Mercurial > repos > jowong > add_sample_as_first_line
changeset 0:231b21337c43 draft
planemo upload for repository https://github.com/jowong4/add_sample_name_as_first_line_of_file commit 462cf96a681fad46e20321feec5996d1e558a0d3
| author | jowong |
|---|---|
| date | Thu, 27 Sep 2018 17:05:18 -0400 |
| parents | |
| children | 492848eff35d |
| files | add_sample_name_as_first_line.py add_sample_name_as_first_line.xml test-data/ABC_1.fastq.gz test-data/test.tab test-data/test_with_header.tab |
| diffstat | 5 files changed, 6399 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_sample_name_as_first_line.py Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,23 @@ +import sys +import argparse +import re + +def Parser(): + the_parser = argparse.ArgumentParser(description="add sample name as first line of a tab file") + the_parser.add_argument('--input', required=True, action="store", type=str, help="input tab file") + the_parser.add_argument('--output', required=True, action="store", type=str, help="output file") + the_parser.add_argument('--sample', required=True, action="store", type=str, help="sample name to add as the first line of input file") + args = the_parser.parse_args() + return args + +args=Parser() + +sample_name = re.sub('[_12]*.fastq.gz', '', args.sample.rstrip().lstrip()) + +with open(args.input) as input: + with open(args.output, 'w') as output: + output.write(sample_name+"\n") + for line in input: + output.write(line) + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/add_sample_name_as_first_line.xml Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,33 @@ +<tool id="my_addName" name="Add sample name as first line" version="0.1.0"> + <description>to an existing tabular file</description> + <command interpreter="python">add_sample_name_as_first_line.py + --input "$input" + --sample "$input2.element_identifier" + --output "$output" + </command> + <inputs> + <param format="tabular" name="input" type="data" label="to Dataset" /> + <param name="input2" format="data" type="data" label="sample" /> + </inputs> + <outputs> + <data name="output" format="tabular" /> + </outputs> + + <tests> + <test> + <param name="input" value="test.tab" ftype="tabular" /> + <param name="input2" value="ABC_1.fastq.gz" /> + <output name="output" file="test_with_header.tab" ftype="tabular"/> + </test> + </tests> + <help> +**What it does** + +Adds a new line with the name of the sample file and removing [_12].fastq.gz from the name if there is match to the pattern. +Written by Johnathan Kwan Long Wong, johnathanwong4@gmail.com + </help> + <citations> + <citation type="bibtex">@UNPUBLISHED{Johnathan2018, + author = "Johnathan W"}</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ABC_1.fastq.gz Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,2114 @@ +CHROM POS TYPE REF ALT +NC_000962.3 1302 snp C A +NC_000962.3 1977 snp A G +NC_000962.3 2532 snp T C +NC_000962.3 4013 snp T C +NC_000962.3 6112 snp G C +NC_000962.3 7362 snp G C +NC_000962.3 7585 snp G C +NC_000962.3 8452 snp C T +NC_000962.3 9143 snp T C +NC_000962.3 9260 snp G C +NC_000962.3 9304 snp G A +NC_000962.3 11879 snp A G +NC_000962.3 13175 snp A G +NC_000962.3 13298 snp G C +NC_000962.3 13460 snp A G +NC_000962.3 14401 snp A G +NC_000962.3 14785 snp T C +NC_000962.3 15088 snp C T +NC_000962.3 15117 snp C G +NC_000962.3 16526 snp C T +NC_000962.3 21795 snp G A +NC_000962.3 21819 snp A C +NC_000962.3 22961 snp T G +NC_000962.3 23174 snp C A +NC_000962.3 26347 snp C G +NC_000962.3 26959 snp C G +NC_000962.3 27199 snp G A +NC_000962.3 27469 snp A G +NC_000962.3 27473 snp G T +NC_000962.3 27996 snp T C +NC_000962.3 31142 snp C T +NC_000962.3 34044 snp T 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T +NC_000962.3 4111303 snp G C +NC_000962.3 4112429 snp T C +NC_000962.3 4113833 snp C T +NC_000962.3 4115001 snp G C +NC_000962.3 4115029 snp G A +NC_000962.3 4116682 snp T C +NC_000962.3 4116758 snp C T +NC_000962.3 4117161 snp C A +NC_000962.3 4118620 snp G T +NC_000962.3 4119246 snp T C +NC_000962.3 4120983 snp A G +NC_000962.3 4123325 snp C T +NC_000962.3 4125460 snp C T +NC_000962.3 4126087 snp T G +NC_000962.3 4126530 snp G A +NC_000962.3 4130711 snp G C +NC_000962.3 4133907 snp G A +NC_000962.3 4137190 snp T C +NC_000962.3 4138377 snp A G +NC_000962.3 4142689 snp G A +NC_000962.3 4145737 snp A G +NC_000962.3 4148861 snp G A +NC_000962.3 4150036 snp G T +NC_000962.3 4151855 snp A G +NC_000962.3 4155266 snp C G +NC_000962.3 4155903 snp G T +NC_000962.3 4156099 snp C A +NC_000962.3 4156239 snp A G +NC_000962.3 4156503 snp C T +NC_000962.3 4158361 snp A G +NC_000962.3 4159195 snp T C +NC_000962.3 4161725 snp G T +NC_000962.3 4162339 snp A G +NC_000962.3 4163558 snp G C +NC_000962.3 4163954 snp T C +NC_000962.3 4169719 snp C T +NC_000962.3 4171454 snp G A +NC_000962.3 4179089 snp C T +NC_000962.3 4182695 snp G A +NC_000962.3 4187063 snp G A +NC_000962.3 4187485 snp T C +NC_000962.3 4187523 snp A G +NC_000962.3 4187817 snp A G +NC_000962.3 4189721 snp G T +NC_000962.3 4190285 snp T C +NC_000962.3 4190532 snp A C +NC_000962.3 4190596 snp A C +NC_000962.3 4195938 snp G A +NC_000962.3 4197189 snp A G +NC_000962.3 4200220 snp A G +NC_000962.3 4201105 snp G A +NC_000962.3 4202383 snp A C +NC_000962.3 4204441 snp A G +NC_000962.3 4205120 snp A G +NC_000962.3 4210274 snp A G +NC_000962.3 4210876 snp T C +NC_000962.3 4215484 snp G C +NC_000962.3 4216255 snp C G +NC_000962.3 4217557 snp A G +NC_000962.3 4221490 snp C G +NC_000962.3 4222073 snp A G +NC_000962.3 4222882 snp A G +NC_000962.3 4223172 snp T C +NC_000962.3 4231150 snp G A +NC_000962.3 4231530 snp C A +NC_000962.3 4232327 snp A G +NC_000962.3 4236844 snp G A +NC_000962.3 4237383 snp C A +NC_000962.3 4240671 snp C T +NC_000962.3 4241042 snp A G +NC_000962.3 4242643 snp C T +NC_000962.3 4243580 snp G A +NC_000962.3 4244420 snp G C +NC_000962.3 4245969 snp C T +NC_000962.3 4247578 snp G A +NC_000962.3 4247646 snp A C +NC_000962.3 4250022 snp T G +NC_000962.3 4250966 snp G A +NC_000962.3 4251297 snp G C +NC_000962.3 4255922 snp A G +NC_000962.3 4257220 snp A G +NC_000962.3 4261499 snp G A +NC_000962.3 4263279 snp A G +NC_000962.3 4264560 snp G A +NC_000962.3 4269387 snp T G +NC_000962.3 4269606 snp A G +NC_000962.3 4275935 snp A G +NC_000962.3 4276306 snp C T +NC_000962.3 4277032 snp G C +NC_000962.3 4280441 snp C A +NC_000962.3 4281143 snp C G +NC_000962.3 4281272 snp G A +NC_000962.3 4287164 snp A G +NC_000962.3 4287361 snp C T +NC_000962.3 4289953 snp A G +NC_000962.3 4290564 snp G T +NC_000962.3 4290827 snp C G +NC_000962.3 4293107 snp G A +NC_000962.3 4296015 snp G A +NC_000962.3 4296381 snp G T +NC_000962.3 4301972 snp C T +NC_000962.3 4302036 snp T C +NC_000962.3 4303407 snp A C +NC_000962.3 4306155 snp C T +NC_000962.3 4306339 snp G T +NC_000962.3 4307021 snp C T +NC_000962.3 4307179 snp G A +NC_000962.3 4307344 snp C G +NC_000962.3 4313128 snp C T +NC_000962.3 4314645 snp A G +NC_000962.3 4314843 snp G A +NC_000962.3 4316566 snp C G +NC_000962.3 4323006 snp G A +NC_000962.3 4326655 snp G A +NC_000962.3 4329782 snp G A +NC_000962.3 4334425 snp G C +NC_000962.3 4336597 snp C A +NC_000962.3 4336774 snp C T +NC_000962.3 4337574 snp A G +NC_000962.3 4338361 snp C T +NC_000962.3 4338603 snp G A +NC_000962.3 4338732 snp G A +NC_000962.3 4344058 snp T C +NC_000962.3 4345682 snp C T +NC_000962.3 4348418 snp G A +NC_000962.3 4349778 snp G A +NC_000962.3 4351039 snp G T +NC_000962.3 4351759 snp G C +NC_000962.3 4354013 snp G A +NC_000962.3 4355919 snp G T +NC_000962.3 4356110 snp G C +NC_000962.3 4357597 snp C G +NC_000962.3 4357773 snp G A +NC_000962.3 4357946 snp C T +NC_000962.3 4361141 snp G A +NC_000962.3 4363243 snp A C +NC_000962.3 4366195 snp T C +NC_000962.3 4366272 snp G C +NC_000962.3 4367090 snp G A +NC_000962.3 4367649 snp A G +NC_000962.3 4369499 snp G A +NC_000962.3 4372353 snp G C +NC_000962.3 4374228 snp T C +NC_000962.3 4375318 snp G A +NC_000962.3 4375628 snp G T +NC_000962.3 4377033 snp G C +NC_000962.3 4379680 snp C G +NC_000962.3 4382054 snp T C +NC_000962.3 4382275 snp G T +NC_000962.3 4383442 snp T C +NC_000962.3 4383655 snp A G +NC_000962.3 4384007 snp C G +NC_000962.3 4385187 snp A G +NC_000962.3 4386228 snp T C +NC_000962.3 4390380 snp A G +NC_000962.3 4393178 snp A G +NC_000962.3 4394210 snp G C +NC_000962.3 4395387 snp A G +NC_000962.3 4398732 snp G A +NC_000962.3 4399137 snp G A +NC_000962.3 4401400 snp A G +NC_000962.3 4407588 snp T C +NC_000962.3 4407873 snp C A +NC_000962.3 4408920 snp A G +NC_000962.3 4408923 snp C T +NC_000962.3 4410386 snp G T +NC_000962.3 4411016 snp G A
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tab Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,2114 @@ +CHROM POS TYPE REF ALT +NC_000962.3 1302 snp C A +NC_000962.3 1977 snp A G +NC_000962.3 2532 snp T C +NC_000962.3 4013 snp T C +NC_000962.3 6112 snp G C +NC_000962.3 7362 snp G C +NC_000962.3 7585 snp G C +NC_000962.3 8452 snp C T +NC_000962.3 9143 snp T C +NC_000962.3 9260 snp G C +NC_000962.3 9304 snp G A +NC_000962.3 11879 snp A G +NC_000962.3 13175 snp A G +NC_000962.3 13298 snp G C +NC_000962.3 13460 snp A G +NC_000962.3 14401 snp A G +NC_000962.3 14785 snp T C +NC_000962.3 15088 snp C T +NC_000962.3 15117 snp C G +NC_000962.3 16526 snp C T +NC_000962.3 21795 snp G A +NC_000962.3 21819 snp A C +NC_000962.3 22961 snp T G +NC_000962.3 23174 snp C A +NC_000962.3 26347 snp C G +NC_000962.3 26959 snp C G +NC_000962.3 27199 snp G A +NC_000962.3 27469 snp A G +NC_000962.3 27473 snp G T +NC_000962.3 27996 snp T C +NC_000962.3 31142 snp C T +NC_000962.3 34044 snp T C +NC_000962.3 36538 snp T C +NC_000962.3 37031 snp C G +NC_000962.3 39623 snp C G +NC_000962.3 39758 snp A G +NC_000962.3 41151 snp C A +NC_000962.3 42281 snp C A +NC_000962.3 42967 snp G C +NC_000962.3 43945 snp A G +NC_000962.3 46735 snp G A +NC_000962.3 49976 snp C T +NC_000962.3 51781 snp C G +NC_000962.3 51949 snp A G +NC_000962.3 54394 snp A G +NC_000962.3 62049 snp A G +NC_000962.3 63752 snp C T +NC_000962.3 64028 snp C T +NC_000962.3 65159 snp G A +NC_000962.3 65663 snp C G +NC_000962.3 66892 snp C G +NC_000962.3 66937 snp C T +NC_000962.3 68174 snp T C +NC_000962.3 69989 snp G A +NC_000962.3 70267 snp G T +NC_000962.3 70816 snp A G +NC_000962.3 71336 snp G C +NC_000962.3 74737 snp T G +NC_000962.3 75233 snp C A +NC_000962.3 75940 snp G C +NC_000962.3 79479 snp T C +NC_000962.3 80616 snp C G +NC_000962.3 83343 snp C T +NC_000962.3 89200 snp G T +NC_000962.3 89871 snp C T +NC_000962.3 92199 snp T G +NC_000962.3 97696 snp T C +NC_000962.3 98966 snp G C +NC_000962.3 103600 snp A G +NC_000962.3 104712 snp C T +NC_000962.3 104824 snp C A +NC_000962.3 105045 snp G C +NC_000962.3 106126 snp T C +NC_000962.3 115499 snp T G +NC_000962.3 116000 snp T G +NC_000962.3 122109 snp A G +NC_000962.3 123520 snp T C +NC_000962.3 126803 snp A G +NC_000962.3 126853 snp G A +NC_000962.3 132417 snp C G +NC_000962.3 132646 snp G T +NC_000962.3 133839 snp C T +NC_000962.3 137233 snp C T +NC_000962.3 137673 snp G A +NC_000962.3 139756 snp T C +NC_000962.3 139954 snp A C +NC_000962.3 143207 snp T C +NC_000962.3 144433 snp C G +NC_000962.3 144434 snp C T +NC_000962.3 144564 snp C T +NC_000962.3 146087 snp T C +NC_000962.3 146788 snp G A +NC_000962.3 146872 snp C T +NC_000962.3 147970 snp C T +NC_000962.3 149983 snp G C +NC_000962.3 150052 snp G A +NC_000962.3 150602 snp C A +NC_000962.3 150609 snp C T +NC_000962.3 150611 snp C T +NC_000962.3 154191 snp A G +NC_000962.3 154283 snp T C +NC_000962.3 157364 snp C T +NC_000962.3 160976 snp C G +NC_000962.3 162226 snp G A +NC_000962.3 167986 snp C T +NC_000962.3 168787 snp C T +NC_000962.3 177175 snp G C +NC_000962.3 177857 snp G A +NC_000962.3 188800 snp T C +NC_000962.3 189948 snp C G +NC_000962.3 194040 snp C A +NC_000962.3 194681 snp G C +NC_000962.3 195360 snp T C +NC_000962.3 196642 snp C T +NC_000962.3 196874 snp C T +NC_000962.3 199470 snp T G +NC_000962.3 200379 snp C T +NC_000962.3 206339 snp T C +NC_000962.3 206481 snp C G +NC_000962.3 206484 snp G T +NC_000962.3 211993 snp C A +NC_000962.3 215238 snp C T +NC_000962.3 217201 snp T C +NC_000962.3 223942 snp T C +NC_000962.3 225315 snp G A +NC_000962.3 225323 snp T C +NC_000962.3 225668 snp C T +NC_000962.3 226676 snp G A +NC_000962.3 227098 snp T C +NC_000962.3 231114 snp C G +NC_000962.3 233358 snp A C +NC_000962.3 233364 snp G C +NC_000962.3 234477 snp T G +NC_000962.3 235681 snp G A +NC_000962.3 236512 snp C T +NC_000962.3 241465 snp G A +NC_000962.3 243598 snp A G +NC_000962.3 244550 snp A G +NC_000962.3 251575 snp G A +NC_000962.3 251669 snp T C +NC_000962.3 254903 snp C A +NC_000962.3 260282 snp G T +NC_000962.3 261869 snp T C +NC_000962.3 263057 snp T G +NC_000962.3 263149 snp A C +NC_000962.3 264298 snp C A +NC_000962.3 264984 snp C G +NC_000962.3 265554 snp A C +NC_000962.3 272678 snp C T +NC_000962.3 273568 snp G T +NC_000962.3 278681 snp C G +NC_000962.3 281454 snp C A +NC_000962.3 282604 snp A T +NC_000962.3 283614 snp T C +NC_000962.3 285772 snp A C +NC_000962.3 285871 snp A G +NC_000962.3 290374 snp T C +NC_000962.3 291977 snp G A +NC_000962.3 294170 snp G A +NC_000962.3 297236 snp C T +NC_000962.3 297396 snp G A +NC_000962.3 303414 snp C T +NC_000962.3 304923 snp A G +NC_000962.3 308312 snp G A +NC_000962.3 309765 snp C T +NC_000962.3 310973 snp G A +NC_000962.3 311613 snp G T +NC_000962.3 320180 snp A G +NC_000962.3 325505 snp T C +NC_000962.3 326002 snp A G +NC_000962.3 331588 snp G A +NC_000962.3 333212 snp G C +NC_000962.3 333292 snp A G +NC_000962.3 333892 snp G C +NC_000962.3 337820 snp G A +NC_000962.3 337959 snp A C 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snp T C +NC_000962.3 406274 snp T C +NC_000962.3 406599 snp G A +NC_000962.3 412280 snp T G +NC_000962.3 414486 snp C T +NC_000962.3 420008 snp A G +NC_000962.3 420405 snp C T +NC_000962.3 424250 snp A G +NC_000962.3 424932 snp T A +NC_000962.3 425342 snp G A +NC_000962.3 426768 snp C T +NC_000962.3 428384 snp C T +NC_000962.3 428698 snp C T +NC_000962.3 434327 snp A G +NC_000962.3 438271 snp G A +NC_000962.3 439711 snp T C +NC_000962.3 440510 snp G T +NC_000962.3 442988 snp G A +NC_000962.3 445400 snp C T +NC_000962.3 445780 snp C T +NC_000962.3 446747 snp C T +NC_000962.3 447442 snp C T +NC_000962.3 447525 snp G C +NC_000962.3 451029 snp C A +NC_000962.3 452288 snp C T +NC_000962.3 453659 snp C A +NC_000962.3 454295 snp T C +NC_000962.3 454472 snp G C +NC_000962.3 455325 snp C G +NC_000962.3 455329 snp T C +NC_000962.3 456487 snp C A +NC_000962.3 456511 snp G A +NC_000962.3 457452 snp T G +NC_000962.3 459399 snp A C +NC_000962.3 467516 snp G C +NC_000962.3 467526 snp C G +NC_000962.3 467546 snp G C +NC_000962.3 467557 snp A C +NC_000962.3 467564 snp A C +NC_000962.3 467585 snp G C +NC_000962.3 467590 snp T C +NC_000962.3 467621 snp T G +NC_000962.3 467638 snp G T +NC_000962.3 468357 snp A G +NC_000962.3 469042 snp C T +NC_000962.3 471666 snp A G +NC_000962.3 475178 snp T C +NC_000962.3 483935 snp T G +NC_000962.3 485230 snp C T +NC_000962.3 485785 snp T G +NC_000962.3 489935 snp G C +NC_000962.3 491742 snp T C +NC_000962.3 492150 snp G C +NC_000962.3 492655 snp G A +NC_000962.3 495198 snp A G +NC_000962.3 495473 snp C T +NC_000962.3 498531 snp A G +NC_000962.3 498557 snp C A +NC_000962.3 502589 snp C G +NC_000962.3 503354 snp G C +NC_000962.3 505974 snp G A +NC_000962.3 508435 snp C T +NC_000962.3 513257 snp T C +NC_000962.3 514657 snp T G +NC_000962.3 517358 snp T C +NC_000962.3 517411 snp A G +NC_000962.3 519185 snp T G +NC_000962.3 522081 snp A G +NC_000962.3 524891 snp C A +NC_000962.3 527050 snp G A +NC_000962.3 527316 snp C G +NC_000962.3 528354 snp C A 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_with_header.tab Thu Sep 27 17:05:18 2018 -0400 @@ -0,0 +1,2115 @@ +ABC +CHROM POS TYPE REF ALT +NC_000962.3 1302 snp C A +NC_000962.3 1977 snp A G +NC_000962.3 2532 snp T C +NC_000962.3 4013 snp T C +NC_000962.3 6112 snp G C +NC_000962.3 7362 snp G C +NC_000962.3 7585 snp G C +NC_000962.3 8452 snp C T +NC_000962.3 9143 snp T C +NC_000962.3 9260 snp G C +NC_000962.3 9304 snp G A +NC_000962.3 11879 snp A G +NC_000962.3 13175 snp A G +NC_000962.3 13298 snp G C +NC_000962.3 13460 snp A G +NC_000962.3 14401 snp A G +NC_000962.3 14785 snp T C +NC_000962.3 15088 snp C T +NC_000962.3 15117 snp C G +NC_000962.3 16526 snp C T +NC_000962.3 21795 snp G A +NC_000962.3 21819 snp A C +NC_000962.3 22961 snp T G +NC_000962.3 23174 snp C A +NC_000962.3 26347 snp C G +NC_000962.3 26959 snp C G +NC_000962.3 27199 snp G A +NC_000962.3 27469 snp A G +NC_000962.3 27473 snp G T +NC_000962.3 27996 snp T C +NC_000962.3 31142 snp C T +NC_000962.3 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