.795 IA:61:49 d:7057:6670 +EBOV_2014_EM110 6918.0 D1 i 0.6819 lp 0.1015 D1:8:6 D2:1:0 i:7118:6660 +EBOV_2014_EM110 8377.0 IA d 0.2361 lp 3.372 IA:185:215 IAA:2:2 IAAA:1:0 IC:1:0 d:5812:5645 +EBOV_2014_EM110 8462.0 IA d 0.05252999999999999 lp 0.2811 IA:11:24 IAA:0:1 d:6478:5936 +EBOV_2014_EM110 8636.0 A G 0.8571 snp 0.934 A:83:68 C:1:1 G:8682:7329 T:3:0 +EBOV_2014_EM110 8733.0 IA d 0.7619 lp 4.316 IA:461:209 IAA:1:2 d:10300:4549 +EBOV_2014_EM110 8766.0 IA d 0.8299 lp 0.6453 IA:52:43 d:8167:6460 +EBOV_2014_EM110 9486.0 G A 0.6544 snp 0.2292 A:10284:6688 G:25:14 T:1:0 +EBOV_2014_EM110 9687.0 IA d 0.9364 lp 0.1135 IA:6:8 d:7169:5150 +EBOV_2014_EM110 10218.0 G A 0.8966 snp 0.289 A:8828:5650 C:0:11 G:26:16 T:0:1 +EBOV_2014_EM110 10229.0 IA d 0.8701 lp 0.2365 IA:21:15 IAA:1:0 IAAA:1:0 d:9061:6125 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d:644:440 +EBOV_2014_NM042.1 18197.0 G A 0.784 snp 1.13 A:566:746 G:8:7 diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt new file mode 100644 index 000000000..7cce48237 --- /dev/null +++ b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt @@ -0,0 +1,1012 @@ +patient pos var ref pval type freq ct_1 ct_2 ct_3 ct_4 extra1 extra2 +EBOV_2014_EM096 2341.0 A G 0.6266 snp 24.83 A:28:9 G:89:23 +EBOV_2014_EM096 18412.0 T C 0.1972 snp 27.81 C:126:131 T:41:58 +EBOV_2014_EM104 5781.0 G A 0.8902 snp 2.347 A:344:280 G:7:8 +EBOV_2014_EM104 8733.0 IA d 0.5694 lp 2.881 IA:8:6 d:312:160 +EBOV_2014_EM104 10743.0 T C 0.2492 snp 31.99 A:1:1 C:255:166 T:130:69 +EBOV_2014_EM104 11490.0 IA d 0.331 lp 7.7360000000000015 IA:18:9 d:242:80 +EBOV_2014_EM104 12841.0 A G 0.6055 snp 14.18 A:27:28 G:151:182 +EBOV_2014_EM106 1089.0 IT d 0.7096 lp 1.1740000000000002 IT:6:7 ITT:0:1 d:645:448 +EBOV_2014_EM106 2127.0 T C 0.6947 snp 2.384 C:320:376 T:10:7 +EBOV_2014_EM106 4712.0 A G 0.8361 snp 1.773 A:9:9 G:523:474 +EBOV_2014_EM106 7203.0 G A 0.4424 snp 2.106 A:254:628 C:0:1 G:7:12 +EBOV_2014_EM106 8377.0 IA d 0.8472 lp 2.8480000000000003 IA:8:10 d:287:327 +EBOV_2014_EM106 8733.0 IA d 0.05875 lp 4.824 IA:33:8 d:536:273 +EBOV_2014_EM106 11490.0 IA d 0.1467 lp 9.826 IA:51:11 d:420:149 +EBOV_2014_EM106 13985.0 IA d 0.7753 lp 2.083 IA:8:7 d:303:402 +EBOV_2014_EM106 17520.0 IT d 0.05955 lp 5.89 IT:36:12 d:471:296 +EBOV_2014_EM110 565.0 G A 0.1657 snp 9.239 A:8175:6696 C:0:2 G:804:710 +EBOV_2014_EM110 1089.0 IT d 0.6045 lp 1.496 IT:153:117 ITT:1:0 d:10354:7427 +EBOV_2014_EM110 4489.0 G T 9.35e-08 snp 1.151 A:2:0 C:4:0 G:107:28 T:5053:6532 +EBOV_2014_EM110 4976.0 A C 0.01236 snp 36.13 A:3077:3403 C:5661:5794 T:2:0 +EBOV_2014_EM110 5001.0 A G 0.1712 snp 2.5860000000000003 A:250:239 C:2:1 G:9985:8425 T:4:0 +EBOV_2014_EM110 6377.0 IA d 0.9687 lp 0.5175 IA:50:43 d:8303:9576 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0.4544 lp 0.7495 IA:22:16 IAA:2:1 d:2605:2424 +EBOV_2014_G3856.1 7367.0 T C 0.4217 snp 0.3504 A:1:0 C:3015:1818 G:1:0 T:8:9 +EBOV_2014_G3856.1 7405.0 T C 0.6158 snp 0.9996 C:3154:2293 T:30:25 +EBOV_2014_G3856.1 7760.0 T G 0.5678 snp 0.5423 A:2:0 C:1:0 G:3601:2632 T:18:16 +EBOV_2014_G3856.1 8377.0 IA d 0.7737 lp 1.8780000000000001 IA:34:34 d:1839:1714 +EBOV_2014_G3856.1 8462.0 IA d 0.8881 lp 0.3526 IA:7:7 d:2053:1904 +EBOV_2014_G3856.1 8733.0 IA d 0.1949 lp 4.744 IA:195:80 d:4109:1413 +EBOV_2014_G3856.1 8766.0 IA d 0.968 lp 0.4846 IA:11:15 d:3101:2238 +EBOV_2014_G3856.1 10215.0 C A 0.6927 snp 0.3084 A:3487:2009 C:10:7 +EBOV_2014_G3856.1 10336.0 IA d 0.1197 lp 0.609 IA:30:12 IAA:1:0 IAAAA:1:0 d:4084:2768 +EBOV_2014_G3856.1 10890.0 G A 0.7779 snp 4.281000000000001 A:3479:2849 G:158:125 +EBOV_2014_G3856.1 11490.0 IA d 0.7282 lp 4.209 IA:119:34 d:2749:733 +EBOV_2014_G3856.1 11980.0 IA d 0.2882 lp 1.3659999999999999 IA:68:18 d:4595:1613 +EBOV_2014_G3856.1 12145.0 IT d 0.1754 lp 0.7326 IT:33:22 ITT:0:1 d:3664:3787 +EBOV_2014_G3856.1 12747.0 IA d 0.9991 lp 0.391 IA:6:6 d:1529:1528 +EBOV_2014_G3856.1 13985.0 IA d 0.8498 lp 2.824 IA:40:68 IAA:0:1 d:1410:2306 +EBOV_2014_G3856.1 13986.0 D1 i 0.5454 lp 0.6485 D1:8:17 D2:1:0 i:1450:2379 +EBOV_2014_G3856.1 16049.0 IT d 0.3664 lp 0.5942 IT:16:11 d:2283:2234 +EBOV_2014_G3856.1 17288.0 C A 0.971 snp 0.3014 A:3612:3004 C:9:11 +EBOV_2014_G3856.1 17520.0 IT d 0.005092 lp 3.7489999999999997 IT:150:62 d:3332:2111 +EBOV_2014_G3856.1 17521.0 D1 i 0.5607 lp 0.2112 D1:6:6 D2:1:0 i:3482:2186 +EBOV_2014_G3856.1 18276.0 IA d 0.9907 lp 1.2690000000000001 IA:41:40 IAA:1:1 IAAAA:0:1 d:3194:3107 +EBOV_2014_G3856.1 18398.0 IA d 0.6083 lp 0.3511 IA:8:12 d:2595:3081 +EBOV_2014_G3856.3 10509.0 T C 0.5689 snp 11.03 C:82:39 T:9:6 +EBOV_2014_NM042.1 1089.0 IT d 0.4163 lp 1.996 IT:28:14 d:1247:815 +EBOV_2014_NM042.1 1257.0 A G 0.2945 snp 19.01 A:134:174 G:528:784 +EBOV_2014_NM042.1 1881.0 A G 0.04116 snp 27.85 A:267:207 G:624:604 +EBOV_2014_NM042.1 5931.0 C T 0.966 snp 0.9836 C:8:7 T:797:713 +EBOV_2014_NM042.1 6917.0 IA d 0.08605 lp 1.469 IA:15:6 d:741:668 +EBOV_2014_NM042.1 7678.0 G A 0.8687 snp 1.114 A:947:562 G:11:6 +EBOV_2014_NM042.1 8377.0 IA d 0.3485 lp 3.8139999999999996 IA:19:13 d:396:411 +EBOV_2014_NM042.1 8733.0 IA d 0.2427 lp 4.418 IA:36:24 d:873:425 +EBOV_2014_NM042.1 10218.0 G A 0.9848 snp 2.539 A:692:496 C:0:1 G:18:13 T:1:0 +EBOV_2014_NM042.1 11174.0 G A 0.214 snp 20.56 A:157:326 G:48:77 +EBOV_2014_NM042.1 11490.0 IA d 0.7932 lp 7.153 IA:41:8 d:541:95 +EBOV_2014_NM042.1 11980.0 IA d 0.9833 lp 1.577 IA:15:7 d:939:434 +EBOV_2014_NM042.1 12145.0 IT d 0.3897 lp 1.5219999999999998 IT:12:8 d:643:651 +EBOV_2014_NM042.1 12729.0 G A 0.5515 snp 1.681 A:432:270 G:6:6 +EBOV_2014_NM042.1 13985.0 IA d 0.5921 lp 2.79 IA:14:17 IAAA:1:0 d:435:644 +EBOV_2014_NM042.1 17520.0 IT d 0.2487 lp 6.787000000000001 IT:37:27 d:571:308 +EBOV_2014_NM042.1 18197.0 G A 0.9211 snp 1.0090000000000001 A:607:766 C:0:1 G:6:8 diff --git a/old-scripts/iSNV/iSNV-pipeline.txt b/old-scripts/iSNV/iSNV-pipeline.txt new file mode 100644 index 000000000..7c0ab6a6f --- /dev/null +++ b/old-scripts/iSNV/iSNV-pipeline.txt @@ -0,0 +1,77 @@ +Instructions for calling and validating iSNVs: + +1. Calling of iSNVs using VPHASER V2 + +# PREREQUISITES +bash +export LD_LIBRARY_PATH=/seq/viral/analysis/xyang/programs/Library/pezmaster31-bamtools-e235c55/lib:$LD_LIBRARY_PATH + +# CALCULATE SNPS WITH VPHASER V2 +for sample in EM096_r1 EM104_r1 EM106_r1 EM110_r1 EM111_r1 EM112_r1 EM113_r1 EM115_r1 EM119_r1 EM120_r1 EM121_r1 EM124.1_r1 EM124.2_r1 EM124.3_r1 EM124.4_r1 G3670.1_r1 G3676.1_r1 G3676.2_r1 G3677.1_r1 G3677.2_r1 G3679.1_r1 G3680.1_r1 G3682.1_r1 G3683.1_r1 G3686.1_r1 G3687.1_r1 G3707_r1 G3713.2_r1 G3713.3_r1 G3713.4_r1 G3724_r1 G3729_r1 G3734.1_r1 G3735.1_r1 G3735.2_r1 G3750.1_r1 G3750.2_r1 G3750.3_r1 G3752_r1 G3758_r1 G3764_r1 G3765.2_r1 G3769.1_r1 G3769.2_r1 G3769.3_r1 G3769.4_r1 G3770.1_r1 G3770.2_r1 G3771_r1 G3782_r1 G3786_r1 G3787_r1 G3788_r1 G3789.1_r1 G3795_r1 G3796_r1 G3798_r1 G3799_r1 G3800_r1 G3805.1_r1 G3805.2_r1 G3807_r1 G3808_r1 G3809_r1 G3810.1_r1 G3810.2_r1 G3814_r1 G3816_r1 G3817_r1 G3818_r1 G3819_r1 G3820_r1 G3821_r1 G3822_r1 G3823_r1 G3825.1_r1 G3825.2_r1 G3826_r1 G3827_r1 G3829_r1 G3831_r1 G3834_r1 G3838_r1 G3840_r1 G3841_r1 G3845_r1 G3846_r1 G3848_r1 G3850_r1 G3851_r1 G3856.1_r1 G3856.3_r1 G3857_r1 NM042.1_r1 NM042.2_r1 NM042.3_r1 +do +for directory in /idi/sabeti-scratch/kandersen/analysis/140726_ebola3 +do +for in_directory in $directory/_bams +do +bsub -n 4 -R "span[hosts=1]" -q week -R "rusage[mem=8]" -o $directory/_logs/$sample.log.bsub.txt -P sabeti_align -J $sample.vp1 "mkdir $directory/_pileup/vp/$sample && /gsap/garage-viral/viral/analysis/xyang/programs/VariantCaller/bin/variant_caller -i $in_directory/$sample.realigned.bam -ig 6 -o $directory/_pileup/vp/$sample" +done +done +done + +#output files from this step at: /idi/sabeti-data/kandersen/analysis/140726_ebola3/_pileup/vp +#example output file: “EBOV-EM096-SL-2014.var.raw.txt” + + +2. Remap iSNV calls to consistent reference coordinates + +#remap all variant calls to same library +for i in *.var.raw.txt; do j=${i%%-SL-2014*.var.raw.txt}; k=${j##EBOV-}; echo $k; /seq/viral/analysis/xyang/scripts/align2ref.pl -ref /idi/sabeti-data/rsealfon/viruses/ebolavirus/new_seqs/EBOV_SL_Guinea.fasta.aln.firstseq -seq /idi/sabeti-scratch/kandersen/analysis/140726_ebola3/_refs/$k"_r1.fasta" -oprefix $i.mapped -vc $i; done + +#complete directory of remap script: /seq/viral/analysis/xyang/scripts/align2ref.pl + + +3. Filter iSNV calls + +#filter +for i in *var.raw.txt.mapped.ref.vc.txt ;do perl ../vphaser2_calls/filter_read_bias.pl $i > $i.filtered; echo $i; done + +#the filtering parameters are hard-coded +#complete directory of filtering script: /idi/sabeti-data/rsealfon/viruses/ebolavirus/iSNV_combined/vphaser2_calls/filter_read_bias.pl +#script also attached + + +4. Remap the file names + +#remap names +for i in *.filtered; do j=${i%%-SL-2014.var.raw.txt.mapped.ref.vc.txt.filtered}; k=${j##EBOV-}; mv $i "EBOV_2014_"$k.var.raw.txt.mapped.ref.vc.txt.filtered; done + + +5. Combine all of the different samples sequenced in the same library prep + +#navigate to folder containing all the .var.raw.txt.mapped.ref.vc.txt.filtered files from step 4 +#run attached python script: concat_samples_NXT1.py + +#repeat for validation set, using concat_samples_NXT2.py (this is the same file as _NXT1.py but saves results with a different name + +# ‘patients_all.txt’ is just a file listing all the patient names in that sequencing batch + +#output files (2) from this step: “vphaser_iSNVs_combined_NXT1.txt” and “vphaser_iSNVs_combined_NXT2.txt” + + + +6. Apply frequency filter (code not included) + +#apply only to original set (NXT1), not validation set (NXT2) +#remove all rows from “vphaser_iSNVs_combined_NXT1.txt” where the value in the “freq” column is <0.5 + +#output file from this step: “vphaser_iSNVs_combined_NXT1_freq.txt” + + +7. Validate calls from NXT1 with validation set (NXT2) + +#run attached python script: nextera_validation +#argument 1 = “vphaser_iSNVs_combined_NXT1_freq.txt” +#argument 2 = “vphaser_iSNVs_combined_NXT2.txt” + +#output file from this step: “vphaser_iSNVs_combined_NXT1_freq_validated.txt” +#final list of iSNV calls \ No newline at end of file diff --git a/old-scripts/iSNV/scripts/concat_samples_NXT1.py b/old-scripts/iSNV/scripts/concat_samples_NXT1.py new file mode 100755 index 000000000..6bcb01b71 --- /dev/null +++ b/old-scripts/iSNV/scripts/concat_samples_NXT1.py @@ -0,0 +1,37 @@ +#! /usr/bin/env python + +import pandas as pd +import numpy as np +import sys +import os.path + +if __name__ == "__main__": + + #read in the patient shift file so we have a list of patients + names=pd.read_csv('patients_all.txt',sep='\t') + #save the names of the patients so we can loop through them + names=names.patient + + #initialize the concatenated dataframe + full=pd.DataFrame() + + #column names to use in the dataframe + cols=['pos','var','ref','pval','type','freq','ct_1','ct_2','ct_3','ct_4','extra1','extra2'] + + for name in names: + + #clear data just in case they file doesn't exist in next round + data=[] + + #first check if file exists then save to dataframe + if os.path.exists(name+'.var.raw.txt.mapped.ref.vc.txt.filtered'): + data=pd.read_csv(name+'.var.raw.txt.mapped.ref.vc.txt.filtered',sep='\t',header=None,names=cols) + + #add a column indicating the patient + data.insert(0,'patient',name) + + #now concat the new patient to the whole dataframe + full=pd.concat([full,data],ignore_index=True) + + #now save the final dataframe as a file + full.to_csv('vphaser_iSNVs_combined_NXT1.txt',sep='\t',index=False) \ No newline at end of file diff --git a/old-scripts/iSNV/scripts/concat_samples_NXT2.py b/old-scripts/iSNV/scripts/concat_samples_NXT2.py new file mode 100755 index 000000000..351797eb2 --- /dev/null +++ b/old-scripts/iSNV/scripts/concat_samples_NXT2.py @@ -0,0 +1,37 @@ +#! /usr/bin/env python + +import pandas as pd +import numpy as np +import sys +import os.path + +if __name__ == "__main__": + + #read in the patient shift file so we have a list of patients + names=pd.read_csv('patients_all.txt',sep='\t') + #save the names of the patients so we can loop through them + names=names.patient + + #initialize the concatenated dataframe + full=pd.DataFrame() + + #column names to use in the dataframe + cols=['pos','var','ref','pval','type','freq','ct_1','ct_2','ct_3','ct_4','extra1','extra2'] + + for name in names: + + #clear data just in case they file doesn't exist in next round + data=[] + + #first check if file exists then save to dataframe + if os.path.exists(name+'.var.raw.txt.mapped.ref.vc.txt.filtered'): + data=pd.read_csv(name+'.var.raw.txt.mapped.ref.vc.txt.filtered',sep='\t',header=None,names=cols) + + #add a column indicating the patient + data.insert(0,'patient',name) + + #now concat the new patient to the whole dataframe + full=pd.concat([full,data],ignore_index=True) + + #now save the final dataframe as a file + full.to_csv('vphaser_iSNVs_combined_NXT2.txt',sep='\t',index=False) \ No newline at end of file diff --git a/old-scripts/iSNV/scripts/filter_read_bias.pl b/old-scripts/iSNV/scripts/filter_read_bias.pl new file mode 100644 index 000000000..2708b3289 --- /dev/null +++ b/old-scripts/iSNV/scripts/filter_read_bias.pl @@ -0,0 +1,45 @@ +open FILE, $ARGV[0]; + +$POS_IDX = 0; +$VAR_IDX = 1; +$REF_IDX = 2; +$CT_IDX = 6; +$MIN_READS_FWD = 5; +$MIN_READS_REV = 5; +$STRAND_BIAS_PERC = 10; +$STRAND_BIAS_FRAC = 1.0/$STRAND_BIAS_PERC; +$RATIO_STRAND_BIAS_PERC = 5; +$RATIO_STRAND_BIAS_FRAC = 1.0/$RATIO_STRAND_BIAS_PERC; +while ($line = ) { + chomp $line; + @parts = split /\t/, $line; + for ($i = $CT_IDX; $i <= $#parts; $i++) { + #print "$parts[$i]\n"; + @read_cts = split /:/, $parts[$i]; + #print "$parts2[0]\n"; + #if we are looking at the number of reads for the variant + if ($read_cts[0] eq $parts[$REF_IDX]) { + #print "REF:$read_cts[0]\t$parts[$REF_IDX]\t$read_cts[1]\t$read_cts[2]\n"; + $ref_fwd = $read_cts[1]; + $ref_rev = $read_cts[2]; + } + + if ($read_cts[0] eq $parts[$VAR_IDX]) { + $var_fwd = $read_cts[1]; + $var_rev = $read_cts[2]; + } + } + + #print "$parts[$VAR_IDX]\t$parts[$REF_IDX]\t$ref_fwd\t$ref_rev\t$var_fwd\t$var_rev\n"; + + #pseudocount to get rid of zeroes + $ref_strand_bias = (1.0 * $ref_fwd + 1) / (1.0 * $ref_rev + 1); + $var_strand_bias = (1.0 * $var_fwd + 1) / (1.0 * $var_rev + 1); + $ratio = $ref_strand_bias / $var_strand_bias; + + #print "$ratio\t$STRAND_BIAS_PERC\t$STRAND_BIAS_PERC_2\t$var_fwd\t$var_rev\t$MIN_READS\n"; + if ($ratio < $RATIO_STRAND_BIAS_PERC && $ratio > $RATIO_STRAND_BIAS_FRAC && $var_strand_bias < $STRAND_BIAS_PERC && $var_strand_bias > $STRAND_BIAS_FRAC && $var_fwd > $MIN_READS_FWD && $var_rev > $MIN_READS_REV) { + print "$line\n"; + } +} + diff --git a/old-scripts/iSNV/scripts/nextera_validation.py b/old-scripts/iSNV/scripts/nextera_validation.py new file mode 100755 index 000000000..f18d0dc4f --- /dev/null +++ b/old-scripts/iSNV/scripts/nextera_validation.py @@ -0,0 +1,88 @@ +#! /usr/bin/env python + +import pandas as pd +import numpy as np +import sys + + +def validate(row1, row2): + ''' + This verifies that two libraries describe the same variant at a given position. + If it is a SNP, we require the same two alleles, but in any order. + If it is an indel, we require both to be indels, but do not check the alleles. + ''' + + alleles1 = [row1['ref'], row1['var']] + alleles2 = [row2['ref'], row2['var']] + alleles1 = [a[0].upper() for a in alleles1] + alleles2 = [a[0].upper() for a in alleles2] + return set(alleles1)==set(alleles2) + + +if __name__ == "__main__": + + ''' + This compares two replicate libraries and looks for positions that match. + Used for validation of the batch2 Nextera library. + ''' + + #get file names from the command line + file1 = str(sys.argv[1]) + file2 = str(sys.argv[2]) + #get the files as dataframes + rep1=pd.read_csv(file1,sep='\t') + rep2=pd.read_csv(file2,sep='\t') + + #save list of positions + names=set(rep1.pos) + #save list of acceptable positions, to be filled in + pos = set() + + for name in names: + + #get all the rows with a particular position + temp_rep1 = rep1[rep1.pos == name] + temp_rep2 = rep2[rep2.pos == name] + + #create a list of patients + patients = set(temp_rep1.patient.tolist()) + + escape = False + + for p in patients: + + #get the rep1 row for a given patient + rep1_row = temp_rep1[temp_rep1.patient == p] + #ensure that we have exactly one row in the first library given this patient + #assert rep1_row.shape[0]==1 + #save rep1_row as an object + for index,row in rep1_row.iterrows(): + rep1_row = row + + #get the rep2 row for a given patient + rep2_row = temp_rep2[temp_rep2.patient == p] + + #continue if we have a matching patient + if rep2_row.shape[0]>0: + + #save rep2_row as an object + for index,row in rep2_row.iterrows(): + rep2_row = row + + #look for matching alleles + if validate(rep1_row, rep2_row): + #if we find a position with matching alleles, add the position and exit + pos.add(name) + escape = True + break + + if escape: + break + + #now use pos to filter out positions that dont have duplicates + rep1=rep1[(rep1.pos.isin(pos))] + + #save resulting dataframe to a file + rep1.to_csv(file1.split('.')[0]+'_validated.txt',sep='\t',index=False) + + \ No newline at end of file From 579a0a64e6c2fa9c3060e7876850c46a631db619 Mon Sep 17 00:00:00 2001 From: Danny Park Date: Mon, 29 Dec 2014 09:54:22 -0500 Subject: [PATCH 3/4] add xiao mapper perl script --- old-scripts/iSNV/scripts/align2ref.pl | 289 ++++++++++++++++++++++++++ 1 file changed, 289 insertions(+) create mode 100755 old-scripts/iSNV/scripts/align2ref.pl diff --git a/old-scripts/iSNV/scripts/align2ref.pl b/old-scripts/iSNV/scripts/align2ref.pl new file mode 100755 index 000000000..740051c75 --- /dev/null +++ b/old-scripts/iSNV/scripts/align2ref.pl @@ -0,0 +1,289 @@ +#!/usr/bin/perl + +# Compare a sequence to a reference, measure similarity etc. If variant calling +# result is specified for the assembly, translate the coordinates onto the ref +# prerequisite: specify the path of muscle + +use strict; +use Getopt::Long; +use Data::Dumper; + +my %option = ( + h => '', + ref => '', + seq => '', + oPrefix => '', + mlen => 20, + msim => 0.9, + vc => '', + silent => '', +); + +GetOptions( + "h" => \$option{h}, + "ref=s" => \$option{ref}, + "seq=s" => \$option{seq}, + "oPrefix=s" => \$option{oPrefix}, + "mlen=i" => \$option{mlen}, + "msim=f" => \$option{msim}, + "vc=s" => \$option{vc}, + "silent" => \$option{silent}, +) || printHelp (); + +if ($option{h}) { printHelp();} + +my $oPrefix = $option{oPrefix}; + +unless ($option{ref} && $option{seq} && $oPrefix) { printHelp();} + +# specify the path of muscle +my $musclepath = "/seq/annotation/bio_tools/muscle/3.8/muscle"; + +my $cat_file = $oPrefix.".cat.fa"; +my $aln_file = $oPrefix.".muscle.afa"; + +unless ($option{silent}) { + print "\ncat $option{ref} $option{seq} > $cat_file\n\n"; +} +system ("cat $option{ref} $option{seq} > $cat_file"); +unless ($option{silent}) { + print "\n$musclepath -in $oPrefix.cat.fa -out $aln_file -quiet\n\n"; +} +system("$musclepath -in $oPrefix.cat.fa -out $aln_file -quiet"); + +system ("rm $cat_file"); + +# read in alignment file +open (ALN, "<$aln_file") or die "unable to open file $aln_file to read\n"; +my $ref = ""; +my $seq = ""; +my $cnt = 0; +while (){ + if (/>/) { + $cnt ++; + if ($cnt > 2) { + print "ERR: more than 2 symbol of > found\n"; + exit; + } + } else { + s/\s+//g; # remove whitespace + if ($cnt == 1) { + $ref .= $_; # add sequence + } else { + $seq .= $_; + } + } +} +close (ALN); + +uc($ref); +uc($seq); # convert to upper case + + +# ---- identify alignment region ---- +my $aln_start = -1; +my $aln_end = -1; +identify_aln_region($ref, $seq, $option{mlen}, $option{msim}, \$aln_start, \$aln_end); + +unless ($option{silent}) { + print "aln_start , end = $aln_start, $aln_end \n\n"; +} +#------------------------------------------------------------------------------------------------------------------------------------------------- +# translates the coordinates of $seq to $ref, calculate alignment similarity etc. +my $prefix = substr($ref, 0, $aln_start); +my $suffix = substr($ref, $aln_end + 1, length($ref) - $aln_end - 1); +$prefix =~ s/-//g; +$suffix =~ s/-//g; +my $idx_ref = length ($prefix); +my $ref_len = length($prefix) + length($suffix); + +$prefix = substr($seq, 0, $aln_start); +my $suffix = substr($seq, $aln_end + 1, length($seq) - $aln_end - 1); +$prefix =~ s/-//g; +$suffix =~ s/-//g; +my $idx_seq = length ($prefix); +my $seq_len = length($prefix) + length($suffix); + +my $num_indel = 0; +my $num_subst = 0; + + +# check aligned region + +my %coord_map; # map coordinate of seq to ref + +unless ($option{silent}) { + print "\nAliged Region: aln_start = $aln_start, aln_end = $aln_end \n\n"; +} + +for (my $i = $aln_start; $i <= $aln_end; ++ $i) { + my $ref_base = substr($ref, $i, 1); + my $seq_base = substr($seq, $i, 1); + + if ($ref_base ne '-' && $seq_base ne '-') { + + $coord_map{$idx_seq} = $idx_ref; + + if ($ref_base ne $seq_base) { + unless ($ref_base eq 'N' || $seq_base eq 'N') { # disregard "N"s + ++ $num_subst; + } + } + + ++ $idx_seq; + ++ $idx_ref; + if ($ref_base ne 'N') { ++ $ref_len; } + if ($seq_base ne 'N') { ++ $seq_len; } + + } else { + if ($ref_base ne '-') { + if ($ref_base ne 'N') { ++ $ref_len; } + ++ $idx_ref; + } + if ($seq_base ne '-') { + if ($seq_base ne 'N') { ++ $seq_len; } + ++ $idx_seq; + } + + ++ $num_indel; + } +} + +my $aln_len = $aln_end - $aln_start + 1; +my $similarity = 100-100*($num_indel + $num_subst)/$aln_len; +my $span = 100*$aln_len/$ref_len; +$span = sprintf "%.2f", $span; +$similarity = sprintf "%.2f", $similarity; +#print "\nRef_len\tSeq_len\tAln_len\tSpan(%)\tSubsts\tIndels\tSimilarity(%)\n"; +#print "$ref_len\t$seq_len\t$aln_len\t$span\t$num_subst\t$num_indel\t$similarity\n\n"; + +# read in variant calling file and convert to the ref coordinates; the first column of vc file has to be the coordinates + +my $num_var = 0; +if ($option{vc}) { + + unless ($option{silent}) { + print "\nConvert Variant calling output to the ref coordinates, \n Note: the first column registers the coordinates\n\n"; + } + my $vc_output = $oPrefix.".ref.vc.txt"; + open (OUTPUT, ">$vc_output") or die "unable to open $vc_output to write\n"; + + open (VPH, "<$option{vc}") or die "unable to open file $option{vc} to read\n"; + + while () { + next if /^(\s)*$/; # skip blank lines + my $line = $_; + if ($line !~ /#/) { + ++ $num_var; + my @entries = split ("\t",$line); + my $num = $#entries + 1; + + my $pos = $entries[0]; + -- $pos; + if (exists $coord_map{$pos}) { + my $map_pos = $coord_map{$pos} + 1; + print OUTPUT $map_pos."\t"; + for (my $i = 1; $i < $num; ++ $i) { + chomp($entries[$i]); + print OUTPUT $entries[$i]."\t"; + } + print OUTPUT "\n"; + } else { + + #print "\nErr: Coordinate $pos doesn't exists !\n"; + #exit; + } + } + } # while () + close (VPH); + close (OUTPUT); +} +# ---------------------------------- +if (!$option{silent}) { + print "\nRef_len\tSeq_len\tAln_len\tSpan(%)\tSubsts\tIndels\tSim(%)\tnum_var\n"; + print "$ref_len\t$seq_len\t$aln_len\t$span\t$num_subst\t$num_indel\t$similarity\t$num_var\n"; +} else { + print "$span\t$similarity\t"; +} + +unless ($option{silent}) { + print "\nDONE !\n\n"; +} +# --------------------------------------------------------------------------------------------------------- +# sub functions +# --------------------------------------------------------------------------------------------------------- +sub printHelp { + print "\n--------------------------------------------------------------------\n"; + print "usage: ./align2ref.pl -ref [ref.fa] -seq [seq.fa] -oPrefix [output_prefix]\n\n"; + + print "\t-ref: reference in fasta format onto which assembly will be mapped\n"; + print "\t-seq: sequence to map to reference\n"; + print "\t-oPrefix: output Prefix\n"; + print "\t-mlen: default 20; required to specify the valid alignment region b/t ref and seq\n"; + print "\t-msim: default 0.9; required to specify the valid alignment region similarity\n"; + print "\t\t where no indels occur in the mlen bp of prefix and suffix region\n"; + print "\t-vc: OPT; variant calling result file by vphaser 2 with respect to the sequence\n"; + print "\n--------------------------------------------------------------------\n"; + + exit; +} + +# @brief -- find the start and end coordinates for a given pairwise alignment satisfying +# the alignment shall not contain any indel for at least min_len bases on both ends +sub identify_aln_region { + my $seq = shift; + my $seq2 = shift; + my $min_len = shift; + my $min_sim = shift; + my $start = shift; + my $end = shift; + my $len = length ($seq); + if ($len != length($seq2)) { + print "In identify_aln_region: two input sequences should have identical length"; + exit; + } + + uc ($seq); + uc ($seq2); + my $cnt = 0; + my $diff = 0; + # prefix + for (my $i = 0; $i < $len; ++ $i) { + my $base = substr($seq, $i, 1); + my $base2 = substr($seq2, $i, 1); + + if ($base ne '-' && $base2 ne '-') { + ++ $cnt; + if ($base ne $base2) { ++ $diff; } + if ($cnt >= $min_len && ($diff/$cnt <= 1 - $min_sim)) { + $$start = $i; + last; + } + } else { + $cnt = 0; + $diff = 0; + } + } + $$start -= ($min_len - 1) ; + #suffix + $cnt = 0; + $diff = 0; + for (my $i = $len - 1; $i >= 0; -- $i) { + my $base = substr($seq, $i, 1); + my $base2 = substr($seq2, $i, 1); + if ($base ne '-' && $base2 ne '-') { + ++ $cnt; + if ($base ne $base2) { ++ $diff; } + if ($cnt >= $min_len && ($diff/$cnt <= 1 - $min_sim)) { + $$end = $i; + last; + } + } else { + $cnt = 0; + $diff = 0; + } + } + $$end += ($min_len - 1); +} # identify_aln_region + + From 8de7298c7aa1c516c15b43d79568f1a34316c9db Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 3 Jan 2015 21:23:54 -0500 Subject: [PATCH 4/4] refine assemble min_coverage increase to 2,3 from 1,3 [ci skip] --- pipes/rules/assembly.rules | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/rules/assembly.rules b/pipes/rules/assembly.rules index 453a5c9ea..3721f30d8 100644 --- a/pipes/rules/assembly.rules +++ b/pipes/rules/assembly.rules @@ -164,7 +164,7 @@ rule refine_assembly_1: params: LSF='-W 4:00', logid="{sample}", novoalign_options = "-r Random -l 30 -g 40 -x 20 -t 502", - min_coverage = "1", + min_coverage = "2", tmpf_intervals = config["tmpDir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly3.intervals', tmpf_bam1 = config["tmpDir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly3_pre_rmdup.bam', tmpf_bam2 = config["tmpDir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly3_pre_indel_realign.bam' @@ -190,7 +190,7 @@ rule refine_assembly_2: more conservative and the input consensus sequence has already been refined once and the input reads are the full raw read set (instead of the cleaned read set). We also require higher - minimum read coverage (3 instead of 1) in order to call a + minimum read coverage (3 instead of 2) in order to call a non-ambiguous base. The output of this step is the final assembly for this sample. Final FASTA file is indexed for Picard, Samtools, and Novoalign.