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Difference between revisions of "Get.seqs"

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===accnos option===
 
===accnos option===
To generate an accnos file, you could use the [[list.seqs]] command. Here you should generate a text file containing the following lines:
+
To generate an accnos file, let's first run [[unique.seqs]], [[summary.seqs]], [[screen.seqs]], and [[list.seqs]]:
  
59_10_1
 
59_10_10
 
59_10_11
 
  
Save the file as esophagus.accnos
+
mothur > unique.seqs(fasta=esophagus.fasta)
 +
 +
mothur > summary.seqs(fasta=esophagus.unique.fasta)
 +
 +
Start End NBases Ambigs Polymer
 +
Minimum: 1 831 831 0 4
 +
2.5%-tile: 1 841 841 0 4
 +
25%-tile: 1 857 857 0 5
 +
Median: 1 866 866 0 5
 +
75%-tile: 1 870 870 0 5
 +
97.5%-tile: 1 900 900 5 7
 +
Maximum: 1 1378 1378 20 8
 +
# of Seqs: 656
 +
 +
mothur > screen.seqs(fasta=esophagus.unique.fasta, maxambig=0)
 +
 +
mothur > list.seqs(fasta=esophagus.unique.good.fasta)
 +
 
 +
This generates esophagus.unique.good.accnos, a file with 527 sequences.
  
  
Line 19: Line 34:
 
To use the fasta option, follow this example:
 
To use the fasta option, follow this example:
  
  mothur > get.seqs(accnos=esophagus.accnos, fasta=esophagus.fasta)
+
  mothur > get.seqs(accnos=esophagus.unique.good.accnos, fasta=esophagus.fasta)
  
 
This generates the file esophagus.pick.fasta, which contains the following lines:
 
This generates the file esophagus.pick.fasta, which contains the following lines:
  
  >59_10_1
+
  >9_1_12
  TGCAAGTCGAACGATGAAGCCTAGCTTG...
+
  GCAAGTCGAGGGGAAAC...
  >59_10_10
+
  >9_1_14
  TGCAAGTAGAACGCTGAAGAGAGGAGCT...
+
  GCAAGTCGAGGGGAACG...
  >59_10_11
+
  >9_1_15
  TGCAAGTCGAACGAAACTTTCTTACACC...
+
  GCAAGTCGAGGGGAAAC...
 
+
...
  
 
===name option===
 
===name option===
To use the name option, follow this example (assuming you have used [[unique.seqs]] on esophagus.fasta):
+
To use the name option, follow this example:
  
  mothur > get.seqs(accnos=esophagus.accnos, name=esophagus.names)
+
  mothur > get.seqs(accnos=esophagus.unique.good.accnos, name=esophagus.names)
  
 
This generates the file esophagus.pick.names, which contains the following lines:
 
This generates the file esophagus.pick.names, which contains the following lines:
  
  59_10_10        59_10_10
+
  65_5_22 65_5_22
  59_10_11        59_10_11
+
  65_5_12 65_5_12
  59_10_1 59_10_1
+
  59_7_23 59_7_23
 
+
59_7_7 59_7_7
 +
65_5_28 65_5_28
 +
65_9_13 65_9_13
 +
9_6_11 9_6_11
 +
...
  
 
===group option===
 
===group option===
 
To use the group option, follow this example:
 
To use the group option, follow this example:
  
  mothur > get.seqs(accnos=esophagus.accnos, group=esophagus.groups)
+
  mothur > get.seqs(accnos=esophagus.unique.good.accnos, group=esophagus.groups)
  
 
This generates the file esophagus.pick.groups, which contains the following lines:
 
This generates the file esophagus.pick.groups, which contains the following lines:
  
  59_10_1 C
+
  9_1_12 B
  59_10_10 C
+
  9_1_14 B
  59_10_11 C
+
  9_1_15 B
 
+
9_1_16 B
 +
9_1_18 B
 +
...
  
 
=== alignreport option===
 
=== alignreport option===
Line 59: Line 80:
 
To use the alignreport option, follow this example:
 
To use the alignreport option, follow this example:
  
  mothur > get.seqs(accnos=esophagus.accnos, alignreport=esophagus.align.report)
+
  mothur > get.seqs(accnos=esophagus.unique.good.accnos, alignreport=esophagus.align.report)
  
 
This generates the file esophagus.pick.align.report, which contains the following lines:
 
This generates the file esophagus.pick.align.report, which contains the following lines:
  
  QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+
  QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
  59_10_1 869 176825 1527 kmer 69.84 needleman 1 869 5914 870 1 6 1 93.79
+
  9_1_12 866 108139 1525 kmer 62.17 needleman 1 866 50 917 868 2 0 0 91.36
  59_10_10 868 196718 1542 kmer 78.05 needleman 1 868 49 916 870 2 2 0 95.29
+
  9_1_14 847 134265 1524 kmer 65.71 needleman 1 847 50 896 849 2 2 0 90.81
  59_10_11 870 97946 1560 kmer 92.12 needleman 1 870 51 920 870 0 0 0 99.08
+
  9_1_15 866 108139 1525 kmer 61.47 needleman 1 866 50 917 869 3 1 1 91.02
 +
9_1_16 854 13820 1555 kmer 90.67 needleman 1 854 43 897 859 5 4 1 97.56
 +
...

Revision as of 13:54, 30 July 2009

The get.seqs command takes a list of sequence names and either a fasta, name, group, or align.report file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.


Options

To run get.seqs, you must provide the accnos option and at least one other option. The command will generate a *.pick.* file.

accnos option

To generate an accnos file, let's first run unique.seqs, summary.seqs, screen.seqs, and list.seqs:


mothur > unique.seqs(fasta=esophagus.fasta)

mothur > summary.seqs(fasta=esophagus.unique.fasta)

		Start	End	NBases	Ambigs	Polymer
Minimum:	1	831	831	0	4
2.5%-tile:	1	841	841	0	4
25%-tile:	1	857	857	0	5
Median: 	1	866	866	0	5
75%-tile:	1	870	870	0	5
97.5%-tile:	1	900	900	5	7
Maximum:	1	1378	1378	20	8
# of Seqs:	656

mothur > screen.seqs(fasta=esophagus.unique.fasta, maxambig=0)

mothur > list.seqs(fasta=esophagus.unique.good.fasta)

This generates esophagus.unique.good.accnos, a file with 527 sequences.


fasta option

To use the fasta option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, fasta=esophagus.fasta)

This generates the file esophagus.pick.fasta, which contains the following lines:

>9_1_12
GCAAGTCGAGGGGAAAC...
>9_1_14
GCAAGTCGAGGGGAACG...
>9_1_15
GCAAGTCGAGGGGAAAC...
...

name option

To use the name option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, name=esophagus.names)

This generates the file esophagus.pick.names, which contains the following lines:

65_5_22	65_5_22
65_5_12	65_5_12
59_7_23	59_7_23
59_7_7	59_7_7
65_5_28	65_5_28
65_9_13	65_9_13
9_6_11	9_6_11
...

group option

To use the group option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, group=esophagus.groups)

This generates the file esophagus.pick.groups, which contains the following lines:

9_1_12	B
9_1_14	B
9_1_15	B
9_1_16	B
9_1_18	B
...

alignreport option

To use the alignreport option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, alignreport=esophagus.align.report)

This generates the file esophagus.pick.align.report, which contains the following lines:

QueryName	QueryLength	TemplateName	TemplateLength	SearchMethod	SearchScore	AlignmentMethod	QueryStart	QueryEnd	TemplateStart	TemplateEnd	PairwiseAlignmentLength	GapsInQuery	GapsInTemplate	LongestInsert	SimBtwnQuery&Template	
9_1_12	866	108139	1525	kmer	62.17	needleman	1	866	50	917	868	2	0	0	91.36	
9_1_14	847	134265	1524	kmer	65.71	needleman	1	847	50	896	849	2	2	0	90.81	
9_1_15	866	108139	1525	kmer	61.47	needleman	1	866	50	917	869	3	1	1	91.02	
9_1_16	854	13820	1555	kmer	90.67	needleman	1	854	43	897	859	5	4	1	97.56	
...