count.seqs
The count.seqs / make.table command counts the number of sequences represented by the representative sequence in a name file. If a group file is given, it will also provide the group count breakdown.
Default Settings
To run the command the names of a name-file needs to be provided:
mothur > count.seqs(name=stool.final.names)
This will generate a summary file called, stool.final.seq.count which looks like:
Representative_Sequence total
F21Fcsw_12128 1764
F11Fcsw_6529 1568
F11Fcsw_112161 861
F11Fcsw_56988 480
F11Fcsw_63768 361
M41Fcsw_132742 326
M11Fcsw_34015 414
F31Fcsw_128576 509
F21Fcsw_85352 370
...
Shared
Can be used to transpose the shared file for use with other software packages.
mothur > count.seqs(shared=final.opti_mcc.shared)
OTU_Label total F003D000 F003D002 F003D004 F003D006 F003D008 F003D142 F003D144 F003D146 F003D148 F003D150
Otu0001 6079 409 992 933 953 346 696 474 436 376 464
Otu0002 4658 384 170 393 419 286 744 584 557 491 630
Otu0003 3969 230 418 442 560 359 595 301 348 388 328
Otu0004 3352 167 88 240 354 779 455 173 449 237 410
Otu0005 2643 183 274 379 370 333 229 212 172 137 354
...
Group
If you would like to see how the sequences are spread over your samples provide the group file.
mothur > count.seqs(name=stool.final.names, group=stool.final.groups)
This will generate a summary file called, stool.final.seq.count which looks like:
Representative_Sequence total F11Fcsw F12Fcsw F13Fcsw F14Fcsw F21Fcsw F22Fcsw
F21Fcsw_12128 1764 0 0 0 0 39 31 ...
F11Fcsw_6529 1568 38 17 23 128 26 18 ...
F11Fcsw_112161 861 1 0 2 7 67 52 ...
F11Fcsw_56988 480 9 1 0 3 0 0 ...
F11Fcsw_63768 361 6 2 0 6 28 17 ...
M41Fcsw_132742 326 0 0 0 0 0 0 ...
M11Fcsw_34015 414 9 8 29 23 6 5 ...
...
count
The count parameter allows you to inflate or deflate count tables.
compress
The compress parameter allows you to indicate you want the count table printed in compressed format. Default=t.
mothur > count.seqs(count=final.count_table, compress=f)
Will result in
Representative_Sequence total F003D000 F003D002 F003D004 F003D006 F003D008 F003D142 F003D144 F003D146 F003D148 F003D150
GQY1XT001CFHYQ 467 325 40 22 30 24 6 7 3 7 3
GQY1XT001C44N8 3677 323 132 328 318 232 579 448 426 381 510
GQY1XT001C296C 4652 356 877 754 794 284 538 361 313 0 375
GQY1XT001ARCB1 2202 203 391 220 155 308 126 33 191 289 286
...
mothur > count.seqs(count=final.count_table, compress=t)
Will result in
#Compressed Format: groupIndex,abundance. For example 1,6 would mean the read has an abundance of 6 for group 1.
#1,F003D000 2,F003D002 3,F003D004 4,F003D006 5,F003D008 6,F003D142 7,F003D144 8,F003D146 9,F003D148 10,F003D150
Representative_Sequence total F003D000 F003D002 F003D004 F003D006 F003D008 F003D142 F003D144 F003D146 F003D148 F003D150
GQY1XT001CFHYQ 467 1,325 2,40 3,22 4,30 5,24 6,6 7,7 8,3 9,7 10,3
GQY1XT001C44N8 3677 1,323 2,132 3,328 4,318 5,232 6,579 7,448 8,426 9,381 10,510
GQY1XT001C296C 4652 1,356 2,877 3,754 4,794 5,284 6,538 7,361 8,313 10,375
GQY1XT001ARCB1 2202 1,203 2,391 3,220 4,155 5,308 6,126 7,33 8,191 9,289 10,286
GQY1XT001CFWVZ 1967 1,193 2,152 3,191 4,300 5,228 6,179 7,172 8,161 9,111 10,280
...
GQY1XT001EI480 10 1,8 8,1 9,1
GQY1XT001EDBEC 95 1,9 2,13 3,13 4,7 5,10 6,11 7,8 8,8 9,5 10,11
GQY1XT001D47YY 97 1,10 2,2 3,13 4,21 5,9 6,5 7,11 8,12 9,2 10,12
GQY1XT001CNUHI 19 1,17 2,1 7,1
...
Groups
If you would like to simplify the output because you are only interested in the number of sequence represented by a specific group or set of groups you can use the groups option.
mothur > count.seqs(name=stool.final.names, group=stool.final.groups, groups=F11Fcsw-F12Fcsw)
This will generate a summary file called, stool.final.seq.count which looks like:
Representative_Sequence total F11Fcsw F12Fcsw
F11Fcsw_6529 55 38 17
F11Fcsw_112161 1 1 0
F11Fcsw_56988 10 9 1
F11Fcsw_63768 8 6 2
M11Fcsw_34015 17 9 8
F11Fcsw_455 107 57 50
F11Fcsw_9818 24 23 1
F11Fcsw_46282 3 3 0
...
Note: When you use the groups option, if a representative sequence does not represent any sequences from the groups you requested it is not displayed. Also, the total reflects the total represented from those groups, not total from all groups.
Revisions
- 1.26.0 - added large parameter and alias make.table name.
- 1.34.0 - added shared parameter. Can be used to transpose the shared file for use with other software packages.
- 1.38.0 - removes large parameter
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347
- 1.42.0 - Adds count and compress parameters to count.seqs to inflate or deflate count tables.