# HG changeset patch # User devteam # Date 1447086321 18000 # Node ID 3100886bf698996b47ceae7a0dc729cf58a00d1d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b diff -r 000000000000 -r 3100886bf698 convert_characters.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_characters.py Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,42 @@ +#!/usr/bin/env python +#By, Guruprasad Ananda. + +from galaxy import eggs +import sys, re + +def stop_err(msg): + sys.stderr.write(msg) + sys.exit() + +def main(): + if len(sys.argv) != 4: + stop_err("usage: convert_characters infile from_char outfile") + + try: + fin = open(sys.argv[1],'r') + except: + stop_err("Input file cannot be opened for reading.") + + from_char = sys.argv[2] + + try: + fout = open(sys.argv[3],'w') + except: + stop_err("Output file cannot be opened for writing.") + + char_dict = {'T':'\t','s':'\s','Dt':'\.','C':',','D':'-','U':'_','P':'\|','Co':':'} + from_ch = char_dict[from_char] + '+' #making an RE to match 1 or more occurences. + skipped = 0 + + for line in fin: + line = line.strip() + try: + fout.write("%s\n" %(re.sub(from_ch,'\t',line))) + except: + skipped += 1 + + if skipped: + print "Skipped %d lines as invalid." %skipped + +if __name__ == "__main__": + main() \ No newline at end of file diff -r 000000000000 -r 3100886bf698 convert_characters.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/convert_characters.xml Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,58 @@ + + delimiters to TAB + convert_characters.py "${input}" "${convert_from}" "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Converts all delimiters of a specified type into TABs. Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab. + +----- + +**Example** + +- Input file:: + + chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|- + chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|- + chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+ + chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+ + +- Converting all pipe delimiters of the above file to TABs will get:: + + chrX 151283558 151283724 NM_000808_exon_8_0_chrX_151283559_r 0 - + chrX 151370273 151370486 NM_000808_exon_9_0_chrX_151370274_r 0 - + chrX 151559494 151559583 NM_018558_exon_1_0_chrX_151559495_f 0 + + chrX 151564643 151564711 NM_018558_exon_2_0_chrX_151564644_f 0 + + + + diff -r 000000000000 -r 3100886bf698 test-data/1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1.bed Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - diff -r 000000000000 -r 3100886bf698 test-data/a.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.tab Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,15 @@ +CHR SNP BP A1 TEST NMISS BETA STAT P +1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161 +1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05 +1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05 +1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05 +1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05 +1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233 +1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05 +1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05 +1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982 +1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 +1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 +1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 +1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 +1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 diff -r 000000000000 -r 3100886bf698 test-data/a.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/a.txt Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,15 @@ + CHR SNP BP A1 TEST NMISS BETA STAT P + 1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161 + 1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05 + 1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05 + 1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05 + 1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05 + 1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233 + 1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05 + 1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05 + 1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982 + 1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826 + 1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05 + 1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339 + 1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05 + 1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05 \ No newline at end of file diff -r 000000000000 -r 3100886bf698 test-data/eq-convert.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eq-convert.dat Mon Nov 09 11:25:21 2015 -0500 @@ -0,0 +1,65 @@ +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - 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