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Commit message:
planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty |
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added:
cut_degen.py cut_degen.xml output.fastq output.txt output2.fastq output2.txt readme.txt test-data/output.fastq test-data/output.txt test-data/output2.fastq test-data/output2.txt test-data/test.fastq test-data/test3prime.fastq test.fastq test3prime.fastq |
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| diff -r 000000000000 -r 716cdcccc919 cut_degen.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cut_degen.py Tue Sep 15 14:14:41 2015 -0400 |
| [ |
| @@ -0,0 +1,95 @@ +#This is a version that is meant to work with Fastq files +import Bio +from Bio import SeqUtils +from Bio import SeqIO +import sys + + +#for records and adapter, should be sys.argv[1 and 2] +fastqfile = sys.argv[1] #This is the input fasta file +adapter = sys.argv[2] #This is the input adapter as a string +keepreads = sys.argv[3] #True or false, this will determine whether or not reads are kept. If true, it will keep reads that do not have the adapter in it. If false, it will get rid of those reads. +removeadapters = sys.argv[4] #True or false, if this is True, the adapters will be removed. If true, removes the adapters from the sequences. If false, it keeps them. +end_defn = sys.argv[5] #If 5, the primer is removed from the 5' end of the sequence. If 3, then it is removed from the 3' end of the sequence. +adapter_name = sys.argv[6] #This is the name of the adapter that you can put into the output text file. + + +# Here is the command for the test: python cut_degen.py 'test.fastq' 'GAACWAYWYCT' 'True' 'True' '5' 'test' + +keepreads = str(keepreads) +removeadapters = str(removeadapters) +fastqfile=str(fastqfile) +end_defn = str(end_defn) + +fh = open(fastqfile, mode='r+') +len_adapter = len(adapter) +count_adapter_found = 0 +count_adapter_not_found = 0 +total_seq_count = 0 + +parsed = SeqIO.parse(fh, format="fastq") + +output_fh_name = "output.fastq" + +if fastqfile=="test3prime.fastq": + output_fh_name="output2.fastq" + +output_fh = open(output_fh_name, mode='w+') + +output_text_name = "output.txt" +if fastqfile=="test3prime.fastq": + output_text_name="output2.txt" +output_text_fh = open(output_text_name, mode='w+') + + +for record in parsed: + try: + sequence = str(record.seq) + search = SeqUtils.nt_search(sequence, adapter) #This will search the + index = int(search[1]) #If it finds the adapter, is the starting index from which it was found. + adapter_start = index + adapter_end = index+len_adapter + count_adapter_found +=1 + total_seq_count+=1 + if removeadapters == "True": #if the value is true, it removes the adapters from the sequences. + if end_defn=="5": + record = record[adapter_end:] #If a 5' adapter, you remove adapter from beginning + elif end_defn=="3": + record = record[:adapter_start] #If it is a 3' adapter, you remove the adapter at the end + elif removeadapters == "False": #if the value is false, it does not remove the adapters from the sequences. + record = record + SeqIO.write(record, output_fh, format="fastq") #No matter what, write the reads. + except IndexError: + count_adapter_not_found+=1 + total_seq_count+=1 + record = record + if keepreads=="True": + SeqIO.write(record, output_fh, format="fastq") + elif keepreads=="False": + pass + else: + pass + +output_fh.close() + +percent_cut = 100*(float(count_adapter_found)/float(total_seq_count)) + + +output_text_fh.write("The total number of sequences that were analyzed was %i.\n\n"%total_seq_count) +output_text_fh.write("Adapter was found and removed for %i sequences (%i%% of total).\n\n"%(count_adapter_found, percent_cut)) + +if keepreads =="True": + output_text_fh.write("Sequences that did not contain the adapter were kept.\n\n") +elif keepreads=="False": + output_text_fh.write("Sequences that did not contain the adapter were removed from the dataset.\n\n") +if removeadapters=="True": + output_text_fh.write("The adapters were removed from the dataset.\n\n") +elif removeadapters=="False": + output_text_fh.write("The adapters were not removed from the dataset.\n\n") +if end_defn=="5": + output_text_fh.write("Adapters were removed from the 5\' end.\n\n") +elif end_defn=="3": + output_text_fh.write("Adapters were removed from the 3\'end.\n\n") + +output_text_fh.write("The name of the adapter that was removed was named %s, and had the sequence %s.\n\n"%(adapter_name,adapter)) +output_text_fh.close() \ No newline at end of file |
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| diff -r 000000000000 -r 716cdcccc919 cut_degen.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cut_degen.xml Tue Sep 15 14:14:41 2015 -0400 |
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| @@ -0,0 +1,68 @@ +<tool id="cut_degen" name="Cut degenerate primers from dataset (for Fastq)" version="0.1.0"> + <description> Degenerate primer removal tool for Fastq files</description> + <requirements> + <requirement type = "package" version = "1.9">numpy</requirement> + <requirement type = "package" version = "1.65">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + + <command interpreter="python">cut_degen.py $input1 $input2 $input3 $input4 $input5 $input6 + </command> + <inputs> + <param name="input1" type="data" label="Input Fastq file" help="Please add a valid Fastq file!" format="fastq"/> + <param name="input2" type="text" label="Input adaptor" help="This will work also with degenerate adaptors. Type the adaptor here..." size="4x25" area="true"/> + <param name="input3" type="select" label="Keep reads without adaptor?" help="This is a True/False option, if True, reads that lack the adaptor will be kept. If false, they will be deleted from the dataset."> + <option value="True">True</option> + <option value="False">False</option> + </param> + <param name="input4" type="select" label = "Remove adaptors?" help="This is True/False option, if True, removes adaptors from sequences. If false, keeps the adaptors in the sequences."> + <option value="True">True</option> + <option value="False">False</option> + </param> + <param name="input5" type="select" multiple="False" label="5' or 3' end" help="Enter '5' to remove the primer from the 5' end, and enter '3' to remove the primer from the 3' end"> + <option value="5">5</option> + <option value="3">3</option> + </param> + <param name="input6" type="text" label="Adaptor name" help="Enter an identifier for your adaptor to be recorded in the output .txt file" size="4x25" area="true"> + </param> + </inputs> + <outputs> + <data name="output1" format="text" from_work_dir="output.txt" label="Degenerate adaptor removal on ${input1.name}(REPORT)"/> + <data name="output2" format="fastq" from_work_dir="output.fastq" label="Degenerate adaptor removal on ${input1.name}(READS)"/> + </outputs> + <tests> + <test> + <param name="input1" value="test.fastq"/> + <param name="input2" value="ACCTGCCTGCCG"/> + <param name="input3" value="True"/> + <param name="input4" value="True"/> + <param name="input5" value="5"/> + <param name="input6" value="UniA"/> + <output name="output1" file="output.txt"/> + <output name="output2" file="output.fastq"/> + </test> + <test> + <param name="input1" value="test3prime.fastq"/> + <param name="input2" value="GCTCGGTGGCGT"/> + <param name="input3" value="True"/> + <param name="input4" value="True"/> + <param name="input5" value="3"/> + <param name="input6" value="UniB"/> + <output name="output1" file="output2.txt"/> + <output name="output2" file="output2.fastq"/> + </test> + </tests> + <help> +This program takes Fastq files and removes a given degenerate primer sequence. There are a few arguments that you can put in: + 1) You can check whether or not to keep reads that do not have the adaptor in it. + 2) You can check whether or not to remove the adaptor sequences from your reads. + 3) You can choose whether to cut adaptors from the 5', or 3' end of the molecules. + 4) You can add an identifier for the adaptor which will show up in the output text file. + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 716cdcccc919 output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\n+GGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\n++\n+C=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\n+@RCTKY:00023:00605\n+GGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\n++\n+D=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\n+@RCTKY:00015:00987\n+GGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\n++\n+C@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\n+@RCTKY:00108:00179\n+GGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\n++\n+C?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\n+@RCTKY:00105:00949\n+GGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\n++\n+<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\n+@RCTKY:00147:01305\n+GGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\n++\n+D?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\n+@RCTKY:00185:00378\n+GGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\n++\n+;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-\n+@RCTKY:00173:01077\n+GGTACTGGTTGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTACTTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCCAGCGGGGG\n++\n+C>CCCCCACACC@CDDCCBBBCACC6>>;;1;;<7<<1/8;+"..b'TCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCCTATACCAGTCATTTATTTTGAC\n++\n+C=?>?CCACACC@>>>CCCCCA??<7<888,:CD?CC18282888,8::@@E9?;;;;;BBBCCCC@CCACC@CCCACCCCC??>?CAC>>?CC@CCCCCCCCDDAB9>>BBEE5;;8828288,8===>???;:88?882:4:@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\n+@RCTKY:03703:02392\n+GGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\n++\n+C?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\n+@RCTKY:03731:02359\n+GGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\n++\n+C=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\n+@RCTKY:03741:02381\n+GGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\n++\n+;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\n+@RCTKY:03758:01997\n+GGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\n++\n+>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\n+@RCTKY:03754:02056\n+GGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\n++\n+>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output.txt Tue Sep 15 14:14:41 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +The total number of sequences that were analyzed was 166. + +Adapter was found and removed for 165 sequences (99% of total). + +Sequences that did not contain the adapter were kept. + +The adapters were removed from the dataset. + +Adapters were removed from the 5' end. + +The name of the adapter that was removed was named UniA, and had the sequence ACCTGCCTGCCG. + |
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| diff -r 000000000000 -r 716cdcccc919 output2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output2.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\n++\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\n+@RCTKY:00023:00605\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\n++\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\n+@RCTKY:00015:00987\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\n++\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\n+@RCTKY:00108:00179\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\n++\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\n+@RCTKY:00105:00949\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\n++\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\n+@RCTKY:00147:01305\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTA\n++\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@\n+@RCTKY:00185:00378\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\n++\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-\n+@RCTKY:00173:01077\n+TAAGGAGAACGATACCTGCCTGCCGGGTA"..b'CCCCCDDAB9>>BBEE5;;8828288,8===>???;:88?882:4:@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\n+@RCTKY:03703:02392\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\n++\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\n+@RCTKY:03731:02359\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\n++\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\n+@RCTKY:03741:02381\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTA\n++\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=\n+@RCTKY:03758:01997\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\n++\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\n+@RCTKY:03754:02056\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\n++\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 output2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output2.txt Tue Sep 15 14:14:41 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +The total number of sequences that were analyzed was 166. + +Adapter was found and removed for 28 sequences (16% of total). + +Sequences that did not contain the adapter were kept. + +The adapters were removed from the dataset. + +Adapters were removed from the 3'end. + +The name of the adapter that was removed was named UniB, and had the sequence GCTCGGTGGCGT. + |
| b |
| diff -r 000000000000 -r 716cdcccc919 readme.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Tue Sep 15 14:14:41 2015 -0400 |
| b |
| @@ -0,0 +1,3 @@ +This is a tool for Galaxy that removes degenerate primers from sequences. + +MORE DETAIL IN FUTURE |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\n+GGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\n++\n+C=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\n+@RCTKY:00023:00605\n+GGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\n++\n+D=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\n+@RCTKY:00015:00987\n+GGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\n++\n+C@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\n+@RCTKY:00108:00179\n+GGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\n++\n+C?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\n+@RCTKY:00105:00949\n+GGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\n++\n+<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\n+@RCTKY:00147:01305\n+GGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\n++\n+D?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\n+@RCTKY:00185:00378\n+GGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\n++\n+;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-\n+@RCTKY:00173:01077\n+GGTACTGGTTGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTACTTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCCAGCGGGGG\n++\n+C>CCCCCACACC@CDDCCBBBCACC6>>;;1;;<7<<1/8;+"..b'TCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCCTATACCAGTCATTTATTTTGAC\n++\n+C=?>?CCACACC@>>>CCCCCA??<7<888,:CD?CC18282888,8::@@E9?;;;;;BBBCCCC@CCACC@CCCACCCCC??>?CAC>>?CC@CCCCCCCCDDAB9>>BBEE5;;8828288,8===>???;:88?882:4:@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\n+@RCTKY:03703:02392\n+GGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\n++\n+C?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\n+@RCTKY:03731:02359\n+GGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\n++\n+C=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\n+@RCTKY:03741:02381\n+GGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\n++\n+;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\n+@RCTKY:03758:01997\n+GGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\n++\n+>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\n+@RCTKY:03754:02056\n+GGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\n++\n+>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.txt Tue Sep 15 14:14:41 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +The total number of sequences that were analyzed was 166. + +Adapter was found and removed for 165 sequences (99% of total). + +Sequences that did not contain the adapter were kept. + +The adapters were removed from the dataset. + +Adapters were removed from the 5' end. + +The name of the adapter that was removed was named UniA, and had the sequence ACCTGCCTGCCG. + |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/output2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\n++\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\n+@RCTKY:00023:00605\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\n++\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\n+@RCTKY:00015:00987\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\n++\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\n+@RCTKY:00108:00179\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\n++\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\n+@RCTKY:00105:00949\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\n++\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\n+@RCTKY:00147:01305\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTA\n++\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@\n+@RCTKY:00185:00378\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\n++\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-\n+@RCTKY:00173:01077\n+TAAGGAGAACGATACCTGCCTGCCGGGTA"..b'CCCCCDDAB9>>BBEE5;;8828288,8===>???;:88?882:4:@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\n+@RCTKY:03703:02392\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\n++\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\n+@RCTKY:03731:02359\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\n++\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\n+@RCTKY:03741:02381\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTA\n++\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=\n+@RCTKY:03758:01997\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\n++\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\n+@RCTKY:03754:02056\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\n++\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/output2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.txt Tue Sep 15 14:14:41 2015 -0400 |
| b |
| @@ -0,0 +1,12 @@ +The total number of sequences that were analyzed was 166. + +Adapter was found and removed for 28 sequences (16% of total). + +Sequences that did not contain the adapter were kept. + +The adapters were removed from the dataset. + +Adapters were removed from the 3'end. + +The name of the adapter that was removed was named UniB, and had the sequence GCTCGGTGGCGT. + |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\r\n++\r\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\r\n+@RCTKY:00023:00605\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\r\n++\r\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\r\n+@RCTKY:00015:00987\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\r\n++\r\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\r\n+@RCTKY:00108:00179\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\r\n++\r\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\r\n+@RCTKY:00105:00949\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\r\n++\r\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\r\n+@RCTKY:00147:01305\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\r\n+@RCTKY:00185:00378\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\r\n++\r\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-"..b':@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\r\n+@RCTKY:03703:02392\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\r\n++\r\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\r\n+@RCTKY:03731:02359\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\r\n++\r\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\r\n+@RCTKY:03741:02381\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\r\n+@RCTKY:03758:01997\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\r\n++\r\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\r\n+@RCTKY:03754:02056\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\r\n++\r\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\r\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 test-data/test3prime.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3prime.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\r\n++\r\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\r\n+@RCTKY:00023:00605\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\r\n++\r\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\r\n+@RCTKY:00015:00987\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\r\n++\r\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\r\n+@RCTKY:00108:00179\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\r\n++\r\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\r\n+@RCTKY:00105:00949\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\r\n++\r\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\r\n+@RCTKY:00147:01305\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\r\n+@RCTKY:00185:00378\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\r\n++\r\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-"..b':@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\r\n+@RCTKY:03703:02392\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\r\n++\r\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\r\n+@RCTKY:03731:02359\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\r\n++\r\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\r\n+@RCTKY:03741:02381\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\r\n+@RCTKY:03758:01997\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\r\n++\r\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\r\n+@RCTKY:03754:02056\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\r\n++\r\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\r\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 test.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\r\n++\r\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\r\n+@RCTKY:00023:00605\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\r\n++\r\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\r\n+@RCTKY:00015:00987\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\r\n++\r\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\r\n+@RCTKY:00108:00179\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\r\n++\r\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\r\n+@RCTKY:00105:00949\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\r\n++\r\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\r\n+@RCTKY:00147:01305\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\r\n+@RCTKY:00185:00378\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\r\n++\r\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-"..b':@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\r\n+@RCTKY:03703:02392\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\r\n++\r\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\r\n+@RCTKY:03731:02359\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\r\n++\r\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\r\n+@RCTKY:03741:02381\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\r\n+@RCTKY:03758:01997\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\r\n++\r\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\r\n+@RCTKY:03754:02056\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\r\n++\r\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\r\n' |
| b |
| diff -r 000000000000 -r 716cdcccc919 test3prime.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test3prime.fastq Tue Sep 15 14:14:41 2015 -0400 |
| b |
| b"@@ -0,0 +1,664 @@\n+@RCTKY:00012:00600\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACAGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGATATCCT\r\n++\r\n+;;7>>0<<8//----)-;;7;AC>AC=CACBB6;;;;7;AACC=@?DADC<@:::/:@@4::/:=B5:888)6<<<8:48BB@;;;BBBAAA?@@788;A;;7;;;;@;;7;C>A;;>;;<>CCDCAAACEAE>>;;;;;.;A::4:5::/::::B@<B>0/0*00*8288888=,8888*131-'-2-.---'---)6<6<5;;;/;AAA0?>C?>=CD@@?>>>110<8<;???@BCCC@CCDC@AB;;;;;:;:::/::4::;;;;::4:2:::4:C::8::89==?288888888/*/:*0/*0//*.6./)-88,6<7=9@@BBE?66777(/--.-'-\r\n+@RCTKY:00023:00605\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTACTGAGCCTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATCTTCTCACTGACCGTAACCTAAATACTACATTCCTTCGACCC\r\n++\r\n+;C7;7;6606<66;;>;??ACDD@CD=@??CCAFDDC>;;;;;04;;@CC4::;;1;;;6;C0;6;6;;;0:@:::C@C>>???;B?CCCCACC>>:?C<;7;;;;;;;?ABAD??<;;7;;>CC??@@@>>@>;0>>;/;;0/*0*/:6::BCCB5==:::@::5=98@AAAA6>?<<*>:;;=AA:0000*...);B:;>?CC8???A9<<//////;6;;BB7>?CBCB@@?>?=1@>>1@100;<0;??B@;;;1;;6;;;B9:..3;6:).)----6==A=>=>C999C=?@@BDACCC;>;;@;/0/*/+/8<//0;*\r\n+@RCTKY:00015:00987\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACTGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTTAATTTTATTACTACAATTATTAATA\r\n++\r\n+BB@C@CBCAE?>>CB?<?>>>?DACC@DD??@ADA??;;@;;;;?ADDCC5@@CADCCDACCACAC@CCC<??CCCCACC???C?>>CCCC@C@DC:::/.)0/0A=8;;;;;0>@CCDACC???CCCCC>?>?CCCCC6::888,82888*8===<76//*/*./1:'.8\r\n+@RCTKY:00108:00179\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACTGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAACCCCAGCATCTCTCAATACCAACACCCTCTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGTCTCCGGAT\r\n++\r\n+CCACACCDACCDECCAC@@??EDBCC?CC@??ACC@@=?AABC=CCCACDADCCC?CCC2==9=@C@CCE>?????C@C???CCCCCCC@@=@@>BC8??B??;;;@@B?=:9=:8:@C5==::C8:=>@===AB8888*88882:<@C;AA@@::6:::8B=@@=@6::800-0><-00000899;;;=C::5:5:BBA7A8828888<88:4=2>>B.8292:667,17)87<<*888828::::==BCC=C>68800///-'-'11\r\n+@RCTKY:00105:00949\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTACCCCCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCT\r\n++\r\n+BB>?>@CCAC?@???@<?@@@AD7<<1;CCCDACC@;6;B;;;1<;;;;;+;;;;1;BB7;;1;7<6<;;6;/00;;8<@CCCCCCCCDCCACCACCAC?@??CBBC@@?@CACCDC;;6<<;AB>?@DCACACC>>>>/<;//*08;;6>0;>?;6:<0//*/06@<@BB@::;7777(70/.'-48./\r\n+@RCTKY:00147:01305\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGTTGAACAGTTTACCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGGTTCTTCGGCCATCCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+CC@B@BAB?B?>==C>BCCACEDADD?CCCCCBCACCACCCCB>;;;1;@?CCCACCCCACDAC@A>;;;1;AACCCADDDCCCC@@@CDCACA???C???AECECCC=>?DD?D>>??AD??>DC??>DADACCCDDE:DC??>;=ACC6BB<??:;882:4=:@C?>???AB<BEEE3B@??;?BB???BBB@@;;;3;??<?AE@@@9???@???A<??BAA:?>>5::>>=???@@=AA???C5::BBCDCAAA;AB=AABBCCAA=A:??B>BCB@@BBB?:;;=@AA;;000737737918//*0/00-;CD<@CBCACECC>;:::::/0///<8C>?>>@@@>??>AC??>@CCACCCAC@B@<::5:<<:88,8828:BB@<888870/*///\r\n+@RCTKY:00185:00378\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACTGTATATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATCTAGGGGCAGTTAATTTCATCACACGATTATTAACATGAAACCCCCCATGT\r\n++\r\n+CC@C@ABD=@@CCC@A@@?<;BC7;;1;7;6B@CDFEA???DCD?>>ADCACCCC>CCB488,82828::/21212B>@@AA;;;?AAA@@>B;6871700*088=@@@?AA=A;;:??58:<<888<88288888CC2?;;;:?9?A;:/0:00/---6-./).-64::::*/////(0/.-"..b':@@@BB8>><<*80005000////*/::*::/:CCCC9CCCAA@A@@=88;6;;CCDACCCCCC@@=??;89<<-700017>ACCA@::=9>CAFFCC@<>??E=A=A48;;@@@ACACBCCA888:4:@@=A=@<<,8888==885:A48:?>>8?@@@BBBB,:88<0000(000*0077:5:000/8816866-6/.\r\n+@RCTKY:03703:02392\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGATGAACAGTTTATCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCCCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAACCACATTCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCGTATCAA\r\n++\r\n+CC@C@CDE@CCDE??>?CDACCCACC?CACCCACCCCACCCCC>C>?:??;;;;E9??B>BB;B>B>BBB6;;???E?CBBBB@@@BB????BB>BC>CCCACCCC>CE>>>@CDDCC@>;;;CC???@@9<7<888<<2<88:7;?GG;ACDD??>@CCEF>>>@CAC@@?<<,8888*88:;>BB:::00,0;>;CC?DDEDC9>>=C=C=>>C;;@ACDCDD@CCDACCCC@CCDCCACACC??>?DFCCBAAAB;BB=AADD???@?D=AAB=???BBBBB=@@@=@BBB@@@CC;??2>=,:7;BBB?;::,88:87:8888288888*8<8::4:::4/..-----.)\r\n+@RCTKY:03731:02359\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACAGTTTATCCTCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATCCTTTGATCCAGCAGGAGGGGGAGATCCTATTCTCTATCAACACCTATTCTGATTCTTTGGCCACCCCGAAGTCTAGCTGGTGCGTATCACCGCACCTGGACCCTA\r\n++\r\n+;60;7<AB>BCCCCCA???ADCC@CC=CACCCADACC?BC:::/=C?=@A?C?CAC???@CDACAC=AAD>BB??CC@@BBBBAAAA@@@D?D????CBBB>BBB@@@BBBBD<C???A6;;DDCCAABC?B=???BBB5@@BB>B>BBB7;;7;AA@@@>B>BB=@=@BBB;;33333(3-..3;999B???BB@A@C6;;?<??AABB;???BBBA@=@@@??<;;;?BBBB>BB@@@;??BAAA>BBB???BBBB6>>?DD???BBB>B>B;;8;CCBBABE>B;;8...///08836<166)///*///88*//*88AA=A8000500000(/./885???=AE@@@AAA=ACC7>?C?70/0>6;;:1:5A=????2<:17000;;;C<6000000788:6:>00,/75000*/.\r\n+@RCTKY:03741:02381\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACTGGATGAACAGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACTTGTGACTGCCGTTCTTTTACTCCTATCGCTACCCGTTCTAGCTGCCGGAATTACTATACTTCTCACTGACCGTAACCTAAATACTACATTCTTCGACCCAGCGGGGGGAGTGACCCCATCTATACCAGCATTTATTTTGGTCTTGGCCACCCGAAGTCTAGCTCGGTGGCGT\r\n++\r\n+BCACACCC:??DCCC@CCC?@CC6;;1;@@@B@BB><6;@;;;1;@@9;?>@CIG@CCC@CC>CADADFG=CCCCCDACCCBCCCCCCCCCACCACCACCC@???C??B>DCACDCDDCACCCCCCCBEEAE7=:@@CC7B;;;;?=AC<CBBBBB>B??;;7:A=A=?><8//)/888(7/0067777700*000*>F>CCCEE:>:;C;B;;;?>:?>??DCDACCCCC??A=@B?BCDD5@;;;=;??DCCCCDE?>>;;BAAA@BB?E<@=@>@CCCCCCD@CC?????BCA??;=@=<??8;;;BBBCD?CC?B;;:>2<888<<<<)>>@@@@@@5@;;;ACBB>;;;:?@:@;;;-717//*/*/1///)-:3116?=??64;>882::8\r\n+@RCTKY:03758:01997\r\n+TAAGGAGAACGATACCTGCCTGCCGGGTACAGGATGAACAGTTTATCCCCCACTTGCAGGTAACCTTGCCCATGCAGGAGCATCAGTAGACCTTACGATCTTCTCTCTGCATTTAGCAGGTGTGTCATCAATTCTAGGGGCAGTTAATTTTATTACTACAATTATTAATATGAAACCCCCAGCAATCTCACAGTATCAAACACCTCTCTTTGTGTGAGCCGTGCTTGTAACTGCCGTACTTCTACTCCTATCACTACCCGTTCTAGCTGCCGGCATTACTATGCTTCTAACTGATCGTAATTTAAATACCACATTCTTTGATCCAGCAGGAGGGGGTAGATCCTATTCTCTATCAACACCTATTCTGGTATTTCTTGCCACCCGGACGACCCGAATCTCGAGTCGGGT\r\n++\r\n+;>7;=ADDB@@@DCCACCCA@@@7;>1>CCDC@CDDCACCCEE?C;>>??5>DCACCCCAEEAC@BA>>;:>D==?C@CCDCCCCCCCCBB?B?C@??;;;?AAABBBCCCCD?DCC>>>?BBBC;;;AA=@=A???EE7BB??<?>BBB5@@=@@;;;C;?<??;?>BBB???9?AAA39.//-.088?BC@@@BBCC<BBB>BBAAAD<@@@ABBBB>BB@??8;;C>BBBB>BBB@@=@CCBB@?BBBBBC;;;?6;;>BCDD???A>B>AAB>ABBBBCCC?C??<?BB;;:C<>6;;366)///)/000*000*/:886;B;::500000(////883;;;<??:00:0/*0::57??=@@B9>>>>6>=<@A8;;C<C;???A;;399-007//0/0/68-.\r\n+@RCTKY:03754:02056\r\n+TAAGGAGAACGATACCTGCCTGCCGGGAACTGGTTGAACTGTTTACCCTCCACTTTCAGGAAACCTTGCCCACGCAGGAGCGTCAGTAGACCTAACAATCTTCTCTCTCCACCTAGCAGGTGTATCATCAATTCTAGGGGCAGTTAATTTCATCACCACGATTATTAACATGAAACCCCCAGCAATCTCTCAATACCAAACACCCCTCTTTGTATGAGCCGTACCTTGTGATGTCTCCTTTC\r\n++\r\n+CD??=@DC@@?DDDD@CCCACCC;>>;>@CDDBDADC@CDCCC>CCC>CC?;;;B;???=AA;A=A=???9?AA;;:>BBCBBBCCBBB448;B???;?BB=???ABCC?DD;?ABB@@=@BAAAAA???;?<?B?>??2??@@=@;??8>=<>:;6:BB@A=AA=@=@@@@BE;AAAA0??BE;????@??;?BC5:8,88888*8<<A;A@@@@@@B>B>0.-/3::;:;0000/)//)0\r\n' |