| Next changeset 1:d0a296afe83a (2016-03-18) |
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lookup/._.DS_Store lookup/._lookup.py lookup/._lookup.xml lookup/._readme.txt lookup/lookup.py lookup/lookup.xml lookup/readme.txt lookup/test-data/._.DS_Store lookup/test-data/input/._.DS_Store lookup/test-data/input/._chr_length.txt lookup/test-data/input/._qtlcart.z.filepart.txt lookup/test-data/input/chr_length.txt lookup/test-data/input/markers_filled_in.txt lookup/test-data/input/qtlcart.z.filepart.txt lookup/test-data/output/._.DS_Store lookup/test-data/output/._chr_summary.txt lookup/test-data/output/._lookup.txt lookup/test-data/output/chr_summary.txt lookup/test-data/output/lookup.txt |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/lookup.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lookup/lookup.py Fri Mar 18 05:12:00 2016 -0400 |
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| b'@@ -0,0 +1,280 @@\n+"""\n+@summary: The information from the Markers file and the QTL Cartographer Z file,\n+are combined to proportionally estimate a base pair position at each 2cM interval.\n+The Lookup file can then serve as a lookup table to convert between base pair positions centimorgan positions.\n+@author: nanette.coetzer@gmail.com\n+@version 5\n+\n+"""\n+import optparse, sys\n+import subprocess\n+import tempfile\n+import os, re\n+\n+def stop_err( msg ):\n+ sys.stderr.write( "%s\\n" % msg )\n+ sys.exit()\n+ \n+def __main__():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option("-i", "--input1", default=None, dest="input1", \n+ help="Markers file")\n+ parser.add_option("-j", "--input2", default=None, dest="input2", \n+ help="QTL Cartographer Z file")\n+ parser.add_option("-k", "--input3", default=None, dest="input3", \n+ help="Chromosome length file")\n+ parser.add_option("-o", "--output1", default=None, dest="output1", \n+ help="Lookup file")\n+ parser.add_option("-p", "--output2", default=None, dest="output2", \n+ help="Lookup summary file")\n+ \n+ (options, args) = parser.parse_args()\n+ \n+ try:\n+ open(options.input1, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the Markers file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the Markers file:\\n" + str(e))\n+ \n+ try:\n+ open(options.input2, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the QTL Cartographer Z file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the QTL Cartographer Z file:\\n" + str(e))\n+ \n+ try:\n+ open(options.input3, "r").close()\n+ except TypeError, e:\n+ stop_err("You need to supply the Chromosome length file:\\n" + str(e))\n+ except IOError, e:\n+ stop_err("Can not open the Chromosome length file:\\n" + str(e))\n+\n+\n+ ##############################################\n+\n+ in1 = open(options.input1,\'r\') # Markers.txt\n+ prev_c = "0"\n+ count = 0\n+ marker_dict = {} # For each unique chr + marker, store the cM + bp positions\n+ last_marker_dict = {} # For the last marker on each chr, store the cM + bp positions [reason: these intervals are not included in the z.txt file, so add separately]\n+\n+ for line in in1: # markers file\n+ count += 1\n+ if line.startswith("c"):\n+ # skip the header line\n+ if count != 1:\n+ # use info in each line to populate marker_dict\n+ i = line.strip().split("\\t")\n+ marker_dict[i[0]+"\\t"+i[1]] = i[3]+"\\t"+i[4]\n+ chr = i[0]\n+ if chr != prev_c and prev_c != "0":\n+ # if the chr number changes, add previous marker info to last_marker_dict\n+ last_marker_dict[prev_c+"\\t"+prev_m] = prev_cM+"\\t"+prev_bp\n+ prev_c = i[0]\n+ prev_m = i[1]\n+ prev_cM = i[3]\n+ prev_bp = i[4]\n+ else:\n+ # no header row\n+ # use info in each line to populate marker_dict\n+ i = line.strip().split("\\t")\n+ marker_dict[i[0]+"\\t"+i[1]] = i[3]+"\\t"+i[4]\n+ chr = i[0]\n+ if chr != prev_c and prev_c != "0":\n+ # if the chr number changes, add previous marker info to last_marker_dict\n+ last_marker_dict[prev_c+"\\t"+prev_m] = prev_cM+"\\t"+prev_bp\n+ prev_c = i[0]\n+ prev_m = i[1]\n+ prev_cM = i[3]\n+ prev_bp = i[4]\n+ \n+ # add the last marker (on last chr) info to last_marker_dict\n+ last_marker_dict[prev_c+"\\t"+prev_m] = prev_cM+"\\t"+prev_bp\n+ in1.close()\n+ \n+ ##############################################\n+ \n+ in1 = open(options.input1,\'r\') \n+ s2_l2 = {} # For each unique chr + marker, store '..b' s1 = float(s1_l1[c+"\\t"+m].split("\\t")[0])\n+ l1 = float(s1_l1[c+"\\t"+m].split("\\t")[1])\n+ s2 = float(s2_l2[c+"\\t"+m].split("\\t")[0])\n+ l2 = float(s2_l2[c+"\\t"+m].split("\\t")[1])\n+ v1 = float(p)*100-0.01\n+ x2 = int(round((((v1-s1)*(l2-s2)/(l1-s1))+s2),0))\n+ check1 = "done"\n+ id += 1\n+ temp_outfile.write(str(id)+"\\t"+str(c)+"\\t"+str(m)+"\\t"+str(p)+"\\t"+str(float(p)*100-0.01)+"\\t"+str(x2)+"\\n")\n+ # store previous chr and marker\n+ prev_m = m\n+ prev_c = c\n+ # do not go on to the other blocks in the z.txt file\n+ if ans == 0 and check1 == "done":\n+ check2 = "stop"\n+ # add the last marker of the last chromosome\n+ id += 1\n+ add_m = int(prev_m)+1\n+ add_cM = last_marker_dict[prev_c+"\\t"+str(add_m)].split("\\t")[0]\n+ add_bp = last_marker_dict[prev_c+"\\t"+str(add_m)].split("\\t")[1]\n+ add_p = (float(add_cM) + 0.01)/100\n+ temp_outfile.write(str(id)+"\\t"+str(prev_c)+"\\t"+str(add_m)+"\\t"+str(add_p)+"\\t"+str(add_cM)+"\\t"+str(add_bp)+"\\n")\n+ \n+ in2.close() \n+ temp_outfile.close()\n+ \n+ ##############################################\n+ \n+ # Aim1: add cM_length column\n+ # Aim2: create lookup summary file\n+ temp_infile = open(lookup_temp,\'r\')\n+ in3 = open(options.input3,\'r\') # chr_length.txt\n+ out1 = open(options.output1,\'w\') # lookup.txt\n+ out2 = open(options.output2,\'w\') # lookup_summary.txt \n+ \n+ out2.write("chr\\tmarkers\\tcM\\tbp\\tinterval positions\\tbins\\n")\n+ chr_dict = {}\n+ for line in in3:\n+ l = line.strip().split("\\t")\n+ if l[0].startswith("chr"):\n+ chr = l[0][3:]\n+ else:\n+ chr = l[0]\n+ chr_dict[chr] = l[1]\n+ \n+ tot_num_int_pos = 0\n+ count = 0\n+ # calc totals for summary file\n+ tot_markers = 0\n+ tot_bp = 0\n+ tot_cM = 0\n+ tot_int_pos = 0\n+ tot_bins = 0\n+ for line in temp_infile:\n+ l = line.strip().split("\\t")\n+ if count == 0:\n+ out1.write(line.strip()+"\\n")\n+ if count > 1:\n+ if l[4] != "0.0":\n+ length_cm = float(l[4])-float(prev_cm)\n+ out1.write(prev_line+"\\t"+str(length_cm)+"\\n")\n+ else:\n+ # always the end of a chromosome\n+ out1.write(prev_line+"\\t0\\n")\n+ # summary file\n+ pl = prev_line.split("\\t")\n+ num_int_pos = int(pl[0]) - tot_num_int_pos\n+ tot_num_int_pos += num_int_pos\n+ out2.write(str(pl[1])+"\\t"+str(pl[2])+"\\t"+str(pl[4])+"\\t"+chr_dict[pl[1]]+"\\t"+str(num_int_pos)+"\\t"+str(num_int_pos-1)+"\\n")\n+ # calc totals for summary file\n+ tot_markers += int(pl[2])\n+ tot_bp += int(chr_dict[pl[1]])\n+ tot_cM += float(pl[4])\n+ tot_int_pos += num_int_pos\n+ tot_bins += (num_int_pos-1) \n+ prev_line = line.strip()\n+ prev_cm = l[4] \n+ count += 1\n+ # the end of the last chromosome\n+ out1.write(prev_line+"\\t0\\n")\n+ # summary file\n+ pl = prev_line.split("\\t")\n+ num_int_pos = int(pl[0]) - tot_num_int_pos\n+ tot_num_int_pos += num_int_pos\n+ out2.write(str(pl[1])+"\\t"+str(pl[2])+"\\t"+str(pl[4])+"\\t"+chr_dict[pl[1]]+"\\t"+str(num_int_pos)+"\\t"+str(num_int_pos-1)+"\\n")\n+ # calc totals for summary file\n+ tot_markers += int(pl[2])\n+ tot_bp += int(chr_dict[pl[1]])\n+ tot_cM += float(pl[4])\n+ tot_int_pos += num_int_pos\n+ tot_bins += (num_int_pos-1)\n+ out2.write("Total\\t"+str(tot_markers)+"\\t"+str(tot_cM)+"\\t"+str(tot_bp)+"\\t"+str(tot_int_pos)+"\\t"+str(tot_bins)+"\\n")\n+ \n+ temp_infile.close()\n+ in3.close()\n+ out1.close()\n+ out2.close()\n+ \n+ ##############################################\n+ \n+if __name__=="__main__": \n+ __main__()\n+\n+\n+\n' |
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| @@ -0,0 +1,98 @@ +<tool id="lookup5" name="Lookup table" version="5.0.0"> + <description> for 2cM intervals</description> + <command interpreter="python"> + lookup.py --input1 $input1 --input2 $input2 --input3 $input3 --output1 $output1 --output2 $output2 + </command> + <inputs> + <param label="Markers file" name="input1" type="data" format="tabular" help="Tabular file giving marker positions in cM and bp"></param> + <param label="QTL Cartographer Z file" name="input2" type="data" format="tabular" help="QTL Cartographer output file (.z)"></param> + <param label="Chromosome length file" name="input3" type="data" format="tabular" help="A tabular file giving the length of each chromosome in bp"></param> + </inputs> + <outputs> + <data format="tabular" name="output1" /> + <data format="tabular" name="output2" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + </test> + </tests> + <help> + +**What it does** + +The information from the Markers file and the QTL Cartographer Z file, are combined to proportionally estimate a base pair position at each “QTL Cartographer bin” (e.g. 2 cM intervals). + +The Lookup file can then serve as a lookup table to convert between base pair and centimorgan positions. + +------- + +**Example input files** + +Markers file, each row correspond to a marker (5 columns; only a part of the file is shown):: + + chr marker name cM bp + 1 1 marker1 0 2038278 + 1 2 marker2 7.53 3649871 + 1 3 marker3 18.77 6155281 + 1 4 marker4 38.71 12398322 + 1 5 marker5 44.62 14171692 + 1 6 marker6 48.73 16529505 + +QTL Cartographer Z file, each row correspond to a 2cM interval (the example shows part of the important part of the Z file, the first 3 data columns of the first block). Note: Headers is fine and will be ignored:: + + 1 1 0.0001 … + 1 1 0.0201 … + 1 1 0.0401 … + 1 1 0.0601 … + 1 2 0.0754 … + 1 2 0.0954 … + 1 2 0.1154 … + 1 2 0.1354 … + 1 2 0.1554 … + 1 2 0.1754 … + 1 3 0.1878 … + 1 3 0.2078 … + 1 3 0.2278 … + 1 3 0.2478 … + +Chromosome length file, each row correspond to a chromosome (2 columns; only a part of the file is shown):: + + chr1 301354135 + chr2 237068873 + chr3 232140174 + chr4 241473504 + chr5 217872852 + chr6 169174353 + +------- + +**Example output files** + + +Lookup output file, each row correspond to a 2 cM interval (7 columns; only a part of the file is shown):: + + int.id chr marker int cM bp length_cM + 1 1 1 0.0001 0.0 2038278 2.0 + 2 1 1 0.0201 2.0 2466324 2.0 + 3 1 1 0.0401 4.0 2894370 2.0 + 4 1 1 0.0601 6.0 3322416 1.53 + 5 1 2 0.0754 7.53 3649871 2.0 + 6 1 2 0.0954 9.53 4095673 2.0 + 7 1 2 0.1154 11.53 4541476 2.0 + 8 1 2 0.1354 13.53 4987278 2.0 + +Chromosome summary file, each row correspond to a chromosome (6 columns; only a part of the file is shown). The last row gives the total across the genome:: + + chr markers cM bp int_positions bins + 1 27 324.4 301354135 177 176 + 2 14 169.11 237068873 92 91 + 3 19 221.29 232140174 123 122 + 4 20 188.37 241473504 105 104 + 5 20 203.82 217872852 110 109 + 6 17 195.85 169174353 106 105 + Total 117 1302.84 1399083891 713 707 + + </help> +</tool> |
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| @@ -0,0 +1,23 @@ +====================================================================== +lookup +====================================================================== +### This is the first tool in the eQTL backend pipeline: +lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment + +Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2 + +The information from the Markers file and the QTL Cartographer Z file, are combined to proportionally estimate a base pair position at each “QTL Cartographer bin” (e.g. 2 cM intervals). + +The Lookup file can then serve as a lookup table to convert between base pair and centimorgan positions. + + +--------------- +Installation +--------------- + +The eQTL backend pipeline is available for: +* command line usage +* integration into Galaxy servers + + +Requirements: Python 2.7 \ No newline at end of file |
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| @@ -0,0 +1,10 @@ +chr1 301354135 +chr2 237068873 +chr3 232140174 +chr4 241473504 +chr5 217872852 +chr6 169174353 +chr7 176764762 +chr8 175793759 +chr9 156750706 +chr10 150189435 |
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| @@ -0,0 +1,168 @@ +c m name position bp +1 1 phi056 0 2038278 +1 2 bnl5.62 7.53 3649871 +1 3 umc1041 18.77 6155281 +1 4 umc157a 38.71 12398322 +1 5 bnlg1178 44.62 14171692 +1 6 bnlg1429 48.73 16529505 +1 7 bnlg1627 53.21 19099579 +1 8 umc11a 69.97 34953249 +1 9 bnlg439 81.87 43691550 +1 10 bnlg2238 96.1 55080425 +1 11 Bnlg1811_U 112.7 70769880 +1 12 bnlg2086 126.83 83645415 +1 13 csu61b 142.69 182103378 +1 14 bnlg1057 148.97 187786747 +1 15 umc1122 164.28 201642220 +1 16 Bnlg615_U 179.12 214414467 +1 17 umc1128 187.24 224258054 +1 18 umc166b 193.42 232921226 +1 19 dupssr12 202.13 239614066 +1 20 phi011 236.08 258364379 +1 21 bnlg1720 255.86 265677051 +1 22 umc106a 264.8 274711300 +1 23 umc147b 275.03 279156575 +1 24 umc1111_P 297.09 288742379 +1 25 bnlg2331 300.19 289782293 +1 26 bnlg2123 315.03 293638366 +1 27 bnl6.32 324.4 297960786 +2 1 phi402893 0 0 +2 2 bnlg1297 13.27 4886669 +2 3 bnlg2042 39.27 9448411 +2 4 umc44b 64.9 16770080 +2 5 csu40 82.04 29945330 +2 6 umc135 90.6 41225839 +2 7 csu54a 101.03 202292680 +2 8 umc55a 111.74 204665019 +2 9 umc14b 117.09 205850080 +2 10 csu154a 132.62 209290082 +2 11 umc150b 141.48 216243952 +2 12 umc1551 150.04 222962363 +2 13 umc36a 166.24 232719775 +2 14 csu109a 169.11 232597010 +3 1 umc32a 0 1728599 +3 2 phi104127 11.75 3478905 +3 3 bnlg1325 25.59 5584239 +3 4 bnlg1447 42.13 10480185 +3 5 umc92a 51.24 18998903 +3 6 bnlg1019a 61.28 26311926 +3 7 phi053 72.02 126236672 +3 8 bnlg420 78.14 131839576 +3 9 umc1307 80.5 134000173 +3 10 Phi073_U 103.41 154974444 +3 11 Bnlg1449_U 129.78 170385368 +3 12 bnl10.24a 136.79 172445457 +3 13 umc7b 155.09 188628682 +3 14 umc3b 161.21 194040777 +3 15 umc16a 177.56 205295752 +3 16 bnlg1108_P 188.53 210942501 +3 17 umc63a 199.15 215787299 +3 18 bnlg1182 213.6 218323475 +3 19 bnlg1754 221.29 221572836 +4 1 umc1017 0 3000150 +4 2 umc1294 19 9800436 +4 3 phi021 29.59 13398617 +4 4 umc1550 35.93 14854630 +4 5 umc1652 53.08 26377276 +4 6 bnlg490 56.16 31306569 +4 7 csu100 70.25 138632126 +4 8 umc156a 74.88 151082461 +4 9 bnlg2291 92.21 169546722 +4 10 umc19 98.38 173459774 +4 11 mmc0341 111.28 180441002 +4 12 umc133a 120.25 185840441 +4 13 umc15a 127.9 190445314 +4 14 csu11b 137.66 213203122 +4 15 npi593a 147.32 235727756 +4 16 bnlg589 151.57 236733272 +4 17 umc1720_P 168.62 237711073 +4 18 bnlg1337 174.2 239340357 +4 19 phi019 183.39 240106933 +4 20 phi006 188.37 240113625 +5 1 bnl8.33 0 2146924 +5 2 npi409 3.2 3323363 +5 3 umc147a 26.02 6833880 +5 4 umc90 33.58 7996873 +5 5 umc107b 40.23 10931346 +5 6 Bnlg105_U 49.92 13812558 +5 7 bnlg1046 61.78 18701376 +5 8 umc166a 77.21 29622131 +5 9 bnl6.22 86.7 58602104 +5 10 csu36b 94.42 81155806 +5 11 DupSSR10_U 99.7 142483423 +5 12 bnl5.71a 111.11 171279125 +5 13 umc1155_P 125 180186737 +5 14 npi237 133.32 186693818 +5 15 umc54 141.11 192786386 +5 16 bnlg1346 164.31 206798092 +5 17 bnlg118 178.93 211725482 +5 18 umc1225 190.83 213266752 +5 19 umc104b 197.54 214709273 +5 20 bnlg1885 203.82 215925616 +6 1 umc85a 0 8273758 +6 2 bnlg426 5.62 26720000 +6 3 umc36c 14.54 52764451 +6 4 umc1572_P 29.03 95072085 +6 5 Bnlg2191_U 35.86 93209180 +6 6 bnlg2151 41.59 91540201 +6 7 umc1887 60.99 102720868 +6 8 umc65a 65.27 104450640 +6 9 umc1014 71.72 108318724 +6 10 bnlg1922 88.87 120739290 +6 11 umc1413_P 115.82 132889642 +6 12 mmc0241 125.56 145315870 +6 13 umc1424_P 139.38 156535165 +6 14 umc36 159.76 160413911 +6 15 umc39 162.3 160897327 +6 16 bnlg1740 182.22 164688526 +6 17 umc2059 195.85 167982181 +7 1 csu13 0 31559916 +7 2 bnlg1094 9.03 37849898 +7 3 umc1393 20.6 120353640 +7 4 bnlg1808 30.83 124221648 +7 5 bnl15.21 41.06 133433921 +7 6 bnlg339 45.2 137162055 +7 7 bnlg155 55.44 146549156 +7 8 bnlg1805 63.19 153653651 +7 9 bnl14.07 76.33 161953186 +7 10 umc1125 87.63 168401834 +7 11 phi082 106.31 173555272 +7 12 umc1799 111.16 174794439 +8 1 npi114a 0 1343362 +8 2 umc1327 10.74 5029298 +8 3 npi110a 25.44 10073134 +8 4 umc103a 38.73 16837007 +8 5 bnlg669 50.14 22644064 +8 6 umc1858 67.47 112531956 +8 7 umc1562_P 83.31 125903217 +8 8 umc48a 96.08 152590459 +8 9 asg52a 99.31 161067852 +8 10 umc150a 102.89 162695789 +8 11 umc1384 118.2 169657722 +8 12 umc7 127.86 171320074 +8 13 bnlg1056 130.99 171858704 +8 14 umc39b 141.31 175793759 +9 1 bnlg1272 0 0 +9 2 umc113a 17.94 8587716 +9 3 umc1170_P 27.5 13164001 +9 4 umc105a 45.94 17907945 +9 5 umc81 65.05 49143473 +9 6 bnl8.17 92.13 127209814 +9 7 umc1231 97.81 133216162 +9 8 umc1733 120.51 145339770 +9 9 bnlg1588 124.78 147653489 +9 10 bnlg1375 140.38 150981541 +9 11 umc1137 158.78 153303149 +10 1 phi118 0 2646499 +10 2 npi285a 15.02 5005541 +10 3 umc1337_P 32.57 8605609 +10 4 umc130 46.05 13554868 +10 5 bnlg1079 52.99 77294622 +10 6 umc1115 75.17 126586743 +10 7 npi232a 81.55 130961755 +10 8 umc44a 90.62 137286534 +10 9 umc182 98.67 138463335 +10 10 bnlg236 104.6 140002858 +10 11 bnl7.49a 117.63 143385654 +10 12 bnlg1450 130.53 146292510 +10 13 umc1038 147.48 149743465 |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/input/qtlcart.z.filepart.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lookup/test-data/input/qtlcart.z.filepart.txt Fri Mar 18 05:12:00 2016 -0400 |
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| b'@@ -0,0 +1,6395 @@\n+# 1286098096 -filetype Zmapqtl.out \n+#\n+#\tQTL Cartographer v. 1.17j, 28 January 2005\n+#\tThis output file (qtlcart.z) was created by Zmapqtl...\n+#\n+#\tIt is 11:28:16 on Sunday, 03 October 2010\n+#\n+#\n+#The position is from the left telomere on the chromosome\n+-window 10.00 Window size for models 5 and 6\n+-background 5 Background parameters in model 6\n+-Model 6 Model number\n+-trait 1 Analyzed trait [P_R_07_GLS]\n+-cross Ri1 Cross\n+#\n+# Note that our Likelihood ratio test statistic compares two nested hypotheses\n+# and is two times the negative natural log of the ratio of the likelihoods. For example,\n+# assume that hypothesis H0 is nested within H1 and that they have likelihoods L0 and L1 respectively.\n+# Then, the "Likelihood Ratio Test Statistic" is -2ln(L0/L1). \n+#\n+# Test Site * Like. Ratio Test Statistics * Additive * Dominance * Misc. HT\n+ c m position H0:H1 R2(0:1) TR2(0:1) H1:a S1 .... .... .... .... .... .... .... ..... .... ..... ..... .... .....\n+-s\n+ 1 1 0.0001 0.7233321 0.0040282 0.3147929 0.0601882 1.6314381 0.0000000 0.0000000 0.0000000 0.0000000 0.5577471 0.0000000 0.0000000 0.5577471 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 1 0.0201 1.1327049 0.0073165 0.3180812 0.0804974 1.3500086 0.0000000 0.0000000 0.0000000 0.0000000 0.5550705 0.0000000 0.0000000 0.5550705 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 1 0.0401 1.5139369 0.0097797 0.3205444 0.0926732 1.0757188 0.0000000 0.0000000 0.0000000 0.0000000 0.5530655 0.0000000 0.0000000 0.5530655 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 1 0.0601 1.7691612 0.0102683 0.3210330 0.0948925 0.8942868 0.0000000 0.0000000 0.0000000 0.0000000 0.5526678 0.0000000 0.0000000 0.5526678 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.0754 1.8688871 0.0095348 0.3202995 0.0916252 0.8033057 0.0000000 0.0000000 0.0000000 0.0000000 0.5532649 0.0000000 0.0000000 0.5532649 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.0954 1.9727642 0.0114691 0.3222338 0.0999176 0.8352817 0.0000000 0.0000000 0.0000000 0.0000000 0.5516904 0.0000000 0.0000000 0.5516904 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.1154 2.0089015 0.0126575 0.3234223 0.1045969 0.8730175 0.0000000 0.0000000 0.0000000 0.0000000 0.5507230 0.0000000 0.0000000 0.5507230 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.1354 1.9560809 0.0126176 0.3233824 0.1042794 0.9053248 0.0000000 0.0000000 0.0000000 0.0000000 0.5507555 0.0000000 0.0000000 0.5507555 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.1554 1.8156977 0.0112879 0.3220527 0.0986898 0.9279529 0.0000000 0.0000000 0.0000000 0.0000000 0.5518378 0.0000000 0.0000000 0.5518378 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 1 2 0.1754 1.6136905 0.0091072 0.3198720 0.0888867 0.9472451 0.0000000 0.0000000 0.0000000 0.0000000 0.5536129 '..b' 0.4077579 0.0000000 0.0000000 0.4077579 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.5128 0.8681007 0.0083793 0.3781382 0.0744203 0.5359337 0.0000000 0.0000000 0.0000000 0.0000000 0.4081249 0.0000000 0.0000000 0.4081249 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.5328 0.7441624 0.0071538 0.3769127 0.0686817 0.5369829 0.0000000 0.0000000 0.0000000 0.0000000 0.4089292 0.0000000 0.0000000 0.4089292 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.5528 0.6101156 0.0055609 0.3753198 0.0605112 0.5459142 0.0000000 0.0000000 0.0000000 0.0000000 0.4099746 0.0000000 0.0000000 0.4099746 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.5728 0.4814455 0.0039797 0.3737385 0.0511777 0.5608467 0.0000000 0.0000000 0.0000000 0.0000000 0.4110124 0.0000000 0.0000000 0.4110124 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.5928 0.3692398 0.0026733 0.3724321 0.0419546 0.5790913 0.0000000 0.0000000 0.0000000 0.0000000 0.4118698 0.0000000 0.0000000 0.4118698 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.6128 0.2780789 0.0017212 0.3714800 0.0336883 0.5981916 0.0000000 0.0000000 0.0000000 0.0000000 0.4124946 0.0000000 0.0000000 0.4124946 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 3 0.6328 0.2074711 0.0010815 0.3708403 0.0267361 0.6164375 0.0000000 0.0000000 0.0000000 0.0000000 0.4129145 0.0000000 0.0000000 0.4129145 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.6491 0.1632715 0.0007362 0.3704950 0.0220892 0.6299663 0.0000000 0.0000000 0.0000000 0.0000000 0.4131411 0.0000000 0.0000000 0.4131411 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.6691 0.1574630 0.0008394 0.3705982 0.0235837 0.6339413 0.0000000 0.0000000 0.0000000 0.0000000 0.4130733 0.0000000 0.0000000 0.4130733 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.6891 0.1464623 0.0008966 0.3706555 0.0243823 0.6407389 0.0000000 0.0000000 0.0000000 0.0000000 0.4130358 0.0000000 0.0000000 0.4130358 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.7091 0.1294678 0.0008729 0.3706318 0.0240768 0.6507566 0.0000000 0.0000000 0.0000000 0.0000000 0.4130513 0.0000000 0.0000000 0.4130513 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.7291 0.1072471 0.0007554 0.3705142 0.0224260 0.6636726 0.0000000 0.0000000 0.0000000 0.0000000 0.4131285 0.0000000 0.0000000 0.4131285 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.7491 0.0824539 0.0005720 0.3703308 0.0195502 0.6782752 0.0000000 0.0000000 0.0000000 0.0000000 0.4132488 0.0000000 0.0000000 0.4132488 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 \n+ 2 4 0.7691 0.0586561 0.0003786 0.3701374 0.0159438 0.6927732 0.0000000 0.0000000 0.0000000 0.0\n' |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/output/._.DS_Store |
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| Binary file lookup/test-data/output/._.DS_Store has changed |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/output/._chr_summary.txt |
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| Binary file lookup/test-data/output/._chr_summary.txt has changed |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/output/._lookup.txt |
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| Binary file lookup/test-data/output/._lookup.txt has changed |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/output/chr_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lookup/test-data/output/chr_summary.txt Fri Mar 18 05:12:00 2016 -0400 |
| b |
| @@ -0,0 +1,12 @@ +chr markers cM bp interval positions bins +1 27 324.4 301354135 177 176 +2 14 169.11 237068873 92 91 +3 19 221.29 232140174 123 122 +4 20 188.37 241473504 105 104 +5 20 203.82 217872852 110 109 +6 17 195.85 169174353 106 105 +7 12 111.16 176764762 63 62 +8 14 141.31 175793759 77 76 +9 11 158.78 156750706 85 84 +10 13 147.48 150189435 81 80 +Total 167 1861.57 2058582553 1019 1009 |
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| diff -r 000000000000 -r 38b3c04b5a67 lookup/test-data/output/lookup.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lookup/test-data/output/lookup.txt Fri Mar 18 05:12:00 2016 -0400 |
| b |
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