List file with seq within each OTU separated by a comma

Hi All!

I would like to generate a .list file that has the names of sequences within each OTU separated by a comma.

Something like this…

http://www.mothur.org/wiki/List_file

I was refering to the Marine community analysis page and When I ran

mothur > read.otu(list=pool.fn.list, group=pool.groups, label=unique-0.03-0.05-0.10)

Four files were generated these include pool.fn.shared, pool.fn.A.rabund, pool.fn.B.rabund, and pool.fn.C.rabund.

No .list files were generated.

I need columns that contain the names of sequences within each OTU separated by a comma.

Hope you can help…

[b]Thanks Heaps

Cheers

Neil[/b]

I am assuming you want a list file for each of your groups? We don’t currently have a command to parse a list file, but it is on the list for the next release. In the meantime here is a work around. If you create a file with the names of the sequences from the group you want, you can use the get.seqs command to create a list file with only those names in it. http://www.mothur.org/wiki/Get.seqs

Hello Westcott,

Thank you for your reply.

I need to generate a list file as defined in http://www.mothur.org/wiki/List_file

The Esophageal community analysis working folder contains three files

esophagus.fn.B.list
esophagus.fn.C.list
esophagus.fn.D.list

Which command was used to generate these files?

The Marine community analysis page mentions that list files (i.e., gos.fn.GS011.list, gos.fn.GS012.list, …, and gos.fn.GS122a.list). are generated when the read.otu command is used…From http://www.mothur.org/wiki/Marine_community_analysis

But when I used the read.otu command

mothur > read.otu(list=neil.fn.list, group=neil.good.groups, label=unique-0.03-0.05-0.10)

Four files including neil.fn.shared, neil.fn.B.rabund, neil.fn.D.rabund, and neil.fn.C.rabund. were generated (I have samples B, C and D in my group file)

Once again I need a list file that contains data as shown in http://www.mothur.org/wiki/List_file

The file ending in “list” contains data indicating the sequences that cluster together within an OTU. Like the rabund and sabund files, the first column represents the distance that sequences were assigned to OTUs. If you are making your own rabund file you can make the label anything without spaces. The number in the second column is the number of OTUs that have been formed. Subsequent columns contain the names of sequences within each OTU separated by a comma. At this time these are not sorted according to any rule.

Sample output of 98_sq_phylip_amazon.fn.list, which can be download in the AmazonData.zip file:

unique 96 U68589 U68590 U68591 U68592 U68593 U68594 U68595 U68596 U68597 U68598 U68599 U68600
U68601 U68602 U68603 U68605 U68606 U68607 U68608 U68609 U68610 U68611 U68612 U68613 U68614
U68615 U68616 U68617 U68620,U68618 U68619 U68621 U68622 U68623 U68624 U68625 U68626 U68627
U68628 U68629 U68630 U68631 U68632 U68633 U68634 U68635 U68636 U68637 U68638 U68639 U68640
U68667,U68641 U68642 U68643 U68644 U68645 U68646 U68647 U68648 U68649 U68651 U68652 U68653
U68654 U68655 U68656 U68657 U68658 U68659 U68660 U68661 U68662 U68663 U68664 U68665 U68666
U68668 U68669 U68670 U68671 U68672 U68673 U68674 U68675 U68676 U68677 U68678 U68679 U68680
U68681 U68682 U68683 U68684 U68685 U68686 U68687 U68688
0.00 95 U68589 U68590 U68591 U68592 U68593 U68594 U68595 U68596 U68597 U68598 U68599 U68600
U68601 U68602 U68603 U68605 U68606 U68607 U68608 U68609 U68610 U68611 U68612 U68613 U68614
U68680,U68615 U68616 U68617 U68620,U68618 U68619 U68621 U68622 U68623 U68624 U68625 U68626
U68627 U68628 U68629 U68630 U68631 U68632 U68633 U68634 U68635 U68636 U68637 U68638 U68639
U68640 U68667,U68641 U68642 U68643 U68644 U68645 U68646 U68647 U68648 U68649 U68651 U68652
U68653 U68654 U68655 U68656 U68657 U68658 U68659 U68660 U68661 U68662 U68663 U68664 U68665
U68666 U68668 U68669 U68670 U68671 U68672 U68673 U68674 U68675 U68676 U68677 U68678 U68679
U68681 U68682 U68683 U68684 U68685 U68686 U68687 U68688
0.01 93 U68589 U68590 U68591 U68592 U68593 U68594 U68595 U68596 U68597 U68598 U68599 U68600
U68601 U68602 U68603 U68605 U68606 U68607 U68608 U68609 U68610 U68611 U68612 U68613 U68614
U68680,U68615 U68616 U68617 U68620,U68618 U68619 U68621 U68622 U68623 U68624 U68625 U68626
U68627 U68628 U68629 U68630 U68636,U68631 U68632 U68633 U68634 U68635 U68637 U68638 U68639
U68640 U68667,U68641 U68642 U68643 U68644 U68645 U68646 U68647 U68648 U68649 U68651 U68652
U68653 U68654 U68655 U68656 U68657 U68658 U68659 U68660 U68661 U68662 U68663 U68664
U68688,U68665 U68666 U68668 U68669 U68670 U68671 U68672 U68673 U68674 U68675 U68676 U68677
U68678 U68679 U68681 U68682 U68683 U68684 U68685 U68686 U68687

Hope this is an adequate description of my query…

Many Thanks

Cheers!

Neil

It seems we have missed a reference on the wiki. :oops: The read.otu command used to parse the list file, but we changed it to output .rabund files instead of .list files to improve speed. The only way to do what you want in mothur currently is to use the get.seqs command. Sorry for the confusion.